diff --git a/.github/workflows/qc.yml b/.github/workflows/qc.yml index 4c560cf..8e96293 100644 --- a/.github/workflows/qc.yml +++ b/.github/workflows/qc.yml @@ -19,7 +19,7 @@ jobs: ontology_qc: # The type of runner that the job will run on runs-on: ubuntu-latest - container: obolibrary/odkfull:v1.4 + container: obolibrary/odkfull:v1.4.3 # Steps represent a sequence of tasks that will be executed as part of the job steps: diff --git a/.gitignore b/.gitignore index 3e5c002..45bda8f 100644 --- a/.gitignore +++ b/.gitignore @@ -41,3 +41,5 @@ pyproject.toml poetry.lock .idea/* src/templates/.~lock.vibso_classes.tsv\# +docs/images/.$VIBSO_T-Box_graph_views.drawio.bkp +*.dtmp diff --git a/README.md b/README.md index 1f9c213..48d1506 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,5 @@ [![License: CC-BY 4.0](https://img.shields.io/badge/License-CC%20BY%204.0-green.svg)](https://creativecommons.org/licenses/by/4.0/) -![Build Status](https://github.com/NFDI4Chem/VibrationSpectroscopyOntology/workflows/CI/badge.svg) +[![CI](https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/actions/workflows/qc.yml/badge.svg)](https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/actions/workflows/qc.yml) # Vibrational Spectroscopy Ontology _Work In Progress - NOT READY FOR PRODUCTION!_ diff --git a/docs/contributing.md b/docs/contributing.md index 8b07dc6..99511df 100644 --- a/docs/contributing.md +++ b/docs/contributing.md @@ -7,6 +7,5 @@ There are different ways in which you can help: * [Open up a new issue](https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/new/choose): For any kind of contributions we rely on the GitHub infrastructure for documentation. Thus, it is always preferred that you use one of our issue templates to let us know what needs to be done and how you might plan on contributing, before working on a pull request (PR). (However, feel free to do a quick PR patch for any typos off course.) * Use [this template](https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/new?assignees=&labels=&template=bug_report.md&title=) to file bugs within the ontology or its CI/CD pipeline, - * [this one](https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/new?assignees=&labels=New+Term+Request&template=new-term-request-issue-template.md&title=%5BNTR%5D) to make a new term request, + * [this one](https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/new?assignees=&labels=New+Term+Request&template=new-term-request-issue-template.md&title=%5BNTR%5D) to make a new term request (but please read the [How to add new terms to VIBSO section](ntr_workflow.md) first), * or [this one](https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/new?assignees=&labels=documentation&template=documentation-related-issue.md&title=%5BDocs%5D) to help us improve this documentation and ask questions about VIBSO. -* [Add new terms to VIBSO](ntr_workflow.md). diff --git a/docs/design_patterns.md b/docs/design_patterns.md index 71eb20c..aadd44f 100644 --- a/docs/design_patterns.md +++ b/docs/design_patterns.md @@ -1,22 +1,55 @@ # Design Patterns & Decisions -**This page is still a stub and will be updated regularly in the iterative development of VIBSO to document modeling decisions and design patterns.** +**This page will be updated regularly in the iterative development of VIBSO to document modeling decisions and design patterns.** -Following best practices in ontology development, we will reuse well established design patterns whenever possible. +Following best practices in ontology development, we will reuse established design patterns whenever possible. Since most ontologies we reuse are OBO Foundry based, we also reuse their design patterns to be logically sound and interoperable. Some of these patterns are provided in the logical definitions of the reused classes in form of asserted `rdfs:subclassOf` or `rdfs:equivalentTo` axioms. Others are only implicitly provided in the textual definitions of the reused terms and the domain and range restrictions of suitable OBO relations. -## Planned Process Pattern - OBI's way of modeling [data and values](https://github.com/obi-ontology/obi/wiki/Data-and-Values) is a very prominent pattern in many OBO ontologies and thus one we also use. Please read their documentation in order to understand how we model values and data. Here is an illustrative example graphic from that documentation: ![measurement process pattern example](images/data_john_mass.png) Using this OBI pattern allows us to differentiate data values of qualities (aka attributes) of a material entity, such as the spectroscope or sample, into data values that represent settings and those that represent measurements. From a data repository use case perspective, we might not need this fine-grained approach and defining qualities/attributes and their value specifications might suffice. Yet in order to allow the integration of VIBSO in Electronic Lab Notebooks, such a differentiation will most likely be very useful. +## VIBSO TBox -Lars Vogt and Tobias Kuhn demonstrate the use of this pattern within a grander research context as follows (cited from their preprint [DOI:10.13140/RG.2.2.13742.59203](http://doi.org/10.13140/RG.2.2.13742.59203), p.8): -![measurement process pattern example](images/Fig4_10.13140_RG.2.2.13742.59203.png) +Here you can see VIBSO's current terminology box that focuses on vibrational Raman spectroscopy and which also shows how VIBSO depends on reusing existing ontology classes, relations and design patterns. - > Figure 3: A detailed machine-actionable representation of the metadata relating to a weight measurement datum documented as an RDF ABox graph. The representation takes the form of an ABox semantic graph following the RDF syntax. The graph documents a mass measurement process using a balance. It relates an instance of mass measurement assay (OBI:0000445) with instances of various other classes from different ontologies, specifying who conducted the measurement, where and when it took place, following which protocol and using which device (i.e., balance). The graph furthermore specifies the particular material entity that served as subject and thus as input of the measurement process (i.e., ‘objectX’), and it specifies the data that is the output of the observation, which is contained in a particular weight measurement assertion. +![Raman spectroscopy terminology box](images/VIBSO_Raman_Tbox.png) +This TBox is supposed to be updated iteratively whenever a new term is being discussed for inclusion. We hope that it might be easier for domain experts to define technical terms in this ontological framework by adding them here first. -## Vibrational Raman Spectroscopy +A higher resolution HTML version with links to the used terms in the NFDI4Chem Terminology Service can be found [here](images/VIBSO_TBox_graph_views.html). -Here you can see the first draft of VIBSO's terminology box that focuses on vibrational Raman spectroscopy and which also shows how VIBSO depend on reusing existing ontology classes, relations and design patterns. The initially identified needed terms, depicted here with a red border, were derived from a Raman spectrometer output. +The source file to edit the TBox with the [draw.io](https://draw.io) app is [here](images/VIBSO_T-Box_graph_views.drawio). -![Raman spectroscopy terminology box](images/VIBSO_Raman_Tbox.png) +## Assay Pattern +As the scope of VIBSO covers the definitions of various types of vibrational spectroscopy assays and their specific research information outputs, we need to reuse the class `assay` from the Ontology for Biomedical Investigations (OBI). It is defined as: + + A planned process that has the objective to produce information about a material entity (the evaluant) by examining it. + +Along with this textual definition, the logical axioms asserted on this class constitute a core design pattern of OBO based ontologies, which can be represented graphically like this: + +![OBI_asserted_assay_pattern](images/OBI_asserted_assay_pattern.png) + +## Assay Pattern with Device Settings +Since we also want to say what kind of devices were used in VIBSO specific assays and how these were set, we extend the assay pattern by importing these classes and relations: + +![OBI_asserted_assay_pattern](images/OBO_setting_pattern.png) + +## Assay Pattern with Data Transformation, Investigation and Sampling +To zoom out a bit further, this is the pattern proposed to be able to also express: + +* who performed an assay, +* what kind of data transformations where performed on the data output of an assay, +* what kind of sampling process was done before the assay, +* and in which grander investigation process the assay is a part of. + +![OBI_asserted_assay_pattern](images/OBO_Investigation_Assay_Pattern.png) + +----- + +## Measurement Example KG of the Assay Pattern +Lars Vogt and Tobias Kuhn demonstrate the use of the OBO assay pattern within a grander research context as follows (cited from their preprint [DOI:10.13140/RG.2.2.13742.59203](http://doi.org/10.13140/RG.2.2.13742.59203), p.8): +![measurement process pattern example](images/Fig4_10.13140_RG.2.2.13742.59203.png) + + > Figure 3: A detailed machine-actionable representation of the metadata relating to a weight measurement datum documented as an RDF ABox graph. The representation takes the form of an ABox semantic graph following the RDF syntax. The graph documents a mass measurement process using a balance. It relates an instance of mass measurement assay (OBI:0000445) with instances of various other classes from different ontologies, specifying who conducted the measurement, where and when it took place, following which protocol and using which device (i.e., balance). The graph furthermore specifies the particular material entity that served as subject and thus as input of the measurement process (i.e., ‘objectX’), and it specifies the data that is the output of the observation, which is contained in a particular weight measurement assertion. -What is needed next are iterative reviews of this draft by domain experts to expand it and to ensure that the [competency questions](competency_questions.md) of VIBSO can be answered. \ No newline at end of file +## Quality & Quantity Pattern +![measurement process pattern example](images/data_john_mass.png) + Since we are reusing OBO ontologies and their patterns, we also try to reuse OBI's way of modeling [data and values](https://github.com/obi-ontology/obi/wiki/Data-and-Values). Please read their documentation for more background. + Using this OBI pattern allows us to differentiate data values of qualities (aka attributes) of a material entity, such as the spectroscope or sample, into data values that represent settings and those that represent measurements. From a data repository use case perspective, we might not need this fine-grained approach and defining qualities/attributes and their value specifications might suffice. Yet in order to allow the integration of VIBSO in Electronic Lab Notebooks, such a differentiation will most likely be very useful. +Although this pattern seems to work in many OBO use cases, we need to see, if we have to adjust it for our needs. Other ontologies like QUDT or SIO use slightly different patterns to model qualities and their quantitative representations. \ No newline at end of file diff --git a/docs/development_approach.md b/docs/development_approach.md index eb6ded5..8154b07 100644 --- a/docs/development_approach.md +++ b/docs/development_approach.md @@ -29,9 +29,11 @@ In both TSV templates there are the following columns: * **term replaced by**: This column should be used to provide the term that replaces a deprecated term. This is important to ensure backwards compatibility. In the **vibso_classes.tsv**, there is also the column: + * **super class**: This column is to be used to provide the parent of the owl:Class that is being defined. It is fine to use the label of the parent class here instead of its IRI or CURIE, as long as the class is already an [imported term](ntr_workflow.md#importing terms). In the **vibso_classes.tsv**, there are also the columns: + * **super property**: This column is to be used to provide the parent of the `owl:ObjectProperty` or `owl:DatatypeProperty` that is being defined, via its label. * **inverse property**: This column can be used to define the inverse of an `owl:ObjectProperty`, via its label. * **domain**: This column can be used to restrict an `owl:ObjectProperty` in terms of being allowed to be used only on a certain subject. diff --git a/docs/images/OBI_asserted_assay_pattern.png b/docs/images/OBI_asserted_assay_pattern.png new file mode 100644 index 0000000..03f46cc Binary files /dev/null and b/docs/images/OBI_asserted_assay_pattern.png differ diff --git a/docs/images/OBO_Investigation_Assay_Pattern.png b/docs/images/OBO_Investigation_Assay_Pattern.png new file mode 100644 index 0000000..1c95331 Binary files /dev/null and b/docs/images/OBO_Investigation_Assay_Pattern.png differ diff --git a/docs/images/OBO_assay_pattern_example_instances.png b/docs/images/OBO_assay_pattern_example_instances.png new file mode 100644 index 0000000..28da229 Binary files /dev/null and b/docs/images/OBO_assay_pattern_example_instances.png differ diff --git a/docs/images/OBO_setting_pattern.png b/docs/images/OBO_setting_pattern.png new file mode 100644 index 0000000..4318e89 Binary files /dev/null and b/docs/images/OBO_setting_pattern.png differ diff --git a/docs/images/Raman spectroscopy T-Box-Raman T-Box.drawio.png b/docs/images/Raman spectroscopy T-Box-Raman T-Box.drawio.png deleted file mode 100644 index f4f99fe..0000000 Binary files a/docs/images/Raman spectroscopy T-Box-Raman T-Box.drawio.png and /dev/null differ diff --git a/docs/images/Raman_spectroscopy_T-Box.drawio b/docs/images/Raman_spectroscopy_T-Box.drawio deleted file mode 100644 index 9013ef9..0000000 --- a/docs/images/Raman_spectroscopy_T-Box.drawio +++ /dev/null @@ -1,2520 +0,0 @@ - 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- bfo:qualityro:has roleText is not SVG - cannot display \ No newline at end of file diff --git a/docs/images/VIBSO_T-Box_graph_views.drawio b/docs/images/VIBSO_T-Box_graph_views.drawio new file mode 100644 index 0000000..a78972f --- /dev/null +++ b/docs/images/VIBSO_T-Box_graph_views.drawio @@ -0,0 +1,2362 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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+ + + + + + + + + + + + + + + + + + diff --git a/docs/images/VIBSO_TBox_graph_views.html b/docs/images/VIBSO_TBox_graph_views.html new file mode 100644 index 0000000..06ac2ee --- /dev/null +++ b/docs/images/VIBSO_TBox_graph_views.html @@ -0,0 +1,11 @@ + + + + +VIBSO_T-Box_graph_views + + +
+ + + \ No newline at end of file diff --git a/docs/ntr_workflow.md b/docs/ntr_workflow.md index 421fd15..336f7b7 100644 --- a/docs/ntr_workflow.md +++ b/docs/ntr_workflow.md @@ -12,9 +12,9 @@ Whenever you identify a term missing in VIBSO and you have found a suitable cand Once it is decided to be needed, a pull request (PR) can be made to include it in the imports. For this it needs either be added in one of the existing text files where such term imports get declared (see [/src/ontology/imports](https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/tree/main/src/ontology/imports)) and from which the OWL import modules are build automatically, according to the standard import workflow documented in [here](odk-workflows/UpdateImports.md). If the term is from an ontology that is not yet being used as an import module in VIBSO the [managing imports workflow](odk-workflows/RepoManagement.md#managing-imports) needs to be triggered. ## New Term Requests -When you've identified a term that is needed within the scope of VIBSO and which is not yet defined in an existing compatible ontology, please file a [new term request (NRT) issue](https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/new?assignees=&labels=New+Term+Request&template=new-term-request-issue-template.md&title=%5BNTR%5D). - This issue should then be used to engage the community in discussing the label, definition, position in the hierarchy as well as possible axiomatization. Once the discussion has reached a consensus, someone from the VIBSO team or maybe you, will have to make a PR in which the discussed changes to VIBSO will be implemented and can be reviewed. +When you've identified a term that is needed within the scope of VIBSO and which is not yet defined in an existing compatible ontology, a new term request (NTR) should be filed in VIBSO's issue tracker. This issue should then be used to engage the community in discussing the label, definition, position in the hierarchy as well as possible axiomatization. Once the discussion has reached a consensus, someone from the VIBSO team or maybe you, will have to make a PR in which the discussed changes to VIBSO will be implemented and can be reviewed. +Please [check the open NTR issues](https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues?q=is%3Aissue+is%3Aopen+label%3A%22New+Term+Request%22) to make sure none exists for this term already. If it does, feel free to participate in the discussion. Else, please use this [issue template](https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/new?assignees=&labels=New+Term+Request&template=new-term-request-issue-template.md&title=%5BNTR%5D) to file your NTR. ## Adding New Terms to the TSV Template diff --git a/src/ontology/Makefile b/src/ontology/Makefile index 879f6da..c6469d9 100644 --- a/src/ontology/Makefile +++ b/src/ontology/Makefile @@ -1,7 +1,7 @@ # ---------------------------------------- # Makefile for vibso # Generated using ontology-development-kit -# ODK Version: v1.4.1 +# ODK Version: v1.4.3 # ---------------------------------------- # IMPORTANT: DO NOT EDIT THIS FILE. To override default make goals, use vibso.Makefile instead @@ -43,7 +43,7 @@ REPORT_PROFILE_OPTS = OBO_FORMAT_OPTIONS = SPARQL_VALIDATION_CHECKS = owldef-self-reference iri-range label-with-iri multiple-replaced_by SPARQL_EXPORTS = basic-report class-count-by-prefix edges xrefs obsoletes synonyms -ODK_VERSION_MAKEFILE = v1.4.1 +ODK_VERSION_MAKEFILE = v1.4.3 TODAY ?= $(shell date +%Y-%m-%d) OBODATE ?= $(shell date +'%d:%m:%Y %H:%M') diff --git a/src/ontology/example_instances.ttl b/src/ontology/example_instances.ttl index c81982b..f06de8c 100644 --- a/src/ontology/example_instances.ttl +++ b/src/ontology/example_instances.ttl @@ -1,12 +1,161 @@ -@prefix ex: . +@prefix : . +@prefix ex: . +@prefix DOI: . +@prefix ROR: . +@prefix dce: . @prefix obo: . @prefix owl: . @prefix rdf: . +@prefix xml: . +@prefix xsd: . +@prefix prov: . +@prefix rdfs: . +@prefix skos: . +@prefix ORCID: . +@prefix schema: . +@prefix dcterms: . +@prefix wikipedia: . +@base . -ex:_RamanSpectrometerX rdf:type owl:NamedIndividual , - obo:CHMO_0001235 ; - obo:OBI_0000293 ex:_objective_magnification_factor_setting_for_RamanSpectroscopeX . + rdf:type owl:Ontology ; + owl:imports , + , + , + , + , + , + , + , + , + ; + dcterms:contributor , + , + ; + dcterms:creator , + "VIBSO Workgroup"@en ; + dcterms:description "_WIP - NOT READY FOR PRODUCTION_ The Vibration Spectroscopy Ontology (VIBSO) is used to represent information regarding the excution and analysis of vibrational spectroscopy assays." ; + dcterms:license ; + dcterms:title "Vibrational Spectroscopy Ontology" . -ex:_objective_magnification_factor_setting_for_RamanSpectroscopeX rdf:type owl:NamedIndividual , - obo:VIBSO_0000014 ; - obo:OBI_0002815 "100x" . +################################################################# +# Annotation properties +################################################################# + +### http://purl.org/dc/terms/contributor +dcterms:contributor rdf:type owl:AnnotationProperty ; + rdfs:label "contributor" . + + +### http://purl.org/dc/terms/creator +dcterms:creator rdf:type owl:AnnotationProperty ; + rdfs:label "creator" . + + +### http://purl.org/dc/terms/description +dcterms:description rdf:type owl:AnnotationProperty ; + rdfs:label "description" . + + +### http://purl.org/dc/terms/license +dcterms:license rdf:type owl:AnnotationProperty ; + rdfs:label "license" . + + +### http://purl.org/dc/terms/title +dcterms:title rdf:type owl:AnnotationProperty ; + rdfs:label "title" . + + +### https://schema.org/affiliation + rdf:type owl:AnnotationProperty . + + +################################################################# +# Classes +################################################################# + +### http://purl.obolibrary.org/obo/NCBITaxon_9606 +obo:NCBITaxon_9606 rdfs:subClassOf obo:OBI_0100026 ; + rdfs:label "person" . + + +################################################################# +# Individuals +################################################################# + +### https://example.instances/AssayObjective_O +ex:AssayObjective_O rdf:type owl:NamedIndividual , + obo:OBI_0000441 . + + +### https://example.instances/Assay_A +ex:Assay_A rdf:type owl:NamedIndividual , + obo:OBI_0000070 ; + obo:BFO_0000055 ex:EvaluantRole_R ; + obo:OBI_0000293 ex:MaterialEntity_M ; + obo:OBI_0000299 ex:DataItem_D ; + obo:OBI_0000417 ex:AssayObjective_O ; + dce:description """The assay A is planned to produce as a specified output the data item D which is a specific kind of information about the material entity M, which has the evaluant role R that gets realized in this planned observation process. + +This example instance is part of the ontology to demonstrate the OBI assay pattern. The type and number of relations between this instance and other example instances are based on the subclassOf and equivalentTo axioms asserted on OBIs assay."""@en . + + +### https://example.instances/DataItem_D +ex:DataItem_D rdf:type owl:NamedIndividual , + obo:IAO_0000027 ; + obo:IAO_0000136 ex:MaterialEntity_M . + + +### https://example.instances/EvaluantRole_R +ex:EvaluantRole_R rdf:type owl:NamedIndividual , + obo:BFO_0000023 . + + +### https://example.instances/MaterialEntity_M +ex:MaterialEntity_M rdf:type owl:NamedIndividual , + obo:BFO_0000040 ; + obo:RO_0000087 ex:EvaluantRole_R . + + +### https://orcid.org/0000-0002-1595-3213 + rdf:type owl:NamedIndividual ; + rdfs:label "Philip Strömert" ; + , + , + "VIBSO Workgroup"@en . + + +### https://orcid.org/0000-0002-2239-3955 + rdf:type owl:NamedIndividual ; + rdfs:label "Giacomo Lanza" ; + , + , + "VIBSO Workgroup"@en . + + +### https://orcid.org/0000-0002-4378-6061 + rdf:type owl:NamedIndividual ; + rdfs:label "Johannes Hunold" ; + , + , + "VIBSO Workgroup"@en . + + +### https://ror.org/04aj4c181 + rdf:type owl:NamedIndividual ; + rdfs:label "German National Library of Science and Technology Hannover"@en , + "Technische Informationsbibliothek (TIB)"@de . + + +### https://ror.org/05r3f7h03 + rdf:type owl:NamedIndividual ; + rdfs:label "German National Metrology Institute"@en , + "Physikalisch-Technische Bundesanstalt (PTB)"@de . + + +### https://www.wikidata.org/wiki/Q96678459 + rdf:type owl:NamedIndividual ; + rdfs:label "NFDI4Chem" . + + +### Generated by the OWL API (version 4.5.25.2023-02-15T19:15:49Z) https://github.com/owlcs/owlapi diff --git a/src/ontology/imports/bfo_import.owl b/src/ontology/imports/bfo_import.owl index caa3f3f..bd0c91f 100644 --- a/src/ontology/imports/bfo_import.owl +++ b/src/ontology/imports/bfo_import.owl @@ -7,9 +7,9 @@ Prefix(rdfs:=) Ontology( - + Annotation( ) -Annotation(owl:versionInfo "2023-06-21") +Annotation(owl:versionInfo "2023-11-27") Declaration(Class()) Declaration(Class()) diff --git a/src/ontology/imports/chmo_import.owl b/src/ontology/imports/chmo_import.owl index 2be2b1d..78aa028 100644 --- a/src/ontology/imports/chmo_import.owl +++ b/src/ontology/imports/chmo_import.owl @@ -12,8 +12,8 @@ xmlns:terms="http://purl.org/dc/terms/" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - - 2023-06-21 + + 2023-11-27 @@ -2581,5 +2581,5 @@ - + diff --git a/src/ontology/imports/iao_import.owl b/src/ontology/imports/iao_import.owl index f4fda27..52e9148 100644 --- a/src/ontology/imports/iao_import.owl +++ b/src/ontology/imports/iao_import.owl @@ -7,9 +7,9 @@ Prefix(rdfs:=) Ontology( - + Annotation( ) -Annotation(owl:versionInfo "2023-06-21") +Annotation(owl:versionInfo "2023-11-27") Declaration(Class()) Declaration(Class()) diff --git a/src/ontology/imports/obi_import.owl b/src/ontology/imports/obi_import.owl index 0f6340a..c6e32e9 100644 --- a/src/ontology/imports/obi_import.owl +++ b/src/ontology/imports/obi_import.owl @@ -12,9 +12,9 @@ xmlns:terms="http://purl.org/dc/terms/" xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#"> - - 2023-06-21 - + + 2023-11-27 + @@ -217,7 +217,7 @@ - + @@ -225,7 +225,7 @@ - + @@ -233,7 +233,7 @@ - + @@ -241,7 +241,7 @@ - + @@ -249,7 +249,7 @@ - + @@ -274,7 +274,7 @@ PERSON: Larry Hunter PERSON: Melanie Coutot - + has_specified_input @@ -290,7 +290,7 @@ A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of. Alan Ruttenberg PERSON:Bjoern Peters - + is_specified_input_of @@ -314,7 +314,7 @@ PERSON: Larry Hunter PERSON: Melanie Courtot - + has_specified_output @@ -331,7 +331,7 @@ Alan Ruttenberg PERSON:Bjoern Peters - + is_specified_output_of @@ -347,7 +347,7 @@ BP, AR, PPPB branch PPPB branch derived modified according to email thread from 1/23/09 in accordince with DT and PPPB branch - + achieves_planned_objective @@ -361,7 +361,7 @@ This relation obtains between an objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process. OBI OBI - + objective_achieved_by @@ -376,7 +376,7 @@ A relation between a planned process and a continuant where the continuant can be a person, organization or device (such as a robot controlled by software workflow management system) that performs the planned process. OBI OBI - + The 'has performer' relation covers the need to report on who performed a planned processed. It has to cover processes done by People or Devices (such as a robot controlled by software WF management system). has performer @@ -386,7 +386,7 @@ - + @@ -394,7 +394,7 @@ - + @@ -414,7 +414,7 @@ - + @@ -422,7 +422,7 @@ - + @@ -430,7 +430,7 @@ - + @@ -438,7 +438,7 @@ - + @@ -475,7 +475,7 @@ - + @@ -495,7 +495,7 @@ - + @@ -503,7 +503,7 @@ - + @@ -511,7 +511,7 @@ - + @@ -525,7 +525,7 @@ - + @@ -545,7 +545,7 @@ - + @@ -578,7 +578,7 @@ objectives is a planned process. This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call) 6/11/9: Edited at workshop. Used to include: is initiated by an agent - + planned process @@ -604,7 +604,7 @@ objectives is a planned process. Is a material entity that is created or changed during material processing. PERSON: Alan Ruttenberg - + processed material @@ -641,7 +641,7 @@ editor = PRS Could add specific objective specification study - + investigation @@ -672,7 +672,7 @@ editor = PRS GROUP: Role Branch OBI Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. - + evaluant role @@ -741,15 +741,16 @@ editor = PRS assay Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house. - A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies. + A planned process that has the objective to produce information about a material entity (the evaluant) by examining it. 12/3/12: BP: the reference to the 'physical examination' is included to point out that a prediction is not an assay, as that does not require physical examiniation. + Discussion on OBI call 2023-05-01 resulted in an agreement to revise the textual definition of 'assay'. https://github.com/obi-ontology/obi/issues/1683. PlanAndPlannedProcess Branch measuring scientific observation OBI branch derived study assay any method - + assay @@ -771,7 +772,7 @@ editor = PRS PlanAndPlannedProcess Branch study OBI branch derived - + sample preparation for assay @@ -791,7 +792,7 @@ editor = PRS Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. May 28 2013. Updated definition taken from ReO based on discussions initiated in Philly 2011 workshop. Former defnition described a narrower view of reagents in chemistry that restricts bearers of the role to be chemical entities ("a role played by a molecular entity used to produce a chemical reaction to detect, measure, or produce other substances"). Updated definition allows for broader view of reagents in the domain of biomedical research to include larger materials that have parts that participate chemically in a molecular reaction or interaction. - + (copied from ReO) Reagents are distinguished from instruments or devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in or have parts that participate in some chemical interaction or reaction during their intended participation in some technique. By contrast, instruments do not participate in a chemical reaction/interaction during the technique. @@ -836,7 +837,7 @@ In regard to the statement that reagents are 'distinct' from the speci PERSON: Philippe Rocca Serra material transformation OBI branch derived - + material processing @@ -877,7 +878,7 @@ specimen can later be subject. GROUP: Role Branch OBI - + specimen role @@ -935,7 +936,7 @@ specimen can later be subject. OBI Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. study person role - + Philly2013: Historically, this role would have been borne only by humans or organizations. However, we now also want to enable investigations run by robot scientists such as ADAM (King et al, Science, 2009) investigation agent role @@ -982,7 +983,7 @@ for now. PERSON: Philippe Rocca-Serra PERSON: Susanna Sansone GROUP: OBI - + organization @@ -999,7 +1000,7 @@ for now. PlanAndPlannedProcess Branch OBI branch derived + wikipedia (http://en.wikipedia.org/wiki/Protocol_%28natural_sciences%29) study protocol - + protocol @@ -1028,7 +1029,7 @@ for now. Bjoern Peters Bjoern Peters Plans and Planned Processes Branch - + planning @@ -1045,7 +1046,7 @@ for now. Daniel Schober Frank Gibson Melanie Courtot - + magnify function @@ -1071,7 +1072,7 @@ for now. An image acquisition function is a function to acquire an image of a material Frank Gibson - + image acquisition function @@ -1098,7 +1099,7 @@ for now. Frank Gibson image acquisition device sep:00096 - + image creation device @@ -1115,7 +1116,7 @@ for now. Daniel Schober Frank Gibson Melanie Courtot - + solid support function @@ -1131,7 +1132,7 @@ for now. an objective specification to determine a specified type of information about an evaluated entity (the material entity bearing evaluant role) PPPB branch PPPB branch - + assay objective @@ -1166,7 +1167,7 @@ for now. PERSON: Helen Parkinson PERSON: Melanie Courtot PERSON:Frank Gibson - + measure function @@ -1187,7 +1188,7 @@ for now. PERSON: Philippe Rocca-Serra artifact creation objective GROUP: OBI PlanAndPlannedProcess Branch - + material transformation objective @@ -1216,7 +1217,7 @@ for now. Manufacturer role is a role which inheres in a person or organization and which is realized by a manufacturing process. GROUP: Role Branch OBI - + manufacturer role @@ -1238,7 +1239,7 @@ for now. a quality inheres_in some device and is concretization of some (device_setting_specification and is_about a quality of the device There is some question of whether 'device setting' is really best modelled as a quality. To be revisited after assay terms have been worked through. See https://github.com/obi-ontology/obi/issues/133 PERSON: Frank Gibson - + device setting @@ -1284,7 +1285,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ specimen collection 5/31/2012: This process is not necessarily an acquisition, as specimens may be collected from materials already in posession 6/9/09: used at workshop - + specimen collection process @@ -1300,7 +1301,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ A objective specification to obtain a material entity for potential use as an input during an investigation. Bjoern Peters Bjoern Peters - + specimen collection objective @@ -1316,7 +1317,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ A material sample role is a specimen role borne by a material entity that is the output of a material sampling process. 7/13/09: Note that this is a relational role: between the sample taken and the 'sampled' material of which the sample is thought to be representative off. - + material sample role @@ -1345,7 +1346,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ sample population sample - + material sample @@ -1372,7 +1373,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ A device in which a measure function inheres. GROUP:OBI Philly workshop OBI - + measurement device @@ -1400,8 +1401,8 @@ http://sourceforge.net/p/obi/obi-terms/716/ manufacturer - A person or organization that has a manufacturer role - + A person or organization that has a manufacturer role. + manufacturer @@ -1442,7 +1443,7 @@ In the examples above, a reagent is an operational component of a device, but th PERSON: Helen Parkinson instrument OBI development call 2012-12-17. - + device @@ -1470,7 +1471,7 @@ In the examples above, a reagent is an operational component of a device, but th A planned process that captures an image of an object. PERSON: Jie Zheng image acquisition - + image creation @@ -1487,7 +1488,7 @@ In the examples above, a reagent is an operational component of a device, but th specimen ID NIAID GSCID-BRC metadata working group Specimen ID - + NIAID GSCID-BRC specimen identifier @@ -1505,7 +1506,7 @@ In the examples above, a reagent is an operational component of a device, but th NIAID GSCID-BRC metadata working group study title project title - + NIAID GSCID-BRC investigation title @@ -1547,7 +1548,7 @@ In the examples above, a reagent is an operational component of a device, but th PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Comments - + NIAID GSCID-BRC comment on investigation @@ -1571,7 +1572,7 @@ OBI doesn't take position as to when an organism starts or ends being an o This issue is outside the scope of OBI. GROUP: OBI Biomaterial Branch WEB: http://en.wikipedia.org/wiki/Organism - + organism @@ -1601,7 +1602,7 @@ This issue is outside the scope of OBI. PERSON: Philippe Rocca-Serra GROUP: OBI Biomaterial Branch - + specimen @@ -1660,7 +1661,7 @@ This issue is outside the scope of OBI. data processing Branch editors - + data transformation @@ -1677,7 +1678,7 @@ This issue is outside the scope of OBI. Modified definition in 2013 Philly OBI workshop James Malone PERSON: James Malone - + data transformation objective @@ -1693,7 +1694,7 @@ This issue is outside the scope of OBI. solvent role is a role which inheres in a molecular entity capable of ensuring the dissolution of another chemical entity and realized by the process of solvation Philippe Rocca-Serra adpated from wikipedia (http://en.wikipedia.org/wiki/Solvatation) - + solvent role @@ -1721,7 +1722,7 @@ This issue is outside the scope of OBI. A microscope is an instrument which magnifies the view on objects (too small to be viewed by the naked eye) under increased resolution. A microscope can be an optical instrument but also and electronic instrument. There are various kind of optical microscopes, e.g confocal microscope, epifluoresence microscope) PERSON: Phillippe Rocca-Serra wikipedia - + microscope @@ -1743,7 +1744,7 @@ This issue is outside the scope of OBI. A microscope slide is a device usually made of glass which is used as a solid matrix for (biological) material deposited on its surface and which is compatible for use with a microscope instrument PERSON: Phillippe Rocca-Serra OBI biomaterial branch - + microscope slide @@ -1768,7 +1769,7 @@ This issue is outside the scope of OBI. experimental design rediscussed at length (MC/JF/BP). 12/9/08). The definition was clarified to differentiate it from protocol. - + study design @@ -1878,7 +1879,7 @@ This issue is outside the scope of OBI. Person:Alan Ruttenberg Person:Helen Parkinson 2009/09/28 Alan Ruttenberg. Fucoidan-use-case - + is member of organization @@ -2014,7 +2015,7 @@ This issue is outside the scope of OBI. See tracker: https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_id=177891&atid=886178 Person: Jie Zheng - + has organization member @@ -2092,5 +2093,5 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + diff --git a/src/ontology/imports/omo_import.owl b/src/ontology/imports/omo_import.owl index deef468..ca2d68b 100644 --- a/src/ontology/imports/omo_import.owl +++ b/src/ontology/imports/omo_import.owl @@ -7,9 +7,9 @@ Prefix(rdfs:=) Ontology( - -Annotation( ) -Annotation(owl:versionInfo "2023-06-21") + +Annotation( ) +Annotation(owl:versionInfo "2023-11-27") Declaration(Class()) Declaration(Class()) @@ -58,6 +58,7 @@ Declaration(NamedIndividual()) Declaration(NamedIndividual()) Declaration(NamedIndividual()) Declaration(NamedIndividual()) +Declaration(NamedIndividual()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -102,6 +103,11 @@ Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -120,7 +126,7 @@ Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -190,7 +196,7 @@ We don't have definitions of 'meaning' or 'expression' or 'property'. For 'refer Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. -We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. "@en) +We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with."@en) AnnotationAssertion( "PERSON:Daniel Schober"@en) AnnotationAssertion( "GROUP:OBI:"@en) AnnotationAssertion(rdfs:label "definition"@en) @@ -509,7 +515,7 @@ AnnotationAssertion( ) AnnotationAssertion( "2023-03-03"^^xsd:date) AnnotationAssertion(rdfs:label "abbreviation") -SubAnnotationPropertyOf( ) +SubAnnotationPropertyOf( ) # Annotation Property: (ambiguous synonym) @@ -518,7 +524,7 @@ AnnotationAssertion( ) AnnotationAssertion( "2023-03-03"^^xsd:date) AnnotationAssertion(rdfs:label "ambiguous synonym") -SubAnnotationPropertyOf( ) +SubAnnotationPropertyOf( ) # Annotation Property: (dubious synonym) @@ -527,7 +533,7 @@ AnnotationAssertion( ) AnnotationAssertion( "2023-03-03"^^xsd:date) AnnotationAssertion(rdfs:label "dubious synonym") -SubAnnotationPropertyOf( ) +SubAnnotationPropertyOf( ) # Annotation Property: (layperson synonym) @@ -537,7 +543,7 @@ AnnotationAssertion( ) AnnotationAssertion( "2023-03-03"^^xsd:date) AnnotationAssertion(rdfs:label "layperson synonym") -SubAnnotationPropertyOf( ) +SubAnnotationPropertyOf( ) # Annotation Property: (plural form) @@ -547,7 +553,7 @@ AnnotationAssertion( ) AnnotationAssertion( "2023-03-03"^^xsd:date) AnnotationAssertion(rdfs:label "plural form") -SubAnnotationPropertyOf( ) +SubAnnotationPropertyOf( ) # Annotation Property: (UK spelling synonym) @@ -557,7 +563,7 @@ AnnotationAssertion( ) AnnotationAssertion( "2023-03-03"^^xsd:date) AnnotationAssertion(rdfs:label "UK spelling synonym") -SubAnnotationPropertyOf( ) +SubAnnotationPropertyOf( ) # Annotation Property: (misspelling) @@ -566,7 +572,7 @@ AnnotationAssertion( ) AnnotationAssertion( "2023-03-03"^^xsd:date) AnnotationAssertion(rdfs:label "misspelling") -SubAnnotationPropertyOf( ) +SubAnnotationPropertyOf( ) # Annotation Property: (misnomer) @@ -575,7 +581,58 @@ AnnotationAssertion( ) AnnotationAssertion( "2023-03-03"^^xsd:date) AnnotationAssertion(rdfs:label "misnomer") -SubAnnotationPropertyOf( ) +SubAnnotationPropertyOf( ) + +# Annotation Property: (previous name) + +AnnotationAssertion( "MAPT, the gene that encodes the Tau protein, has a previous name DDPAC. Note: in this case, the name type is more specifically the gene symbol.") +AnnotationAssertion( "A synonym type for names that have been used as primary labels in the past.") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "2023-07-25"^^xsd:date) +AnnotationAssertion(rdfs:label "previous name") +SubAnnotationPropertyOf( ) + +# Annotation Property: (legal name) + +AnnotationAssertion( "The legal name for Harvard University (https://ror.org/03vek6s52) is President and Fellows of Harvard College") +AnnotationAssertion( "A synonym type for the legal entity name") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "2023-07-27"^^xsd:date) +AnnotationAssertion(rdfs:label "legal name") +SubAnnotationPropertyOf( ) + +# Annotation Property: (International Nonproprietary Name) + +AnnotationAssertion( "CHEBI:46195 has been assigned the english International Nonproproprietary Name (INN) \"paracetamol\". In some cases such as this one, the INN might be the same as the ontology's primary label") +AnnotationAssertion( "The International Nonproprietary Name (INN) is a standardize name for a pharmaceutical drug or active ingredient issued by the World Health Organization (WHO) meant to address the issues with country- or language-specific brand names. These are issued in several languages, including English, Latin, French, Russian, Spanish, Arabic, and Chinese.") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "2023-09-30"^^xsd:date) +AnnotationAssertion( "INN") +AnnotationAssertion(rdfs:label "International Nonproprietary Name") +SubAnnotationPropertyOf( ) + +# Annotation Property: (latin term) + +AnnotationAssertion( "nasopharynx (UBERON:0001728) has the latin name \"pars nasalis pharyngis") +AnnotationAssertion( "A synonym type for describing Latin term synonyms.") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "2023-10-12"^^xsd:date) +AnnotationAssertion(rdfs:label "latin term") +SubAnnotationPropertyOf( ) + +# Annotation Property: (acronym) + +AnnotationAssertion( "NASA is an word acronym for the US National Aeronautics and Space Administration because the acronym is pronounced. FBI is an initialism (also known as alphabetism) for the US Federal Bureau of Investigation since the letters are pronounced one at a time. JPEG is an acronym for Joint Photographic Experts Group but does not count as a word acronym nor an initialism since it is mixed how it is pronounced.") +AnnotationAssertion( "A synonym type for describing abbreviations that are a part of the full name's words, such as initialisms or alphabetisms.") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "2023-11-01"^^xsd:date) +AnnotationAssertion(rdfs:label "acronym") +SubAnnotationPropertyOf( ) # Annotation Property: (has broad synonym) @@ -1009,6 +1066,16 @@ AnnotationAssertion( "out of scope") ClassAssertion( ) +# Individual: (domain entity does not exist) + +AnnotationAssertion( "The term was added to the ontology on the assumption it was a valid domain entity, but it turns out the entity does not exist in reality."@en) +AnnotationAssertion( "This obsolesence reason should be used conservatively. For example: Obsoleting class that describes a breed of cow based on a record in an existing database, that was later retracted as faulty (breed does not exist). Do not use this term to obsolete a historic concept (that was once valid, but not anymore). "@en) +AnnotationAssertion( ) +AnnotationAssertion( "https://github.com/information-artifact-ontology/ontology-metadata/issues/136") +AnnotationAssertion( "https://orcid.org/0000-0002-4142-7153") +AnnotationAssertion(rdfs:label "domain entity does not exist") +ClassAssertion( ) + DifferentIndividuals( ) DifferentIndividuals( ) diff --git a/src/ontology/imports/pato_import.owl b/src/ontology/imports/pato_import.owl index 251f1f8..7426452 100644 --- a/src/ontology/imports/pato_import.owl +++ b/src/ontology/imports/pato_import.owl @@ -7,9 +7,9 @@ Prefix(rdfs:=) Ontology( - + Annotation( ) -Annotation(owl:versionInfo "2023-06-21") +Annotation(owl:versionInfo "2023-11-27") Declaration(Class()) Declaration(Class()) diff --git a/src/ontology/imports/ro_import.owl b/src/ontology/imports/ro_import.owl index df3eed2..4e93321 100644 --- a/src/ontology/imports/ro_import.owl +++ b/src/ontology/imports/ro_import.owl @@ -7,9 +7,9 @@ Prefix(rdfs:=) Ontology( - -Annotation( ) -Annotation(owl:versionInfo "2023-06-21") + +Annotation( ) +Annotation(owl:versionInfo "2023-11-27") Declaration(Class()) Declaration(Class()) @@ -26,6 +26,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) @@ -166,10 +167,7 @@ Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -194,6 +192,10 @@ Declaration(AnnotationProperty()) # Annotation Properties ############################ +# Annotation Property: (example of usage) + +AnnotationAssertion(rdfs:label "example of usage") + # Annotation Property: (definition) AnnotationAssertion(rdfs:label "definition") @@ -265,6 +267,7 @@ AnnotationAssertion( "part of"@en) AnnotationAssertion(rdfs:seeAlso ) AnnotationAssertion(rdfs:seeAlso ) +AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Part_of"^^xsd:anyURI) AnnotationAssertion(rdfs:seeAlso "http://www.obofoundry.org/ro/#OBO_REL:part_of") SubObjectPropertyOf( ) InverseObjectProperties( ) @@ -327,7 +330,7 @@ AnnotationAssertion( "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other."@en) AnnotationAssertion( "is preceded by"@en) AnnotationAssertion( "preceded_by"@en) -AnnotationAssertion( "http://www.obofoundry.org/ro/#OBO_REL:preceded_by") +AnnotationAssertion( "http://www.obofoundry.org/ro/#OBO_REL:preceded_by") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "preceded by"@en) SubObjectPropertyOf( ) @@ -397,7 +400,7 @@ AnnotationAssertion( "a relation between a process and a continuant, in which the continuant is somehow involved in the process"@en) AnnotationAssertion( "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time."@en) AnnotationAssertion( "has_participant"@en) -AnnotationAssertion( "http://www.obofoundry.org/ro/#OBO_REL:has_participant") +AnnotationAssertion( "http://www.obofoundry.org/ro/#OBO_REL:has_participant") AnnotationAssertion(rdfs:label "has participant"@en) ObjectPropertyDomain( ) ObjectPropertyRange( ) @@ -510,7 +513,7 @@ SubObjectPropertyOf( (has regulatory component activity) AnnotationAssertion( "A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B.") -AnnotationAssertion( "dos") +AnnotationAssertion( ) AnnotationAssertion( "2017-05-24T09:30:46Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label "has regulatory component activity") SubObjectPropertyOf( ) @@ -519,7 +522,7 @@ SubObjectPropertyOf( (has negative regulatory component activity) AnnotationAssertion( "A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B.") -AnnotationAssertion( "dos") +AnnotationAssertion( ) AnnotationAssertion( "2017-05-24T09:31:01Z"^^xsd:dateTime) AnnotationAssertion(rdfs:comment "By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'.") AnnotationAssertion(rdfs:label "has negative regulatory component activity") @@ -529,7 +532,7 @@ SubObjectPropertyOf( (has positive regulatory component activity) AnnotationAssertion( "A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B.") -AnnotationAssertion( "dos") +AnnotationAssertion( ) AnnotationAssertion( "2017-05-24T09:31:17Z"^^xsd:dateTime) AnnotationAssertion(rdfs:comment "By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'.") AnnotationAssertion(rdfs:label "has positive regulatory component activity") @@ -538,7 +541,7 @@ SubObjectPropertyOf( (has component activity) -AnnotationAssertion( "dos") +AnnotationAssertion( ) AnnotationAssertion( "2017-05-24T09:44:33Z"^^xsd:dateTime) AnnotationAssertion(rdfs:comment "A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B.") AnnotationAssertion(rdfs:label "has component activity") @@ -547,7 +550,7 @@ SubObjectPropertyOf( (has component process) AnnotationAssertion( "w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.") -AnnotationAssertion( "dos") +AnnotationAssertion( ) AnnotationAssertion( "2017-05-24T09:49:21Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label "has component process") SubObjectPropertyOf( ) @@ -556,17 +559,17 @@ ObjectPropertyRange( (directly regulated by) -AnnotationAssertion( "dos") +AnnotationAssertion( ) AnnotationAssertion( "2017-09-17T13:52:24Z"^^xsd:dateTime) -AnnotationAssertion(Annotation( "GOC:dos") rdfs:comment "Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2.") +AnnotationAssertion(Annotation( ) rdfs:comment "Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2.") AnnotationAssertion(rdfs:label "directly regulated by") SubObjectPropertyOf( ) InverseObjectProperties( ) # Object Property: (directly negatively regulated by) -AnnotationAssertion(Annotation( "GOC:dos") "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.") -AnnotationAssertion( "dos") +AnnotationAssertion(Annotation( ) "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.") +AnnotationAssertion( ) AnnotationAssertion( "2017-09-17T13:52:38Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label "directly negatively regulated by") SubObjectPropertyOf( ) @@ -574,8 +577,8 @@ InverseObjectProperties( (directly positively regulated by) -AnnotationAssertion(Annotation( "GOC:dos") "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.") -AnnotationAssertion( "dos") +AnnotationAssertion(Annotation( ) "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.") +AnnotationAssertion( ) AnnotationAssertion( "2017-09-17T13:52:47Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label "directly positively regulated by") SubObjectPropertyOf( ) @@ -583,8 +586,8 @@ InverseObjectProperties( (has effector activity) -AnnotationAssertion(Annotation( "GOC:dos") "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.") -AnnotationAssertion( "dos") +AnnotationAssertion(Annotation( ) "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.") +AnnotationAssertion( ) AnnotationAssertion( "2017-09-22T14:14:36Z"^^xsd:dateTime) AnnotationAssertion(rdfs:comment "This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations.") AnnotationAssertion(rdfs:label "has effector activity") @@ -748,6 +751,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "has input"@en) +AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Has_input"^^xsd:anyURI) SubObjectPropertyOf( ) InverseObjectProperties( ) ObjectPropertyDomain( ) @@ -768,7 +772,7 @@ AnnotationAssertion( "affects") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "acts upstream of or within") -AnnotationAssertion(rdfs:seeAlso ) +AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within"^^xsd:anyURI) SubObjectPropertyOf( ) # Object Property: (causally upstream of, positive effect) @@ -780,6 +784,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y") AnnotationAssertion(rdfs:label "causally upstream of, positive effect") +AnnotationAssertion(rdfs:seeAlso ) SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -791,6 +796,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "causally upstream of, negative effect") +AnnotationAssertion(rdfs:seeAlso ) SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -827,6 +833,7 @@ AnnotationAssertion( "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized.") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "enables"@en) +AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Enables"^^xsd:anyURI) SubObjectPropertyOf( ) InverseObjectProperties( ) @@ -852,7 +859,7 @@ AnnotationAssertion( "actively involved in") AnnotationAssertion( "enables part of") AnnotationAssertion(rdfs:label "involved in"@en) -AnnotationAssertion(rdfs:seeAlso ) +AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Involved_in"^^xsd:anyURI) SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -862,6 +869,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "enabled by"@en) +AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Enabled_by"^^xsd:anyURI) SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -929,6 +937,7 @@ AnnotationAssertion( "indirectly activates") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "indirectly positively regulates"@en) +AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Indirectly_positively_regulates"^^xsd:anyURI) SubObjectPropertyOf( ) SubObjectPropertyOf( ) TransitiveObjectProperty() @@ -940,6 +949,7 @@ AnnotationAssertion( "indirectly inhibits") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "indirectly negatively regulates"@en) +AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Indirectly_negatively_regulates"^^xsd:anyURI) SubObjectPropertyOf( ) SubObjectPropertyOf( ) TransitiveObjectProperty() @@ -1276,6 +1286,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "directly positively regulates") +AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Directly_positively_regulates"^^xsd:anyURI) SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -1289,6 +1300,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "directly negatively regulates") +AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Directly_negatively_regulates"^^xsd:anyURI) SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -1317,7 +1329,7 @@ AnnotationAssertion( "2018-01-26T23:49:30Z"^^xsd:dateTime) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "acts upstream of or within, positive effect") -AnnotationAssertion(rdfs:seeAlso ) +AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect"^^xsd:anyURI) SubObjectPropertyOf( ) # Object Property: (acts upstream of or within, negative effect) @@ -1327,6 +1339,7 @@ AnnotationAssertion( "2018-01-26T23:49:51Z"^^xsd:dateTime) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "acts upstream of or within, negative effect") +AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within,_negative_effect"^^xsd:anyURI) SubObjectPropertyOf( ) # Object Property: (acts upstream of, positive effect) @@ -1337,7 +1350,7 @@ AnnotationAssertion( "2018-01-26T23:53:14Z"^^xsd:dateTime) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "acts upstream of, positive effect") -AnnotationAssertion(rdfs:seeAlso ) +AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Acts_upstream_of,_positive_effect"^^xsd:anyURI) SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -1349,7 +1362,7 @@ AnnotationAssertion( "2018-01-26T23:53:22Z"^^xsd:dateTime) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "acts upstream of, negative effect") -AnnotationAssertion(rdfs:seeAlso ) +AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Acts_upstream_of,_negative_effect"^^xsd:anyURI) SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -1359,6 +1372,7 @@ AnnotationAssertion( ) AnnotationAssertion( "2018-03-13T23:55:05Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label "causally upstream of or within, negative effect") +AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect"^^xsd:anyURI) SubObjectPropertyOf( ) # Object Property: (causally upstream of or within, positive effect) @@ -1367,6 +1381,7 @@ AnnotationAssertion( ) AnnotationAssertion( "2018-03-13T23:55:19Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label "causally upstream of or within, positive effect") +AnnotationAssertion(rdfs:seeAlso ) SubObjectPropertyOf( ) # Object Property: (realized in response to) @@ -1379,7 +1394,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion(Annotation( "RO:cjm") "triggered by process") +AnnotationAssertion(Annotation( ) "triggered by process") AnnotationAssertion(rdfs:label "realized in response to"@en) AnnotationAssertion(rdfs:seeAlso "https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit"^^xsd:anyURI) SubObjectPropertyOf( ) @@ -1424,7 +1439,7 @@ ObjectPropertyRange( (indirectly causally upstream of) AnnotationAssertion( "p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q.") -AnnotationAssertion( "pg") +AnnotationAssertion( ) AnnotationAssertion( "2022-09-26T06:07:17Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label "indirectly causally upstream of"@en) SubObjectPropertyOf( ) @@ -1432,7 +1447,7 @@ SubObjectPropertyOf( (indirectly regulates) AnnotationAssertion( "p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q.") -AnnotationAssertion( "pg") +AnnotationAssertion( ) AnnotationAssertion( "2022-09-26T06:08:01Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label "indirectly regulates"@en) SubObjectPropertyOf( ) @@ -1446,7 +1461,7 @@ AnnotationAssertion( ) AnnotationAssertion( "A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input.") AnnotationAssertion( "See github ticket https://github.com/oborel/obo-relations/issues/497") -AnnotationAssertion( "2021-11-08T12:00:00Z") +AnnotationAssertion( "2021-11-08T12:00:00Z"^^xsd:dateTime) AnnotationAssertion( "utilizes") AnnotationAssertion(rdfs:label "device utilizes material"@en) @@ -1496,7 +1511,8 @@ DisjointClasses( ObjectSomeValuesFro # Class: (independent continuant) -AnnotationAssertion( "A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything."@en) +AnnotationAssertion( "b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])"@en) +AnnotationAssertion(rdfs:comment "A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything."@en) AnnotationAssertion(rdfs:label "independent continuant"@en) SubClassOf( ) SubClassOf( ObjectAllValuesFrom( )) @@ -1505,7 +1521,8 @@ DisjointClasses( (process) -AnnotationAssertion( "An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t."@en) +AnnotationAssertion( "p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])"@en) +AnnotationAssertion(rdfs:comment "An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t."@en) AnnotationAssertion(rdfs:label "process"@en) SubClassOf( ) @@ -1531,7 +1548,8 @@ SubClassOf( ObjectAllValuesFrom( (specifically dependent continuant) -AnnotationAssertion( "A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same."@en) +AnnotationAssertion( "b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])"@en) +AnnotationAssertion(rdfs:comment "A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same."@en) AnnotationAssertion(rdfs:label "specifically dependent continuant"@en) SubClassOf( ) SubClassOf( ObjectAllValuesFrom( )) @@ -1545,7 +1563,8 @@ SubClassOf( (generically dependent continuant) -AnnotationAssertion( "A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time."@en) +AnnotationAssertion( "b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])"@en) +AnnotationAssertion(rdfs:comment "A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time."@en) AnnotationAssertion(rdfs:label "generically dependent continuant"@en) SubClassOf( ) SubClassOf( ObjectAllValuesFrom( )) @@ -1637,17 +1656,17 @@ DLSafeRule(Body(ObjectPropertyAtom( V DLSafeRule(Annotation(rdfs:comment "If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.") Annotation(rdfs:label "inferring direct reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) DLSafeRule(Annotation(rdfs:label "inferring direct neg reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) DLSafeRule(Annotation(rdfs:label "inferring direct positive reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "effector input is compound function input") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "Input of effector is input of its parent MF") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:comment "if effector directly regulates X, its parent MF directly regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:comment "if effector directly positively regulates X, its parent MF directly positively regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "if effector directly negatively regulates X, its parent MF directly negatively regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable()))) -DLSafeRule(Annotation(rdfs:label "'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "effector input is compound function input") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "Input of effector is input of its parent MF") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:comment "if effector directly regulates X, its parent MF directly regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:comment "if effector directly positively regulates X, its parent MF directly positively regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "if effector directly negatively regulates X, its parent MF directly negatively regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable()))) +DLSafeRule(Annotation(rdfs:label "'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) ) \ No newline at end of file diff --git a/src/ontology/imports/stato_import.owl b/src/ontology/imports/stato_import.owl index 76ee579..ef67641 100644 --- a/src/ontology/imports/stato_import.owl +++ b/src/ontology/imports/stato_import.owl @@ -7,8 +7,8 @@ Prefix(rdfs:=) Ontology( - -Annotation(owl:versionInfo "2023-06-21") + +Annotation(owl:versionInfo "2023-11-27") Declaration(Class()) Declaration(Class()) diff --git a/src/ontology/vibso-edit.owl b/src/ontology/vibso-edit.owl index 459f3bd..a1b056e 100644 --- a/src/ontology/vibso-edit.owl +++ b/src/ontology/vibso-edit.owl @@ -1,4 +1,5 @@ Prefix(:=) +Prefix(ex:=) Prefix(DOI:=) Prefix(ROR:=) Prefix(dce:=) @@ -27,7 +28,6 @@ Import() Import() Import() Import() -Import() Annotation(dcterms:contributor ) Annotation(dcterms:contributor ) Annotation(dcterms:contributor ) @@ -37,6 +37,11 @@ Annotation(dcterms:description "_WIP - NOT READY FOR PRODUCTION_ The Vibration S Annotation(dcterms:license ) Annotation(dcterms:title "Vibrational Spectroscopy Ontology") +Declaration(NamedIndividual(ex:AssayObjective_O)) +Declaration(NamedIndividual(ex:Assay_A)) +Declaration(NamedIndividual(ex:DataItem_D)) +Declaration(NamedIndividual(ex:EvaluantRole_R)) +Declaration(NamedIndividual(ex:MaterialEntity_M)) Declaration(NamedIndividual()) Declaration(NamedIndividual()) Declaration(NamedIndividual()) @@ -75,6 +80,7 @@ AnnotationAssertion(rdfs:label dcterms:title "title") + ############################ # Classes ############################ @@ -89,6 +95,35 @@ SubClassOf(obo:NCBITaxon_9606 obo:OBI_0100026) # Named Individuals ############################ +# Individual: ex:AssayObjective_O (ex:AssayObjective_O) + +ClassAssertion(obo:OBI_0000441 ex:AssayObjective_O) + +# Individual: ex:Assay_A (ex:Assay_A) + +AnnotationAssertion(dce:description ex:Assay_A "The assay A is planned to produce as a specified output the data item D which is a specific kind of information about the material entity M, which has the evaluant role R that gets realized in this planned observation process. + +This example instance is part of the ontology to demonstrate the OBI assay pattern. The type and number of relations between this instance and other example instances are based on the subclassOf and equivalentTo axioms asserted on OBI's assay."@en) +ClassAssertion(obo:OBI_0000070 ex:Assay_A) +ObjectPropertyAssertion(obo:BFO_0000055 ex:Assay_A ex:EvaluantRole_R) +ObjectPropertyAssertion(obo:OBI_0000293 ex:Assay_A ex:MaterialEntity_M) +ObjectPropertyAssertion(obo:OBI_0000299 ex:Assay_A ex:DataItem_D) +ObjectPropertyAssertion(obo:OBI_0000417 ex:Assay_A ex:AssayObjective_O) + +# Individual: ex:DataItem_D (ex:DataItem_D) + +ClassAssertion(obo:IAO_0000027 ex:DataItem_D) +ObjectPropertyAssertion(obo:IAO_0000136 ex:DataItem_D ex:MaterialEntity_M) + +# Individual: ex:EvaluantRole_R (ex:EvaluantRole_R) + +ClassAssertion(obo:BFO_0000023 ex:EvaluantRole_R) + +# Individual: ex:MaterialEntity_M (ex:MaterialEntity_M) + +ClassAssertion(obo:BFO_0000040 ex:MaterialEntity_M) +ObjectPropertyAssertion(obo:RO_0000087 ex:MaterialEntity_M ex:EvaluantRole_R) + # Individual: (Philip Strömert) AnnotationAssertion(rdfs:label "Philip Strömert") diff --git a/vibso-base.obo b/vibso-base.obo index da17117..38c99b8 100644 --- a/vibso-base.obo +++ b/vibso-base.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: vibso/releases/2023-06-21/vibso-base.owl +data-version: vibso/releases/2023-11-27/vibso-base.owl ontology: vibso/vibso-base property_value: http://purl.org/dc/elements/1.1/type IAO:8000001 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-1595-3213 @@ -10,7 +10,7 @@ property_value: http://purl.org/dc/terms/creator "VIBSO Workgroup" xsd:string property_value: http://purl.org/dc/terms/description "_WIP - NOT READY FOR PRODUCTION_ The Vibration Spectroscopy Ontology (VIBSO) is used to represent information regarding the excution and analysis of vibrational spectroscopy assays." xsd:string property_value: http://purl.org/dc/terms/license https://creativecommons.org/licenses/by/4.0/ property_value: http://purl.org/dc/terms/title "Vibrational Spectroscopy Ontology" xsd:string -property_value: owl:versionInfo "2023-06-21" xsd:string +property_value: owl:versionInfo "2023-11-27" xsd:string [Term] id: NCBITaxon:9606 @@ -42,6 +42,7 @@ is_a: IAO:0000140 property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-1595-3213 property_value: IAO:0000116 "This class should better be defined in a more general device ontology or a domain ontology with the scope of optical devices." xsd:string property_value: IAO:0000118 "integration period setting" xsd:string +property_value: IAO:0000118 "integration time" xsd:string property_value: seeAlso https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/40 [Term] @@ -116,6 +117,8 @@ def: "A setting datum that specifies the number of grooves in a diffraction grat is_a: IAO:0000140 property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-1595-3213 property_value: IAO:0000116 "This class should better be defined in a more general device ontology or a domain ontology with the scope of optical devices." xsd:string +property_value: IAO:0000118 "grating" xsd:string +property_value: IAO:0000118 "grating setting" xsd:string property_value: seeAlso https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/45 [Term] @@ -156,6 +159,8 @@ property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/000 property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-1595-3213 property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-2239-3955 property_value: IAO:0000112 "example:RamanSpectrometerX rdf:type obo:CHMO_0001235 (Raman spectrometer) ;\n obo:OBI_0000293 (has_specified_input) example:objective_magnification_factor_setting_for_RamanSpectrometerX .\nexample:objective_magnification_factor_setting_for_RamanSpectrometerX rdf:type obo:VIBSO_0000014 ;\n obo:OBI_0002815 (has representation) '100 x' ." xsd:string +property_value: IAO:0000118 "magnification" xsd:string +property_value: IAO:0000118 "magnification setting" xsd:string property_value: seeAlso https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/24%20 [Term] diff --git a/vibso-base.owl b/vibso-base.owl index 0497e60..2faa579 100644 --- a/vibso-base.owl +++ b/vibso-base.owl @@ -18,7 +18,7 @@ xmlns:schema1="https://schema.org/" xmlns:wikipedia="https://en.wikipedia.org/wiki/"> - + @@ -28,7 +28,7 @@ _WIP - NOT READY FOR PRODUCTION_ The Vibration Spectroscopy Ontology (VIBSO) is used to represent information regarding the excution and analysis of vibrational spectroscopy assays. Vibrational Spectroscopy Ontology - 2023-06-21 + 2023-11-27 @@ -267,6 +267,7 @@ A setting datum that specifies the length of time that a photo detector is allowed to collect photons before passing the accumulated charge to the A/D converter for processing. The minimum integration time is the shortest integration time the device supports and is dependent on how fast the detector can read out all of the pixel information. Integration time should not be confused with data transfer speed. This class should better be defined in a more general device ontology or a domain ontology with the scope of optical devices. integration period setting + integration time integration time setting @@ -386,6 +387,8 @@ A setting datum that specifies the number of grooves in a diffraction grating device. This class should better be defined in a more general device ontology or a domain ontology with the scope of optical devices. + grating + grating setting groove density setting @@ -449,6 +452,8 @@ example:objective_magnification_factor_setting_for_RamanSpectrometerX rdf:type obo:VIBSO_0000014 ; obo:OBI_0002815 (has representation) '100 x' . A setting datum that specifies the magnification factor of the objective collecting the scattered light. + magnification + magnification setting @@ -770,5 +775,5 @@ Together with the focal point distance, this setting defines the region of inter - + diff --git a/vibso-full.obo b/vibso-full.obo index c20ebd7..521f963 100644 --- a/vibso-full.obo +++ b/vibso-full.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: vibso/releases/2023-06-21/vibso-full.owl +data-version: vibso/releases/2023-11-27/vibso-full.owl subsetdef: attribute_slim "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_gp2term "" @@ -10,6 +10,19 @@ subsetdef: ro-eco "" subsetdef: RO:0002259 "" subsetdef: scalar_slim "" subsetdef: value_slim "" +synonymtypedef: OMO:0003000 "abbreviation" +synonymtypedef: OMO:0003001 "ambiguous synonym" +synonymtypedef: OMO:0003002 "dubious synonym" +synonymtypedef: OMO:0003003 "layperson synonym" +synonymtypedef: OMO:0003004 "plural form" +synonymtypedef: OMO:0003005 "UK spelling synonym" +synonymtypedef: OMO:0003006 "misspelling" +synonymtypedef: OMO:0003007 "misnomer" +synonymtypedef: OMO:0003008 "previous name" +synonymtypedef: OMO:0003009 "legal name" +synonymtypedef: OMO:0003010 "International Nonproprietary Name" +synonymtypedef: OMO:0003011 "latin term" +synonymtypedef: OMO:0003012 "acronym" ontology: vibso/vibso-full property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-1595-3213 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2239-3955 @@ -19,7 +32,7 @@ property_value: http://purl.org/dc/terms/creator "VIBSO Workgroup" xsd:string property_value: http://purl.org/dc/terms/description "_WIP - NOT READY FOR PRODUCTION_ The Vibration Spectroscopy Ontology (VIBSO) is used to represent information regarding the excution and analysis of vibrational spectroscopy assays." xsd:string property_value: http://purl.org/dc/terms/license https://creativecommons.org/licenses/by/4.0/ property_value: http://purl.org/dc/terms/title "Vibrational Spectroscopy Ontology" xsd:string -property_value: owl:versionInfo "2023-06-21" xsd:string +property_value: owl:versionInfo "2023-11-27" xsd:string [Term] id: BFO:0000001 @@ -31,8 +44,8 @@ property_value: IAO:0000112 "the Second World War" xsd:string property_value: IAO:0000112 "Verdi’s Requiem" xsd:string property_value: IAO:0000112 "your body mass index" xsd:string property_value: IAO:0000116 "BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81" xsd:string -property_value: IAO:0000116 "Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000004", comment="per discussion with Barry Smith", http://www.w3.org/2000/01/rdf-schema#seeAlso="http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf"} -property_value: IAO:0000600 "An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/001-001"} +property_value: IAO:0000116 "Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000004", comment="per discussion with Barry Smith", seeAlso="http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf"} +property_value: IAO:0000600 "An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/001-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] @@ -45,15 +58,15 @@ relationship: BFO:0000050 BFO:0000002 {all_only="true"} ! part of continuant property_value: BFO:0000179 "continuant" xsd:string property_value: BFO:0000180 "Continuant" xsd:string property_value: IAO:0000116 "BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240" xsd:string -property_value: IAO:0000116 "Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000007"} -property_value: IAO:0000600 "A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/008-002"} -property_value: IAO:0000601 "if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/126-001"} -property_value: IAO:0000601 "if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/009-002"} -property_value: IAO:0000601 "if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/011-002"} -property_value: IAO:0000602 "(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/009-002"} -property_value: IAO:0000602 "(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/126-001"} -property_value: IAO:0000602 "(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/008-002"} -property_value: IAO:0000602 "(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/011-002"} +property_value: IAO:0000116 "Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000007"} +property_value: IAO:0000600 "A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/008-002"} +property_value: IAO:0000601 "if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/126-001"} +property_value: IAO:0000601 "if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/009-002"} +property_value: IAO:0000601 "if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/011-002"} +property_value: IAO:0000602 "(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/009-002"} +property_value: IAO:0000602 "(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/126-001"} +property_value: IAO:0000602 "(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/008-002"} +property_value: IAO:0000602 "(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/011-002"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] @@ -66,20 +79,20 @@ property_value: BFO:0000179 "occurrent" xsd:string property_value: BFO:0000180 "Occurrent" xsd:string property_value: IAO:0000116 "BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region" xsd:string property_value: IAO:0000116 "BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players." xsd:string -property_value: IAO:0000116 "Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000006", comment="per discussion with Barry Smith"} -property_value: IAO:0000116 "Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000012"} -property_value: IAO:0000600 "An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/077-002"} -property_value: IAO:0000601 "b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/079-001"} -property_value: IAO:0000601 "Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/108-001"} -property_value: IAO:0000602 "(forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/108-001"} -property_value: IAO:0000602 "(forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/079-001"} +property_value: IAO:0000116 "Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process." xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000006", comment="per discussion with Barry Smith"} +property_value: IAO:0000116 "Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame." xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000012"} +property_value: IAO:0000600 "An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/077-002"} +property_value: IAO:0000601 "b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/079-001"} +property_value: IAO:0000601 "Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/108-001"} +property_value: IAO:0000602 "(forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/108-001"} +property_value: IAO:0000602 "(forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/079-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000004 name: independent continuant -def: "A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything." [] -def: "b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/017-002"} +def: "b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])" [] {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/017-002"} +comment: A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. is_a: BFO:0000002 ! continuant disjoint_from: BFO:0000020 ! specifically dependent continuant disjoint_from: BFO:0000031 ! generically dependent continuant @@ -96,11 +109,11 @@ property_value: IAO:0000112 "an orchestra." xsd:string property_value: IAO:0000112 "an organism" xsd:string property_value: IAO:0000112 "the bottom right portion of a human torso" xsd:string property_value: IAO:0000112 "the interior of your mouth" xsd:string -property_value: IAO:0000601 "For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/134-001"} -property_value: IAO:0000601 "For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/018-002"} -property_value: IAO:0000602 "(forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/018-002"} -property_value: IAO:0000602 "(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/134-001"} -property_value: IAO:0000602 "(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/017-002"} +property_value: IAO:0000601 "For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/134-001"} +property_value: IAO:0000601 "For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/018-002"} +property_value: IAO:0000602 "(forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/018-002"} +property_value: IAO:0000602 "(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/134-001"} +property_value: IAO:0000602 "(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/017-002"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] @@ -112,11 +125,11 @@ disjoint_from: BFO:0000140 ! continuant fiat boundary property_value: BFO:0000179 "s-region" xsd:string property_value: BFO:0000180 "SpatialRegion" xsd:string property_value: IAO:0000116 "BFO 2 Reference: Spatial regions do not participate in processes." xsd:string -property_value: IAO:0000116 "Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000002", comment="per discussion with Barry Smith"} -property_value: IAO:0000600 "A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/035-001"} -property_value: IAO:0000601 "All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/036-001"} -property_value: IAO:0000602 "(forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/036-001"} -property_value: IAO:0000602 "(forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/035-001"} +property_value: IAO:0000116 "Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional." xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000002", comment="per discussion with Barry Smith"} +property_value: IAO:0000600 "A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/035-001"} +property_value: IAO:0000601 "All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/036-001"} +property_value: IAO:0000602 "(forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/036-001"} +property_value: IAO:0000602 "(forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/035-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] @@ -128,13 +141,13 @@ disjoint_from: BFO:0000015 ! process disjoint_from: BFO:0000035 ! process boundary property_value: BFO:0000179 "t-region" xsd:string property_value: BFO:0000180 "TemporalRegion" xsd:string -property_value: IAO:0000116 "Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000003", comment="per discussion with Barry Smith"} -property_value: IAO:0000600 "A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/100-001"} -property_value: IAO:0000601 "All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/101-001"} -property_value: IAO:0000601 "Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/119-002"} -property_value: IAO:0000602 "(forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/119-002"} -property_value: IAO:0000602 "(forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/101-001"} -property_value: IAO:0000602 "(forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/100-001"} +property_value: IAO:0000116 "Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000003", comment="per discussion with Barry Smith"} +property_value: IAO:0000600 "A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/100-001"} +property_value: IAO:0000601 "All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/101-001"} +property_value: IAO:0000601 "Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/119-002"} +property_value: IAO:0000602 "(forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/119-002"} +property_value: IAO:0000602 "(forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/101-001"} +property_value: IAO:0000602 "(forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/100-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] @@ -146,8 +159,8 @@ property_value: BFO:0000179 "2d-s-region" xsd:string property_value: BFO:0000180 "TwoDimensionalSpatialRegion" xsd:string property_value: IAO:0000112 "an infinitely thin plane in space." xsd:string property_value: IAO:0000112 "the surface of a sphere-shaped part of space" xsd:string -property_value: IAO:0000600 "A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/039-001"} -property_value: IAO:0000602 "(forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/039-001"} +property_value: IAO:0000600 "A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/039-001"} +property_value: IAO:0000602 "(forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/039-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] @@ -159,24 +172,24 @@ property_value: BFO:0000180 "SpatiotemporalRegion" xsd:string property_value: IAO:0000112 "the spatiotemporal region occupied by a human life" xsd:string property_value: IAO:0000112 "the spatiotemporal region occupied by a process of cellular meiosis." xsd:string property_value: IAO:0000112 "the spatiotemporal region occupied by the development of a cancer tumor" xsd:string -property_value: IAO:0000600 "A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/095-001"} -property_value: IAO:0000601 "All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/096-001"} -property_value: IAO:0000601 "Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/099-001"} -property_value: IAO:0000601 "Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/098-001"} +property_value: IAO:0000600 "A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/095-001"} +property_value: IAO:0000601 "All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/096-001"} +property_value: IAO:0000601 "Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/099-001"} +property_value: IAO:0000601 "Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/098-001"} property_value: IAO:0000601 "Every spatiotemporal region occupies_spatiotemporal_region itself." xsd:string -property_value: IAO:0000601 "Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/107-002"} -property_value: IAO:0000602 "(forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/107-002"} -property_value: IAO:0000602 "(forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/099-001"} -property_value: IAO:0000602 "(forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/096-001"} -property_value: IAO:0000602 "(forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/098-001"} -property_value: IAO:0000602 "(forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/095-001"} +property_value: IAO:0000601 "Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/107-002"} +property_value: IAO:0000602 "(forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/107-002"} +property_value: IAO:0000602 "(forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/099-001"} +property_value: IAO:0000602 "(forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/096-001"} +property_value: IAO:0000602 "(forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/098-001"} +property_value: IAO:0000602 "(forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/095-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000015 name: process -def: "An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t." [] -def: "p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/083-003"} +def: "p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])" [] {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/083-003"} +comment: An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. is_a: BFO:0000003 ! occurrent property_value: BFO:0000179 "process" xsd:string property_value: BFO:0000180 "Process" xsd:string @@ -188,7 +201,7 @@ property_value: IAO:0000112 "the flight of a bird" xsd:string property_value: IAO:0000112 "the life of an organism" xsd:string property_value: IAO:0000112 "your process of aging." xsd:string property_value: IAO:0000116 "BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war)" xsd:string -property_value: IAO:0000602 "(iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/083-003"} +property_value: IAO:0000602 "(iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/083-003"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] @@ -203,10 +216,10 @@ property_value: IAO:0000112 "certain people have a predisposition to colon cance property_value: IAO:0000112 "children are innately disposed to categorize objects in certain ways." xsd:string property_value: IAO:0000112 "the cell wall is disposed to filter chemicals in endocytosis and exocytosis" xsd:string property_value: IAO:0000116 "BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type." xsd:string -property_value: IAO:0000600 "b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/062-002"} -property_value: IAO:0000601 "If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/063-002"} -property_value: IAO:0000602 "(forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/063-002"} -property_value: IAO:0000602 "(forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/062-002"} +property_value: IAO:0000600 "b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/062-002"} +property_value: IAO:0000601 "If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/063-002"} +property_value: IAO:0000602 "(forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/063-002"} +property_value: IAO:0000602 "(forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/062-002"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] @@ -223,10 +236,10 @@ property_value: IAO:0000112 "the disposition of your blood to coagulate" xsd:str property_value: IAO:0000112 "the function of your reproductive organs" xsd:string property_value: IAO:0000112 "the role of being a doctor" xsd:string property_value: IAO:0000112 "the role of this boundary to delineate where Utah and Colorado meet" xsd:string -property_value: IAO:0000600 "To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/058-002"} -property_value: IAO:0000601 "All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/060-002"} -property_value: IAO:0000602 "(forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/060-002"} -property_value: IAO:0000602 "(forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/058-002"} +property_value: IAO:0000600 "To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/058-002"} +property_value: IAO:0000601 "All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/060-002"} +property_value: IAO:0000602 "(forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/060-002"} +property_value: IAO:0000602 "(forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/058-002"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] @@ -236,8 +249,8 @@ is_a: BFO:0000006 ! spatial region disjoint_from: BFO:0000028 ! three-dimensional spatial region property_value: BFO:0000179 "0d-s-region" xsd:string property_value: BFO:0000180 "ZeroDimensionalSpatialRegion" xsd:string -property_value: IAO:0000600 "A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/037-001"} -property_value: IAO:0000602 "(forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/037-001"} +property_value: IAO:0000600 "A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/037-001"} +property_value: IAO:0000602 "(forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/037-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] @@ -253,17 +266,17 @@ property_value: IAO:0000112 "the length of the circumference of your waist" xsd: property_value: IAO:0000112 "the mass of this piece of gold." xsd:string property_value: IAO:0000112 "the shape of your nose" xsd:string property_value: IAO:0000112 "the shape of your nostril" xsd:string -property_value: IAO:0000600 "a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/055-001"} -property_value: IAO:0000601 "If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/105-001"} -property_value: IAO:0000602 "(forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/105-001"} -property_value: IAO:0000602 "(forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/055-001"} +property_value: IAO:0000600 "a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/055-001"} +property_value: IAO:0000601 "If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/105-001"} +property_value: IAO:0000602 "(forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/105-001"} +property_value: IAO:0000602 "(forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/055-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000020 name: specifically dependent continuant -def: "A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same." [] -def: "b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/050-003"} +def: "b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])" [] {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/050-003"} +comment: A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. is_a: BFO:0000002 ! continuant disjoint_from: BFO:0000031 ! generically dependent continuant relationship: BFO:0000050 BFO:0000020 {all_only="true"} ! part of specifically dependent continuant @@ -280,8 +293,8 @@ property_value: IAO:0000112 "the pink color of a medium rare piece of grilled fi property_value: IAO:0000112 "the role of being a doctor" xsd:string property_value: IAO:0000112 "the shape of this hole." xsd:string property_value: IAO:0000112 "the smell of this portion of mozzarella" xsd:string -property_value: IAO:0000116 "Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000005", comment="per discussion with Barry Smith"} -property_value: IAO:0000602 "(iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/050-003"} +property_value: IAO:0000116 "Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc." xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000005", comment="per discussion with Barry Smith"} +property_value: IAO:0000602 "(iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/050-003"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] @@ -299,8 +312,8 @@ property_value: IAO:0000112 "the role of a stone in marking a property boundary" property_value: IAO:0000112 "the role of subject in a clinical trial" xsd:string property_value: IAO:0000112 "the student role" xsd:string property_value: IAO:0000116 "BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives." xsd:string -property_value: IAO:0000600 "b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/061-001"} -property_value: IAO:0000602 "(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/061-001"} +property_value: IAO:0000600 "b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/061-001"} +property_value: IAO:0000602 "(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/061-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] @@ -317,8 +330,8 @@ property_value: IAO:0000112 "the FMA:regional parts of an intact human body." xs property_value: IAO:0000112 "the upper and lower lobes of the left lung" xsd:string property_value: IAO:0000112 "the Western hemisphere of the Earth" xsd:string property_value: IAO:0000116 "BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisions" xsd:string -property_value: IAO:0000600 "b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/027-004"} -property_value: IAO:0000602 "(forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/027-004"} +property_value: IAO:0000600 "b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/027-004"} +property_value: IAO:0000602 "(forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/027-004"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] @@ -329,8 +342,8 @@ disjoint_from: BFO:0000028 ! three-dimensional spatial region property_value: BFO:0000179 "1d-s-region" xsd:string property_value: BFO:0000180 "OneDimensionalSpatialRegion" xsd:string property_value: IAO:0000112 "an edge of a cube-shaped portion of space." xsd:string -property_value: IAO:0000600 "A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/038-001"} -property_value: IAO:0000602 "(forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/038-001"} +property_value: IAO:0000600 "A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/038-001"} +property_value: IAO:0000602 "(forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/038-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] @@ -352,12 +365,12 @@ property_value: IAO:0000112 "the aggregate of blood cells in your body" xsd:stri property_value: IAO:0000112 "the nitrogen atoms in the atmosphere" xsd:string property_value: IAO:0000112 "the restaurants in Palo Alto" xsd:string property_value: IAO:0000112 "your collection of Meissen ceramic plates." xsd:string -property_value: IAO:0000116 "An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000301"} -property_value: IAO:0000116 "An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000011"} +property_value: IAO:0000116 "An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000301"} +property_value: IAO:0000116 "An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000011"} property_value: IAO:0000116 "BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee)." xsd:string -property_value: IAO:0000119 "ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000300"} -property_value: IAO:0000600 "b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/025-004"} -property_value: IAO:0000602 "(forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/025-004"} +property_value: IAO:0000119 "ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158." xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000300"} +property_value: IAO:0000600 "b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/025-004"} +property_value: IAO:0000602 "(forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/025-004"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] @@ -368,8 +381,8 @@ property_value: BFO:0000179 "3d-s-region" xsd:string property_value: BFO:0000180 "ThreeDimensionalSpatialRegion" xsd:string property_value: IAO:0000112 "a cube-shaped region of space" xsd:string property_value: IAO:0000112 "a sphere-shaped region of space," xsd:string -property_value: IAO:0000600 "A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/040-001"} -property_value: IAO:0000602 "(forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/040-001"} +property_value: IAO:0000600 "A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/040-001"} +property_value: IAO:0000602 "(forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/040-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] @@ -393,8 +406,8 @@ property_value: IAO:0000112 "the interior of your refrigerator" xsd:string property_value: IAO:0000112 "the lumen of your gut" xsd:string property_value: IAO:0000112 "the Piazza San Marco" xsd:string property_value: IAO:0000112 "your left nostril (a fiat part – the opening – of your left nasal cavity)" xsd:string -property_value: IAO:0000600 "b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/034-002"} -property_value: IAO:0000602 "(forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/034-002"} +property_value: IAO:0000600 "b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/034-002"} +property_value: IAO:0000602 "(forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/034-002"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] @@ -419,14 +432,14 @@ property_value: IAO:0000116 "BFO 2 Reference: BFO rests on the presupposition th property_value: IAO:0000116 "BFO 2 Reference: Each object is such that there are entities of which we can assert unproblematically that they lie in its interior, and other entities of which we can assert unproblematically that they lie in its exterior. This may not be so for entities lying at or near the boundary between the interior and exterior. This means that two objects – for example the two cells depicted in Figure 3 – may be such that there are material entities crossing their boundaries which belong determinately to neither cell. Something similar obtains in certain cases of conjoined twins (see below)." xsd:string property_value: IAO:0000116 "BFO 2 Reference: To say that b is causally unified means: b is a material entity which is such that its material parts are tied together in such a way that, in environments typical for entities of the type in question,if c, a continuant part of b that is in the interior of b at t, is larger than a certain threshold size (which will be determined differently from case to case, depending on factors such as porosity of external cover) and is moved in space to be at t at a location on the exterior of the spatial region that had been occupied by b at t, then either b’s other parts will be moved in coordinated fashion or b will be damaged (be affected, for example, by breakage or tearing) in the interval between t and t.causal changes in one part of b can have consequences for other parts of b without the mediation of any entity that lies on the exterior of b. Material entities with no proper material parts would satisfy these conditions trivially. Candidate examples of types of causal unity for material entities of more complex sorts are as follows (this is not intended to be an exhaustive list):CU1: Causal unity via physical coveringHere the parts in the interior of the unified entity are combined together causally through a common membrane or other physical covering\\. The latter points outwards toward and may serve a protective function in relation to what lies on the exterior of the entity [13, 47" xsd:string property_value: IAO:0000116 "BFO 2 Reference: ‘objects’ are sometimes referred to as ‘grains’ [74" xsd:string -property_value: IAO:0000600 "b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/024-001"} +property_value: IAO:0000600 "b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/024-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000031 name: generically dependent continuant -def: "A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time." [] -def: "b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/074-001"} +def: "b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])" [] {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/074-001"} +comment: A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. is_a: BFO:0000002 ! continuant relationship: BFO:0000050 BFO:0000031 {all_only="true"} ! part of generically dependent continuant property_value: BFO:0000179 "gdc" xsd:string @@ -434,7 +447,7 @@ property_value: BFO:0000180 "GenericallyDependentContinuant" xsd:string property_value: IAO:0000112 "The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity." xsd:string property_value: IAO:0000112 "the pdf file on your laptop, the pdf file that is a copy thereof on my laptop" xsd:string property_value: IAO:0000112 "the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule." xsd:string -property_value: IAO:0000602 "(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/074-001"} +property_value: IAO:0000602 "(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/074-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] @@ -443,26 +456,26 @@ name: function is_a: BFO:0000016 ! disposition property_value: BFO:0000179 "function" xsd:string property_value: BFO:0000180 "Function" xsd:string -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000112 "the function of a hammer to drive in nails" xsd:string property_value: IAO:0000112 "the function of a heart pacemaker to regulate the beating of a heart through electricity" xsd:string property_value: IAO:0000112 "the function of amylase in saliva to break down starch into sugar" xsd:string property_value: IAO:0000116 "BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc." xsd:string -property_value: IAO:0000600 "A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/064-001"} -property_value: IAO:0000602 "(forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/064-001"} +property_value: IAO:0000600 "A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/064-001"} +property_value: IAO:0000602 "(forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/064-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000035 name: process boundary -def: "p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/084-001"} +def: "p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001])" [] {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/084-001"} is_a: BFO:0000003 ! occurrent property_value: BFO:0000179 "p-boundary" xsd:string property_value: BFO:0000180 "ProcessBoundary" xsd:string property_value: IAO:0000112 "the boundary between the 2nd and 3rd year of your life." xsd:string -property_value: IAO:0000601 "Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/085-002"} -property_value: IAO:0000602 "(forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/085-002"} -property_value: IAO:0000602 "(iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/084-001"} +property_value: IAO:0000601 "Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/085-002"} +property_value: IAO:0000602 "(forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/085-002"} +property_value: IAO:0000602 "(iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/084-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] @@ -474,8 +487,8 @@ property_value: BFO:0000179 "1d-t-region" xsd:string property_value: BFO:0000180 "OneDimensionalTemporalRegion" xsd:string property_value: IAO:0000112 "the temporal region during which a process occurs." xsd:string property_value: IAO:0000116 "BFO 2 Reference: A temporal interval is a special kind of one-dimensional temporal region, namely one that is self-connected (is without gaps or breaks)." xsd:string -property_value: IAO:0000600 "A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/103-001"} -property_value: IAO:0000602 "(forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/103-001"} +property_value: IAO:0000600 "A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/103-001"} +property_value: IAO:0000602 "(forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/103-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] @@ -501,26 +514,26 @@ property_value: IAO:0000112 "the undetached arm of a human being" xsd:string property_value: IAO:0000116 "BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60" xsd:string property_value: IAO:0000116 "BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity." xsd:string property_value: IAO:0000116 "BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here." xsd:string -property_value: IAO:0000600 "A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/019-002"} -property_value: IAO:0000601 "every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/021-002"} -property_value: IAO:0000601 "Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/020-002"} -property_value: IAO:0000602 "(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/021-002"} -property_value: IAO:0000602 "(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/020-002"} -property_value: IAO:0000602 "(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/019-002"} +property_value: IAO:0000600 "A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/019-002"} +property_value: IAO:0000601 "every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/021-002"} +property_value: IAO:0000601 "Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/020-002"} +property_value: IAO:0000602 "(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/021-002"} +property_value: IAO:0000602 "(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/020-002"} +property_value: IAO:0000602 "(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/019-002"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000140 name: continuant fiat boundary -def: "b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/029-001"} +def: "b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001])" [] {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/029-001"} is_a: BFO:0000141 ! immaterial entity property_value: BFO:0000179 "cf-boundary" xsd:string property_value: BFO:0000180 "ContinuantFiatBoundary" xsd:string property_value: IAO:0000116 "BFO 2 Reference: a continuant fiat boundary is a boundary of some material entity (for example: the plane separating the Northern and Southern hemispheres; the North Pole), or it is a boundary of some immaterial entity (for example of some portion of airspace). Three basic kinds of continuant fiat boundary can be distinguished (together with various combination kinds [29" xsd:string property_value: IAO:0000116 "BFO 2 Reference: In BFO 1.1 the assumption was made that the external surface of a material entity such as a cell could be treated as if it were a boundary in the mathematical sense. The new document propounds the view that when we talk about external surfaces of material objects in this way then we are talking about something fiat. To be dealt with in a future version: fiat boundaries at different levels of granularity.More generally, the focus in discussion of boundaries in BFO 2.0 is now on fiat boundaries, which means: boundaries for which there is no assumption that they coincide with physical discontinuities. The ontology of boundaries becomes more closely allied with the ontology of regions." xsd:string -property_value: IAO:0000116 "Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000008"} +property_value: IAO:0000116 "Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions." xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000008"} property_value: IAO:0000601 "Every continuant fiat boundary is located at some spatial region at every time at which it exists" xsd:string -property_value: IAO:0000602 "(iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/029-001"} +property_value: IAO:0000602 "(iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/029-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] @@ -545,14 +558,14 @@ property_value: IAO:0000112 "all lines of latitude and longitude" xsd:string property_value: IAO:0000112 "The Equator" xsd:string property_value: IAO:0000112 "the line separating the outer surface of the mucosa of the lower lip from the outer surface of the skin of the chin." xsd:string property_value: IAO:0000112 "the median sulcus of your tongue" xsd:string -property_value: IAO:0000600 "a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/032-001"} -property_value: IAO:0000602 "(iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/032-001"} +property_value: IAO:0000600 "a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/032-001"} +property_value: IAO:0000602 "(iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/032-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000144 name: process profile -def: "b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/093-002"} +def: "b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002])" [] {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/093-002"} is_a: BFO:0000015 ! process disjoint_from: BFO:0000182 ! history property_value: BFO:0000179 "process-profile" xsd:string @@ -560,21 +573,21 @@ property_value: BFO:0000180 "ProcessProfile" xsd:string property_value: IAO:0000112 "On a somewhat higher level of complexity are what we shall call rate process profiles, which are the targets of selective abstraction focused not on determinate quality magnitudes plotted over time, but rather on certain ratios between these magnitudes and elapsed times. A speed process profile, for example, is represented by a graph plotting against time the ratio of distance covered per unit of time. Since rates may change, and since such changes, too, may have rates of change, we have to deal here with a hierarchy of process profile universals at successive levels" xsd:string property_value: IAO:0000112 "One important sub-family of rate process profiles is illustrated by the beat or frequency profiles of cyclical processes, illustrated by the 60 beats per minute beating process of John’s heart, or the 120 beats per minute drumming process involved in one of John’s performances in a rock band, and so on. Each such process includes what we shall call a beat process profile instance as part, a subtype of rate process profile in which the salient ratio is not distance covered but rather number of beat cycles per unit of time. Each beat process profile instance instantiates the determinable universal beat process profile. But it also instantiates multiple more specialized universals at lower levels of generality, selected from rate process profilebeat process profileregular beat process profile3 bpm beat process profile4 bpm beat process profileirregular beat process profileincreasing beat process profileand so on.In the case of a regular beat process profile, a rate can be assigned in the simplest possible fashion by dividing the number of cycles by the length of the temporal region occupied by the beating process profile as a whole. Irregular process profiles of this sort, for example as identified in the clinic, or in the readings on an aircraft instrument panel, are often of diagnostic significance." xsd:string property_value: IAO:0000112 "The simplest type of process profiles are what we shall call ‘quality process profiles’, which are the process profiles which serve as the foci of the sort of selective abstraction that is involved when measurements are made of changes in single qualities, as illustrated, for example, by process profiles of mass, temperature, aortic pressure, and so on." xsd:string -property_value: IAO:0000600 "b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/094-005"} -property_value: IAO:0000602 "(forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/094-005"} -property_value: IAO:0000602 "(iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/093-002"} +property_value: IAO:0000600 "b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/094-005"} +property_value: IAO:0000602 "(forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/094-005"} +property_value: IAO:0000602 "(iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/093-002"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000145 name: relational quality -def: "b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/057-001"} +def: "b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001])" [] {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/057-001"} is_a: BFO:0000019 ! quality property_value: BFO:0000179 "r-quality" xsd:string property_value: BFO:0000180 "RelationalQuality" xsd:string property_value: IAO:0000112 "a marriage bond, an instance of requited love, an obligation between one person and another." xsd:string property_value: IAO:0000112 "John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married." xsd:string -property_value: IAO:0000602 "(iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/057-001"} +property_value: IAO:0000602 "(iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/057-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] @@ -583,8 +596,8 @@ name: two-dimensional continuant fiat boundary is_a: BFO:0000140 ! continuant fiat boundary property_value: BFO:0000179 "2d-cf-boundary" xsd:string property_value: BFO:0000180 "TwoDimensionalContinuantFiatBoundary" xsd:string -property_value: IAO:0000600 "a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/033-001"} -property_value: IAO:0000602 "(iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/033-001"} +property_value: IAO:0000600 "a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/033-001"} +property_value: IAO:0000602 "(iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/033-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] @@ -596,9 +609,9 @@ property_value: BFO:0000180 "ZeroDimensionalContinuantFiatBoundary" xsd:string property_value: IAO:0000112 "the geographic North Pole" xsd:string property_value: IAO:0000112 "the point of origin of some spatial coordinate system." xsd:string property_value: IAO:0000112 "the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet" xsd:string -property_value: IAO:0000116 "zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000001", comment="requested by Melanie Courtot", http://www.w3.org/2000/01/rdf-schema#seeAlso="ZDRnpiIi:TUJ"} -property_value: IAO:0000600 "a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/031-001"} -property_value: IAO:0000602 "(iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/031-001"} +property_value: IAO:0000116 "zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona." xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000001", comment="requested by Melanie Courtot", seeAlso="ZDRnpiIi:TUJ"} +property_value: IAO:0000600 "a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/031-001"} +property_value: IAO:0000602 "(iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/031-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] @@ -613,8 +626,8 @@ property_value: IAO:0000112 "the moment at which a child is born" xsd:string property_value: IAO:0000112 "the moment at which a finger is detached in an industrial accident" xsd:string property_value: IAO:0000112 "the moment of death." xsd:string property_value: IAO:0000118 "temporal instant." xsd:string -property_value: IAO:0000600 "A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/102-001"} -property_value: IAO:0000602 "(forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/102-001"} +property_value: IAO:0000600 "A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/102-001"} +property_value: IAO:0000602 "(forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/102-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] @@ -623,7 +636,7 @@ name: history is_a: BFO:0000015 ! process property_value: BFO:0000179 "history" xsd:string property_value: BFO:0000180 "History" xsd:string -property_value: IAO:0000600 "A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/138-001"} +property_value: IAO:0000600 "A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/138-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] @@ -1976,7 +1989,7 @@ id: IAO:0000027 name: data item def: "An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements." [] is_a: IAO:0000030 ! information content entity -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "data item" xsd:string property_value: IAO:0000112 "Data items include counts of things, analyte concentrations, and statistical summaries." xsd:string property_value: IAO:0000114 IAO:0000125 @@ -2051,7 +2064,7 @@ id: IAO:0000064 name: algorithm def: "A plan specification which describes the inputs and output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata." [] is_a: IAO:0000104 ! plan specification -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "algorithm" xsd:string property_value: IAO:0000112 "PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies." xsd:string property_value: IAO:0000114 IAO:0000120 @@ -2077,7 +2090,7 @@ id: IAO:0000101 name: image def: "An image is an affine projection to a two dimensional surface, of measurements of some quality of an entity or entities repeated at regular intervals across a spatial range, where the measurements are represented as color and luminosity on the projected on surface." [] is_a: IAO:0000308 ! figure -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "image" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "person:Alan Ruttenberg" xsd:string @@ -2120,7 +2133,7 @@ id: IAO:0000109 name: measurement datum def: "A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device." [] is_a: IAO:0000027 ! data item -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "measurement datum" xsd:string property_value: IAO:0000112 "Examples of measurement data are the recoding of the weight of a mouse as {40,mass,\"grams\"}, the recording of an observation of the behavior of the mouse {,process,\"agitated\"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}." xsd:string property_value: IAO:0000114 IAO:0000125 @@ -2485,14 +2498,14 @@ property_value: IAO:0000111 "EL++ ontology module" xsd:string id: NCBITaxon:9606 name: person is_a: OBI:0100026 ! organism -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl [Term] id: OBI:0000011 name: planned process def: "A process that realizes a plan which is the concretization of a plan specification." [] is_a: BFO:0000015 ! process -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "planned process" xsd:string property_value: IAO:0000111 "planned process" xsd:string property_value: IAO:0000112 "Injecting mice with a vaccine in order to test its efficacy" xsd:string @@ -2513,7 +2526,7 @@ is_a: BFO:0000040 ! material entity intersection_of: BFO:0000040 ! material entity intersection_of: OBI:0000312 OBI:0000094 ! is_specified_output_of material processing relationship: OBI:0000312 OBI:0000094 ! is_specified_output_of material processing -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "processed material" xsd:string property_value: IAO:0000112 "Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples" xsd:string property_value: IAO:0000114 IAO:0000122 @@ -2524,7 +2537,7 @@ id: OBI:0000066 name: investigation def: "a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s)." [] is_a: OBI:0000011 ! planned process -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "investigation" xsd:string property_value: IAO:0000112 "Lung cancer investigation using expression profiling, a stem cell transplant investigation, biobanking is not an investigation, though it may be part of an investigation" xsd:string property_value: IAO:0000114 IAO:0000122 @@ -2542,7 +2555,7 @@ def: "a role that inheres in a material entity that is realized in an assay in w is_a: BFO:0000023 ! role relationship: BFO:0000054 OBI:0000070 {all_only="true"} ! realized in assay relationship: RO:0000052 BFO:0000040 ! characteristic of material entity -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "evaluant role" xsd:string property_value: IAO:0000112 "When a specimen of blood is assayed for glucose concentration, the blood has the evaluant role. When measuring the mass of a mouse, the evaluant is the mouse. When measuring the time of DNA replication, the evaluant is the DNA. When measuring the intensity of light on a surface, the evaluant is the light source." xsd:string property_value: IAO:0000114 IAO:0000122 @@ -2555,17 +2568,18 @@ property_value: IAO:0000232 "Feb 10, 2009. changes after discussion at OBI Cons [Term] id: OBI:0000070 name: assay -def: "A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies." [] +def: "A planned process that has the objective to produce information about a material entity (the evaluant) by examining it." [] is_a: OBI:0000011 ! planned process disjoint_from: OBI:0000339 ! planning disjoint_from: OBI:0200000 ! data transformation relationship: BFO:0000055 OBI:0000067 ! realizes evaluant role relationship: OBI:0000417 OBI:0000441 ! achieves_planned_objective assay objective -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "assay" xsd:string property_value: IAO:0000112 "Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house." xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000116 "12/3/12: BP: the reference to the 'physical examination' is included to point out that a prediction is not an assay, as that does not require physical examiniation." xsd:string +property_value: IAO:0000116 "Discussion on OBI call 2023-05-01 resulted in an agreement to revise the textual definition of 'assay'. https://github.com/obi-ontology/obi/issues/1683." xsd:string property_value: IAO:0000117 "PlanAndPlannedProcess Branch" xsd:string property_value: IAO:0000118 "measuring" xsd:string property_value: IAO:0000118 "scientific observation" xsd:string @@ -2578,7 +2592,7 @@ id: OBI:0000073 name: sample preparation for assay def: "A sample_preparation_for_assay is a protocol_application including material_enrollments and biomaterial_transformations. definition_source: OBI." [] is_a: OBI:0000094 ! material processing -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "sample preparation for assay" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "PlanAndPlannedProcess Branch" xsd:string @@ -2591,7 +2605,7 @@ name: reagent role def: "A role inhering in a biological or chemical entity that is intended to be applied in a scientific technique to participate (or have molecular components that participate) in a chemical reaction that facilitates the generation of data about some entity distinct from the bearer, or the generation of some specified material output distinct from the bearer." [] comment: (copied from ReO)\nReagents are distinguished from instruments or devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in or have parts that participate in some chemical interaction or reaction during their intended participation in some technique. By contrast, instruments do not participate in a chemical reaction/interaction during the technique.\n\nReagents are distinguished from study subjects/evaluants in that study subjects and evaluants are that about which conclusions are drawn and knowledge is sought in an investigation - while reagents, by definition, are not. It should be noted, however, that reagent and study subject/evaluant roles can be borne by instances of the same type of material entity - but a given instance will realize only one of these roles in the execution of a given assay or technique. For example, taq polymerase can bear a reagent role or an evaluant role. In a DNA sequencing assay aimed at generating sequence data about some plasmid, the reagent role of the taq polymerase is realized. In an assay to evaluate the quality of the taq polymerase itself, the evaluant/study subject role of the taq is realized, but not the reagent role since the taq is the subject about which data is generated.\n\nIn regard to the statement that reagents are 'distinct' from the specified outputs of a technique, note that a reagent may be incorporated into a material output of a technique, as long as the IDENTITY of this output is distinct from that of the bearer of the reagent role. For example, dNTPs input into a PCR are reagents that become part of the material output of this technique, but this output has a new identity (ie that of a 'nucleic acid molecule') that is distinct from the identity of the dNTPs that comprise it. Similarly, a biotin molecule input into a cell labeling technique are reagents that become part of the specified output, but the identity of the output is that of some modified cell specimen which shares identity with the input unmodified cell specimen, and not with the biotin label. Thus, we see that an important criteria of 'reagent-ness' is that it is a facilitator, and not the primary focus of an investigation or material processing technique (ie not the specified subject/evaluant about which knowledge is sought, or the specified output material of the technique). is_a: BFO:0000023 ! role -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "reagent role" xsd:string property_value: IAO:0000112 "Buffer, dye, a catalyst, a solvating agent." xsd:string property_value: IAO:0000114 IAO:0000120 @@ -2608,7 +2622,7 @@ is_a: OBI:0000011 ! planned process relationship: OBI:0000293 BFO:0000040 {all_only="true"} ! has_specified_input material entity relationship: OBI:0000299 OBI:0000047 ! has_specified_output processed material relationship: OBI:0000417 OBI:0000456 ! achieves_planned_objective material transformation objective -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "material processing" xsd:string property_value: IAO:0000112 "A cell lysis, production of a cloning vector, creating a buffer." xsd:string property_value: IAO:0000114 IAO:0000122 @@ -2625,7 +2639,7 @@ id: OBI:0000112 name: specimen role def: "a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation" [] is_a: BFO:0000023 ! role -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "specimen role" xsd:string property_value: IAO:0000112 "liver section; a portion of a culture of cells; a nemotode or other animal once no longer a subject (generally killed); portion of blood from a patient." xsd:string property_value: IAO:0000114 IAO:0000122 @@ -2644,7 +2658,7 @@ def: "A role borne by an entity and that is realized in a process that is part o comment: Philly2013: Historically, this role would have been borne only by humans or organizations. However, we now also want to enable investigations run by robot scientists such as ADAM (King et al, Science, 2009) is_a: BFO:0000023 ! role relationship: BFO:0000054 OBI:0000066 {all_only="true"} ! realized in investigation -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "investigation agent role" xsd:string property_value: IAO:0000112 "The person perform microarray experiments and submit microarray results (including raw data, processed data) with experiment description to ArrayExpress." xsd:string property_value: IAO:0000114 IAO:0000122 @@ -2661,7 +2675,7 @@ id: OBI:0000245 name: organization def: "An entity that can bear roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members." [] is_a: BFO:0000040 ! material entity -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "organization" xsd:string property_value: IAO:0000112 "PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods." xsd:string property_value: IAO:0000114 IAO:0000122 @@ -2677,7 +2691,7 @@ id: OBI:0000272 name: protocol def: "A plan specification which has sufficient level of detail and quantitative information to communicate it between investigation agents, so that different investigation agents will reliably be able to independently reproduce the process." [] is_a: IAO:0000104 ! plan specification -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "protocol" xsd:string property_value: IAO:0000112 "PCR protocol, has objective specification, amplify DNA fragment of interest, and has action specification describes the amounts of experimental reagents used (e..g. buffers, dNTPS, enzyme), and the temperature and cycle time settings for running the PCR." xsd:string property_value: IAO:0000114 IAO:0000122 @@ -2689,7 +2703,7 @@ property_value: OBI:0001847 "study protocol" xsd:string id: OBI:0000339 name: planning def: "a process of creating or modifying a plan specification" [] -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "planning" xsd:string property_value: IAO:0000112 "The process of a scientist thinking about and deciding what reagents to use as part of a protocol for an experiment. Note that the scientist could be human or a \"robot scientist\" executing software." xsd:string property_value: IAO:0000114 IAO:0000122 @@ -2703,7 +2717,7 @@ id: OBI:0000369 name: magnify function def: "A magnify function is a function to increase the size of a transmitted object image through the precise arrangement of energy diffraction elements along an imaging path." [] is_a: BFO:0000034 ! function -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "magnify function" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "Bill Bug" xsd:string @@ -2718,7 +2732,7 @@ def: "An image acquisition function is a function to acquire an image of a mater is_a: OBI:0000453 ! measure function relationship: BFO:0000054 OBI:0001007 {all_only="true"} ! realized in image creation relationship: RO:0000052 OBI:0000398 ! characteristic of image creation device -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "image acquisition function" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "Frank Gibson" xsd:string @@ -2731,7 +2745,7 @@ is_a: OBI:0000832 ! measurement device intersection_of: OBI:0000968 ! device intersection_of: RO:0000085 OBI:0000397 ! has function image acquisition function relationship: RO:0000085 OBI:0000397 ! has function image acquisition function -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "image acquisition device" xsd:string property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000117 "Frank Gibson" xsd:string @@ -2743,7 +2757,7 @@ id: OBI:0000399 name: solid support function def: "A solid support function is a function of a device on which an entity is kept in a defined position and prevented in its movement" [] is_a: BFO:0000034 ! function -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "solid support function" xsd:string property_value: IAO:0000112 "Taped, glued, pinned, dried or molecularly bonded to a solid support" xsd:string property_value: IAO:0000114 IAO:0000122 @@ -2756,7 +2770,7 @@ id: OBI:0000441 name: assay objective def: "an objective specification to determine a specified type of information about an evaluated entity (the material entity bearing evaluant role)" [] is_a: IAO:0000005 ! objective specification -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "assay objective" xsd:string property_value: IAO:0000112 "the objective to determine the weight of a mouse." xsd:string property_value: IAO:0000114 IAO:0000122 @@ -2769,7 +2783,7 @@ name: measure function def: "Measure function is a function that is borne by a processed material and realized in a process in which information about some entity is expressed relative to some reference." [] is_a: BFO:0000034 ! function relationship: RO:0000079 OBI:0000047 ! function of processed material -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "measure function" xsd:string property_value: IAO:0000112 "A glucometer measures blood glucose concentration, the glucometer has a measure function." xsd:string property_value: IAO:0000114 IAO:0000122 @@ -2783,7 +2797,7 @@ id: OBI:0000456 name: material transformation objective def: "an objective specifiction that creates an specific output object from input materials." [] is_a: IAO:0000005 ! objective specification -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "material transformation objective" xsd:string property_value: IAO:0000112 "The objective to create a mouse infected with LCM virus. The objective to create a defined solution of PBS." xsd:string property_value: IAO:0000114 IAO:0000122 @@ -2800,7 +2814,7 @@ id: OBI:0000571 name: manufacturer role def: "Manufacturer role is a role which inheres in a person or organization and which is realized by a manufacturing process." [] is_a: BFO:0000023 ! role -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "manufacturer role" xsd:string property_value: IAO:0000112 "With respect to The Accuri C6 Flow Cytometer System, the organization Accuri bears the role manufacturer role. With respect to a transformed line of tissue culture cells derived by a specific lab, the lab whose personnel isolated the cll line bears the role manufacturer role. With respect to a specific antibody produced by an individual scientist, the scientist who purifies, characterizes and distributes the anitbody bears the role manufacturer role." xsd:string property_value: IAO:0000114 IAO:0000123 @@ -2813,7 +2827,7 @@ name: device setting def: "a quality inheres_in some device and is concretization of some (device_setting_specification and is_about a quality of the device" [] is_a: BFO:0000019 ! quality relationship: RO:0000052 OBI:0000047 ! characteristic of processed material -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "device setting" xsd:string property_value: IAO:0000112 "Examples, 300V for 4 hours, 200mvolts, 37degrees.A knob set a 300 V is the device setting, the protocol stating to set the instrument to 300V is a device setting specification" xsd:string property_value: IAO:0000114 IAO:0000123 @@ -2830,7 +2844,7 @@ intersection_of: OBI:0000417 OBI:0000684 ! achieves_planned_objective specimen c relationship: OBI:0000293 BFO:0000040 ! has_specified_input material entity relationship: OBI:0000299 OBI:0100051 ! has_specified_output specimen relationship: OBI:0000417 OBI:0000684 ! achieves_planned_objective specimen collection objective -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "specimen collection process" xsd:string property_value: IAO:0000112 "drawing blood from a patient for analysis, collecting a piece of a plant for depositing in a herbarium, buying meat from a butcher in order to measure its protein content in an investigation" xsd:string property_value: IAO:0000114 IAO:0000122 @@ -2848,7 +2862,7 @@ id: OBI:0000684 name: specimen collection objective def: "A objective specification to obtain a material entity for potential use as an input during an investigation." [] is_a: IAO:0000005 ! objective specification -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "specimen collection objective" xsd:string property_value: IAO:0000112 "The objective to collect bits of excrement in the rainforest. The objective to obtain a blood sample from a patient." xsd:string property_value: IAO:0000114 IAO:0000122 @@ -2860,7 +2874,7 @@ id: OBI:0000740 name: material sample role def: "A material sample role is a specimen role borne by a material entity that is the output of a material sampling process." [] is_a: OBI:0000112 ! specimen role -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "material sample role" xsd:string property_value: IAO:0000112 "a role borne by a portion of blood taken to represent all the blood in an organism; the role borne by a population of humans with HIV enrolled in a study taken to represent patients with HIV in general." xsd:string property_value: IAO:0000114 IAO:0000125 @@ -2875,7 +2889,7 @@ is_a: OBI:0100051 ! specimen intersection_of: BFO:0000040 ! material entity intersection_of: RO:0000087 OBI:0000740 ! has role material sample role relationship: RO:0000087 OBI:0000740 ! has role material sample role -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "material sample" xsd:string property_value: IAO:0000112 "blood drawn from patient to measure his systemic glucose level. A population of humans with HIV enrolled in a study taken to represent patients with HIV in general." xsd:string property_value: IAO:0000114 IAO:0000123 @@ -2892,7 +2906,7 @@ is_a: OBI:0000968 ! device intersection_of: OBI:0000968 ! device intersection_of: RO:0000085 OBI:0000453 ! has function measure function relationship: RO:0000085 OBI:0000453 ! has function measure function -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "measurement device" xsd:string property_value: IAO:0000112 "A ruler, a microarray scanner, a Geiger counter." xsd:string property_value: IAO:0000114 IAO:0000122 @@ -2902,10 +2916,10 @@ property_value: IAO:0000119 "OBI" xsd:string [Term] id: OBI:0000835 name: manufacturer -def: "A person or organization that has a manufacturer role" [] +def: "A person or organization that has a manufacturer role." [] is_a: BFO:0000040 ! material entity relationship: RO:0000087 OBI:0000571 ! has role manufacturer role -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "manufacturer" xsd:string property_value: IAO:0000114 IAO:0000123 @@ -2915,7 +2929,7 @@ name: device def: "A material entity that is designed to perform a function in a scientific investigation, but is not a reagent." [] is_a: OBI:0000047 ! processed material relationship: RO:0000085 BFO:0000034 ! has function function -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "device" xsd:string property_value: IAO:0000112 "A voltmeter is a measurement device which is intended to perform some measure function." xsd:string property_value: IAO:0000112 "An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure." xsd:string @@ -2932,7 +2946,7 @@ def: "A planned process that captures an image of an object." [] is_a: OBI:0000011 ! planned process relationship: OBI:0000293 BFO:0000040 ! has_specified_input material entity relationship: OBI:0000299 IAO:0000101 ! has_specified_output image -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "image acquisition" xsd:string property_value: IAO:0000112 "Taking a polaroid picture of a patients skin lesion; Using a digital camera to take a picture of a gel" xsd:string property_value: IAO:0000114 IAO:0000123 @@ -2944,7 +2958,7 @@ id: OBI:0001616 name: specimen identifier def: "A CRID symbol denotes a specimen and used to distinguish one specimen from another in an investigation." [] is_a: IAO:0000577 ! centrally registered identifier symbol -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: http://purl.org/dc/elements/1.1/source "NIAID GSCID-BRC" xsd:string property_value: IAO:0000111 "specimen identifier" xsd:string property_value: IAO:0000114 IAO:0000120 @@ -2958,7 +2972,7 @@ id: OBI:0001622 name: investigation title def: "A textual entity that denotes an investigation." [] is_a: OBI:0001898 ! comment on investigation -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: http://purl.org/dc/elements/1.1/source "NIAID GSCID-BRC" xsd:string property_value: IAO:0000111 "investigation title" xsd:string property_value: IAO:0000114 IAO:0000120 @@ -2972,7 +2986,7 @@ id: OBI:0001898 name: comment on investigation def: "A textual entity that is about any of the aspects of an investigation worth noting" [] is_a: IAO:0000300 ! textual entity -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: http://purl.org/dc/elements/1.1/source "NIAID GSCID-BRC" xsd:string property_value: IAO:0000111 "comment on investigation" xsd:string property_value: IAO:0000114 IAO:0000120 @@ -2985,7 +2999,7 @@ id: OBI:0100026 name: organism def: "A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs." [] is_a: BFO:0000040 ! material entity -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "organism" xsd:string property_value: IAO:0000112 "animal" xsd:string property_value: IAO:0000112 "fungus" xsd:string @@ -3005,7 +3019,7 @@ is_a: BFO:0000040 ! material entity intersection_of: BFO:0000040 ! material entity intersection_of: RO:0000087 OBI:0000112 ! has role specimen role relationship: RO:0000087 OBI:0000112 ! has role specimen role -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "specimen" xsd:string property_value: IAO:0000112 "Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen." xsd:string property_value: IAO:0000114 IAO:0000122 @@ -3022,7 +3036,7 @@ def: "A planned process that produces output data from input data." [] is_a: OBI:0000011 ! planned process relationship: OBI:0000293 IAO:0000027 {all_only="true"} ! has_specified_input data item relationship: OBI:0000417 OBI:0200166 ! achieves_planned_objective data transformation objective -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "data transformation" xsd:string property_value: IAO:0000112 "The application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value." xsd:string property_value: IAO:0000114 IAO:0000122 @@ -3044,7 +3058,7 @@ id: OBI:0200166 name: data transformation objective def: "An objective specification to transformation input data into output data" [] is_a: IAO:0000005 ! objective specification -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "data transformation objective" xsd:string property_value: IAO:0000112 "normalize objective" xsd:string property_value: IAO:0000114 IAO:0000122 @@ -3057,7 +3071,7 @@ id: OBI:0302732 name: solvent role def: "solvent role is a role which inheres in a molecular entity capable of ensuring the dissolution of another chemical entity and realized by the process of solvation" [] is_a: BFO:0000023 ! role -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "solvent role" xsd:string property_value: IAO:0000112 "PMID: 18373502.Transfusion. 2008 Mar 25. Solvent/detergent treatment of platelet concentrates enhances the release of growth factors." xsd:string property_value: IAO:0000114 IAO:0000125 @@ -3070,7 +3084,7 @@ name: microscope def: "A microscope is an instrument which magnifies the view on objects (too small to be viewed by the naked eye) under increased resolution. A microscope can be an optical instrument but also and electronic instrument. There are various kind of optical microscopes, e.g confocal microscope, epifluoresence microscope)" [] is_a: OBI:0000398 ! image creation device relationship: RO:0000085 OBI:0000369 ! has function magnify function -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "microscope" xsd:string property_value: IAO:0000112 "PMID:18466942. A light and transmission electron microscope study of hepatic portal tracts in the rhesus monkey (Macacus rhesus). Tissue Cell. 2008 May 6" xsd:string property_value: IAO:0000114 IAO:0000123 @@ -3083,7 +3097,7 @@ name: microscope slide def: "A microscope slide is a device usually made of glass which is used as a solid matrix for (biological) material deposited on its surface and which is compatible for use with a microscope instrument" [] is_a: OBI:0000968 ! device relationship: RO:0000085 OBI:0000399 ! has function solid support function -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "microscope slide" xsd:string property_value: IAO:0000112 "PMID: 9668975.Microscope slide for enhanced analysis of DNA damage using the comet assay." xsd:string property_value: IAO:0000114 IAO:0000123 @@ -3096,7 +3110,7 @@ name: study design def: "A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution." [] is_a: IAO:0000104 ! plan specification relationship: BFO:0000051 OBI:0000272 ! has part protocol -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "study design" xsd:string property_value: IAO:0000112 "a matched pairs study design describes criteria by which subjects are identified as pairs which then undergo the same protocols, and the data generated is analyzed by comparing the differences between the paired subjects, which constitute the results of the executed study design." xsd:string property_value: IAO:0000114 IAO:0000122 @@ -3305,6 +3319,7 @@ is_a: IAO:0000140 ! setting datum property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-1595-3213 property_value: IAO:0000116 "This class should better be defined in a more general device ontology or a domain ontology with the scope of optical devices." xsd:string property_value: IAO:0000118 "integration period setting" xsd:string +property_value: IAO:0000118 "integration time" xsd:string property_value: seeAlso https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/40 [Term] @@ -3379,6 +3394,8 @@ def: "A setting datum that specifies the number of grooves in a diffraction grat is_a: IAO:0000140 ! setting datum property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-1595-3213 property_value: IAO:0000116 "This class should better be defined in a more general device ontology or a domain ontology with the scope of optical devices." xsd:string +property_value: IAO:0000118 "grating" xsd:string +property_value: IAO:0000118 "grating setting" xsd:string property_value: seeAlso https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/45 [Term] @@ -3419,6 +3436,8 @@ property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/000 property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-1595-3213 property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-2239-3955 property_value: IAO:0000112 "example:RamanSpectrometerX rdf:type obo:CHMO_0001235 (Raman spectrometer) ;\n obo:OBI_0000293 (has_specified_input) example:objective_magnification_factor_setting_for_RamanSpectrometerX .\nexample:objective_magnification_factor_setting_for_RamanSpectrometerX rdf:type obo:VIBSO_0000014 ;\n obo:OBI_0002815 (has representation) '100 x' ." xsd:string +property_value: IAO:0000118 "magnification" xsd:string +property_value: IAO:0000118 "magnification setting" xsd:string property_value: seeAlso https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/24%20 [Term] @@ -3601,7 +3620,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "is part of" xsd:string property_value: IAO:0000112 "my brain is part of my body (continuant parthood, two material entities)" xsd:string property_value: IAO:0000112 "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" xsd:string @@ -3621,6 +3640,7 @@ property_value: RO:0040042 BFO:0000031 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:PartOf property_value: seeAlso "http://www.obofoundry.org/ro/#OBO_REL:part_of" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Part_of" xsd:anyURI is_transitive: true is_a: RO:0002131 ! overlaps inverse_of: BFO:0000051 ! has part @@ -3632,7 +3652,7 @@ def: "a core relation that holds between a whole and its part" [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "has part" xsd:string property_value: IAO:0000112 "my body has part my brain (continuant parthood, two material entities)" xsd:string property_value: IAO:0000112 "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" xsd:string @@ -3649,7 +3669,7 @@ is_a: RO:0002131 ! overlaps id: BFO:0000054 name: realized in comment: Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "realized in" xsd:string property_value: IAO:0000112 "this disease is realized in this disease course" xsd:string property_value: IAO:0000112 "this fragility is realized in this shattering" xsd:string @@ -3666,7 +3686,7 @@ inverse_of: BFO:0000055 ! realizes id: BFO:0000055 name: realizes comment: Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "realizes" xsd:string property_value: IAO:0000112 "this disease course realizes this disease" xsd:string property_value: IAO:0000112 "this investigation realizes this investigator role" xsd:string @@ -3681,7 +3701,7 @@ id: BFO:0000062 name: preceded by def: "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco -property_value: http://purl.org/dc/elements/1.1/source "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" xsd:string +property_value: http://purl.org/dc/terms/source "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" xsd:string property_value: IAO:0000111 "preceded by" xsd:string property_value: IAO:0000116 "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." xsd:string property_value: IAO:0000118 "is preceded by" xsd:string @@ -3714,7 +3734,7 @@ is_a: BFO:0000051 ! has part id: IAO:0000136 name: is about def: "A (currently) primitive relation that relates an information artifact to an entity." [] -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000112 "This document is about information artifacts and their representations" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of \"mentions\" relation. Weaken the is_about relationship to be primitive. \n\nWe will try to build it back up by elaborating the various subproperties that are more precisely defined.\n\nSome currently missing phenomena that should be considered \"about\" are predications - \"The only person who knows the answer is sitting beside me\" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic." xsd:string @@ -3747,7 +3767,7 @@ is_a: IAO:0000136 ! is about id: OBI:0000293 name: has_specified_input def: "The inverse property of is_specified_input_of" [] -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "has_specified_input" xsd:string property_value: IAO:0000111 "has_specified_input" xsd:string property_value: IAO:0000112 "see is_input_of example_of_usage" xsd:string @@ -3764,7 +3784,7 @@ is_a: RO:0000057 ! has participant id: OBI:0000295 name: is_specified_input_of def: "A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of." [] -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "is_specified_input_of" xsd:string property_value: IAO:0000112 "some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay" xsd:string property_value: IAO:0000114 IAO:0000122 @@ -3776,7 +3796,7 @@ is_a: RO:0000056 ! participates in id: OBI:0000299 name: has_specified_output def: "The inverse property of is_specified_output_of" [] -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "has_specified_output" xsd:string property_value: IAO:0000111 "has_specified_output" xsd:string property_value: IAO:0000114 IAO:0000122 @@ -3791,7 +3811,7 @@ is_a: RO:0000057 ! has participant id: OBI:0000312 name: is_specified_output_of def: "A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of." [] -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "is_specified_output_of" xsd:string property_value: IAO:0000111 "is_specified_output_of" xsd:string property_value: IAO:0000114 IAO:0000122 @@ -3804,7 +3824,7 @@ is_a: RO:0000056 ! participates in id: OBI:0000417 name: achieves_planned_objective def: "This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process." [] -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "achieves_planned_objective" xsd:string property_value: IAO:0000112 "A cell sorting process achieves the objective specification 'material separation objective'" xsd:string property_value: IAO:0000114 IAO:0000120 @@ -3816,7 +3836,7 @@ property_value: IAO:0000232 "modified according to email thread from 1/23/09 in id: OBI:0000833 name: objective_achieved_by def: "This relation obtains between an objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process." [] -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "objective_achieved_by" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "OBI" xsd:string @@ -3827,7 +3847,7 @@ id: OBI:0001950 name: has performer def: "A relation between a planned process and a continuant where the continuant can be a person, organization or device (such as a robot controlled by software workflow management system) that performs the planned process." [] comment: The 'has performer' relation covers the need to report on who performed a planned processed. It has to cover processes done by People or Devices (such as a robot controlled by software WF management system). -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "has performer" xsd:string property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "OBI" xsd:string @@ -3839,7 +3859,7 @@ id: RO:0000052 name: characteristic of def: "a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence." [] comment: Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "inheres in" xsd:string property_value: IAO:0000112 "this fragility is a characteristic of this vase" xsd:string property_value: IAO:0000112 "this red color is a characteristic of this apple" xsd:string @@ -3853,7 +3873,7 @@ inverse_of: RO:0000053 ! has characteristic id: RO:0000053 name: has characteristic def: "Inverse of characteristic_of" [] -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "bearer of" xsd:string property_value: IAO:0000112 "this apple is bearer of this red color" xsd:string property_value: IAO:0000112 "this vase is bearer of this fragility" xsd:string @@ -3881,7 +3901,7 @@ inverse_of: RO:0000057 ! has participant id: RO:0000057 name: has participant def: "a relation between a process and a continuant, in which the continuant is somehow involved in the process" [] -property_value: http://purl.org/dc/elements/1.1/source "http://www.obofoundry.org/ro/#OBO_REL:has_participant" xsd:string +property_value: http://purl.org/dc/terms/source "http://www.obofoundry.org/ro/#OBO_REL:has_participant" xsd:string property_value: IAO:0000111 "has participant" xsd:string property_value: IAO:0000112 "this blood coagulation has participant this blood clot" xsd:string property_value: IAO:0000112 "this investigation has participant this investigator" xsd:string @@ -3906,7 +3926,7 @@ inverse_of: RO:0000059 ! concretizes id: RO:0000059 name: concretizes def: "A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant." [] -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000112 "A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant)." xsd:string property_value: IAO:0000112 "An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process)." xsd:string domain: BFO:0000020 ! specifically dependent continuant @@ -3917,7 +3937,7 @@ id: RO:0000079 name: function of def: "a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence" [] comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000112 "this catalysis function is a function of this enzyme" xsd:string property_value: IAO:0000116 "A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists." xsd:string property_value: IAO:0000118 "function_of" xsd:string @@ -3954,7 +3974,7 @@ inverse_of: RO:0000087 ! has role id: RO:0000085 name: has function def: "a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence" [] -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000112 "this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)" xsd:string property_value: IAO:0000116 "A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists." xsd:string property_value: IAO:0000118 "has_function" xsd:string @@ -3976,7 +3996,7 @@ is_a: RO:0000053 ! has characteristic id: RO:0000087 name: has role def: "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence" [] -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000112 "this person has role this investigator role (more colloquially: this person has this role of investigator)" xsd:string property_value: IAO:0000116 "A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists." xsd:string property_value: IAO:0000118 "has_role" xsd:string @@ -4007,7 +4027,7 @@ name: has regulatory component activity def: "A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B." [] is_a: RO:0002017 ! has component activity is_a: RO:0002334 ! regulated by -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:30:46Z [Typedef] @@ -4017,7 +4037,7 @@ def: "A relationship that holds between a GO molecular function and a component comment: By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. is_a: RO:0002013 ! has regulatory component activity is_a: RO:0002335 ! negatively regulated by -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:31:01Z [Typedef] @@ -4027,7 +4047,7 @@ def: "A relationship that holds between a GO molecular function and a component comment: By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. is_a: RO:0002013 ! has regulatory component activity is_a: RO:0002336 ! positively regulated by -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:31:17Z [Typedef] @@ -4035,7 +4055,7 @@ id: RO:0002017 name: has component activity comment: A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. is_a: RO:0002018 ! has component process -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:44:33Z [Typedef] @@ -4045,44 +4065,44 @@ def: "w 'has process component' p if p and w are processes, w 'has part' p and domain: BFO:0000015 ! process range: BFO:0000015 ! process is_a: RO:0002180 ! has component -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:49:21Z [Typedef] id: RO:0002022 name: directly regulated by -comment: Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. {xref="GOC:dos"} +comment: Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. {xref="https://orcid.org/0000-0002-7073-9172"} is_a: RO:0002334 ! regulated by inverse_of: RO:0002578 ! directly regulates -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-09-17T13:52:24Z [Typedef] id: RO:0002023 name: directly negatively regulated by -def: "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1." [GOC:dos] +def: "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1." [https://orcid.org/0000-0002-7073-9172] is_a: RO:0002022 ! directly regulated by inverse_of: RO:0002630 ! directly negatively regulates -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-09-17T13:52:38Z [Typedef] id: RO:0002024 name: directly positively regulated by -def: "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1." [GOC:dos] +def: "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1." [https://orcid.org/0000-0002-7073-9172] is_a: RO:0002022 ! directly regulated by inverse_of: RO:0002629 ! directly positively regulates -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-09-17T13:52:47Z [Typedef] id: RO:0002025 name: has effector activity -def: "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity." [GOC:dos] +def: "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity." [https://orcid.org/0000-0002-7073-9172] comment: This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. is_functional: true is_a: RO:0002017 ! has component activity -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-09-22T14:14:36Z [Typedef] @@ -4125,7 +4145,7 @@ subset: ro-eco property_value: IAO:0000114 IAO:0000125 property_value: RO:0001900 RO:0001901 holds_over_chain: BFO:0000050 BFO:0000050 -holds_over_chain: BFO:0000051 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} +holds_over_chain: BFO:0000051 BFO:0000050 {RO:0002582="true"} holds_over_chain: BFO:0000051 RO:0002131 is_symmetric: true is_a: RO:0002323 ! mereotopologically related to @@ -4222,7 +4242,7 @@ def: "c stands in this relationship to p if and only if there exists some p' suc property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has function in" xsd:string property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/reflexivity/ -holds_over_chain: RO:0002215 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} +holds_over_chain: RO:0002215 BFO:0000050 {RO:0002582="true"} is_a: RO:0002328 ! functionally related to is_a: RO:0002500 ! causal agent in process @@ -4250,6 +4270,7 @@ subset: ro-eco property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "consumes" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Has_input" xsd:anyURI domain: BFO:0000015 ! process is_a: RO:0000057 ! has participant inverse_of: RO:0002352 ! input of @@ -4271,7 +4292,7 @@ def: "c acts upstream of or within p if c is enables f, and f is causally upstre subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term synonym: "affects" RELATED [] property_value: IAO:0000112 "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway." xsd:string -property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within +property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within" xsd:anyURI holds_over_chain: RO:0002327 RO:0002418 is_a: RO:0002500 ! causal agent in process @@ -4284,6 +4305,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: RO:0004049 RO:0002411 +property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of,_positive_effect is_a: RO:0002411 ! causally upstream of is_a: RO:0004047 ! causally upstream of or within, positive effect @@ -4295,6 +4317,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: RO:0004050 RO:0002411 +property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of,_negative_effect is_a: RO:0002411 ! causally upstream of is_a: RO:0004046 ! causally upstream of or within, negative effect @@ -4308,7 +4331,7 @@ property_value: IAO:0000118 "inheres in part of" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 property_value: RO:0001900 RO:0001901 property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/reflexivity/ -holds_over_chain: RO:0000052 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} +holds_over_chain: RO:0000052 BFO:0000050 {RO:0002582="true"} is_a: RO:0002502 ! depends on transitive_over: BFO:0000050 ! part of @@ -4333,6 +4356,7 @@ property_value: IAO:0000118 "has" xsd:string property_value: IAO:0000118 "is catalyzing" xsd:string property_value: IAO:0000118 "is executing" xsd:string property_value: IAO:0000232 "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized." xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Enables" xsd:anyURI is_a: RO:0002215 ! capable of inverse_of: RO:0002333 ! enabled by transitive_over: BFO:0000051 ! has part @@ -4351,7 +4375,7 @@ name: part of structure that is capable of def: "this relation holds between c and p when c is part of some c', and c' is capable of p." [] property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "false" xsd:boolean -holds_over_chain: BFO:0000050 RO:0002215 {http://purl.obolibrary.org/obo/RO_0002581="true"} +holds_over_chain: BFO:0000050 RO:0002215 {RO:0002581="true"} is_a: RO:0002328 ! functionally related to [Typedef] @@ -4361,7 +4385,7 @@ def: "c involved_in p if and only if c enables some process p', and p' is part o property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "actively involved in" xsd:string property_value: IAO:0000118 "enables part of" xsd:string -property_value: seeAlso Involved:in +property_value: seeAlso "https://wiki.geneontology.org/Involved_in" xsd:anyURI holds_over_chain: RO:0002327 BFO:0000050 is_a: RO:0000056 ! participates in is_a: RO:0002431 ! involved in or involved in regulation of @@ -4373,6 +4397,7 @@ name: enabled by def: "inverse of enables" [] subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: seeAlso "https://wiki.geneontology.org/Enabled_by" xsd:anyURI is_a: RO:0000057 ! has participant is_a: RO:0002328 ! functionally related to @@ -4440,6 +4465,7 @@ def: "p indirectly positively regulates q iff p is indirectly causally upstream property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "indirectly activates" xsd:string property_value: RO:0002579 RO:0002213 +property_value: seeAlso "https://wiki.geneontology.org/Indirectly_positively_regulates" xsd:anyURI holds_over_chain: RO:0002409 RO:0002409 holds_over_chain: RO:0002629 RO:0002407 holds_over_chain: RO:0002629 RO:0002629 @@ -4455,6 +4481,7 @@ def: "p indirectly negatively regulates q iff p is indirectly causally upstream property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "indirectly inhibits" xsd:string property_value: RO:0002579 RO:0002212 +property_value: seeAlso "https://wiki.geneontology.org/Indirectly_negatively_regulates" xsd:anyURI holds_over_chain: RO:0002630 RO:0002409 holds_over_chain: RO:0002630 RO:0002630 is_transitive: true @@ -4786,6 +4813,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly positively regulates (process to process)" xsd:string property_value: RO:0004049 RO:0002578 +property_value: seeAlso "https://wiki.geneontology.org/Directly_positively_regulates" xsd:anyURI is_a: RO:0002213 ! positively regulates is_a: RO:0002578 ! directly regulates @@ -4799,6 +4827,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly negatively regulates (process to process)" xsd:string property_value: RO:0004050 RO:0002578 +property_value: seeAlso "https://wiki.geneontology.org/Directly_negatively_regulates" xsd:anyURI is_a: RO:0002212 ! negatively regulates is_a: RO:0002578 ! directly regulates @@ -4827,7 +4856,7 @@ id: RO:0004032 name: acts upstream of or within, positive effect subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: RO:0004049 RO:0002264 -property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within,_positive_effect +property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect" xsd:anyURI holds_over_chain: RO:0002327 RO:0004047 is_a: RO:0002264 ! acts upstream of or within created_by: https://orcid.org/0000-0002-6601-2165 @@ -4838,6 +4867,7 @@ id: RO:0004033 name: acts upstream of or within, negative effect subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: RO:0004050 RO:0002264 +property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within,_negative_effect" xsd:anyURI holds_over_chain: RO:0002327 RO:0004046 is_a: RO:0002264 ! acts upstream of or within created_by: https://orcid.org/0000-0002-6601-2165 @@ -4849,7 +4879,7 @@ name: acts upstream of, positive effect def: "c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive" [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: RO:0004049 RO:0002263 -property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_positive_effect +property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of,_positive_effect" xsd:anyURI holds_over_chain: RO:0002327 RO:0002304 is_a: RO:0002263 ! acts upstream of is_a: RO:0004032 ! acts upstream of or within, positive effect @@ -4862,7 +4892,7 @@ name: acts upstream of, negative effect def: "c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative" [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: RO:0004050 RO:0002263 -property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_negative_effect +property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of,_negative_effect" xsd:anyURI holds_over_chain: RO:0002327 RO:0002305 is_a: RO:0002263 ! acts upstream of is_a: RO:0004033 ! acts upstream of or within, negative effect @@ -4873,6 +4903,7 @@ creation_date: 2018-01-26T23:53:22Z id: RO:0004046 name: causally upstream of or within, negative effect property_value: RO:0004050 RO:0002418 +property_value: seeAlso "https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect" xsd:anyURI is_a: RO:0002418 ! causally upstream of or within created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-03-13T23:55:05Z @@ -4881,6 +4912,7 @@ creation_date: 2018-03-13T23:55:05Z id: RO:0004047 name: causally upstream of or within, positive effect property_value: RO:0004049 RO:0002418 +property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of_or_within,_positive_effect is_a: RO:0002418 ! causally upstream of or within created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-03-13T23:55:19Z @@ -4889,7 +4921,7 @@ creation_date: 2018-03-13T23:55:19Z id: RO:0009501 name: realized in response to def: "r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r." [] -synonym: "triggered by process" EXACT [RO:cjm] +synonym: "triggered by process" EXACT [https://orcid.org/0000-0002-6601-2165] property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6996-0040 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6601-2165 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7073-9172 @@ -4945,7 +4977,7 @@ id: RO:0012011 name: indirectly causally upstream of def: "p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q." [] is_a: RO:0002411 ! causally upstream of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2022-09-26T06:07:17Z [Typedef] @@ -4954,7 +4986,7 @@ name: indirectly regulates def: "p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q." [] is_a: RO:0002211 ! regulates is_a: RO:0012011 ! indirectly causally upstream of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2022-09-26T06:08:01Z [Typedef] diff --git a/vibso-full.owl b/vibso-full.owl index f463617..c689d50 100644 --- a/vibso-full.owl +++ b/vibso-full.owl @@ -27,7 +27,7 @@ xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#" xmlns:wikipedia="https://en.wikipedia.org/wiki/"> - + @@ -36,7 +36,7 @@ _WIP - NOT READY FOR PRODUCTION_ The Vibration Spectroscopy Ontology (VIBSO) is used to represent information regarding the excution and analysis of vibrational spectroscopy assays. Vibrational Spectroscopy Ontology - 2023-06-21 + 2023-11-27 @@ -104,6 +104,7 @@ PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + example of usage example of usage @@ -158,6 +159,26 @@ We don't have definitions of 'meaning' or 'expression' Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. +We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. + 2012-04-05: +Barry Smith + +The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. + +Can you fix to something like: + +A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. + +Alan Ruttenberg + +Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. + +On the specifics of the proposed definition: + +We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. + +Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. + We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> @@ -632,7 +653,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] 2023-03-03 abbreviation - + @@ -645,7 +666,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] 2023-03-03 ambiguous synonym - + @@ -658,7 +679,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] 2023-03-03 dubious synonym - + @@ -672,7 +693,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] 2023-03-03 layperson synonym - + @@ -686,7 +707,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] 2023-03-03 plural form - + @@ -700,7 +721,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] 2023-03-03 UK spelling synonym - + @@ -713,7 +734,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] 2023-03-03 misspelling - + @@ -726,7 +747,78 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] 2023-03-03 misnomer - + + + + + + + + + MAPT, the gene that encodes the Tau protein, has a previous name DDPAC. Note: in this case, the name type is more specifically the gene symbol. + A synonym type for names that have been used as primary labels in the past. + + + 2023-07-25 + previous name + + + + + + + + + The legal name for Harvard University (https://ror.org/03vek6s52) is President and Fellows of Harvard College + A synonym type for the legal entity name + + + 2023-07-27 + legal name + + + + + + + + + CHEBI:46195 has been assigned the english International Nonproproprietary Name (INN) "paracetamol". In some cases such as this one, the INN might be the same as the ontology's primary label + The International Nonproprietary Name (INN) is a standardize name for a pharmaceutical drug or active ingredient issued by the World Health Organization (WHO) meant to address the issues with country- or language-specific brand names. These are issued in several languages, including English, Latin, French, Russian, Spanish, Arabic, and Chinese. + + + 2023-09-30 + INN + International Nonproprietary Name + + + + + + + + + nasopharynx (UBERON:0001728) has the latin name "pars nasalis pharyngis + A synonym type for describing Latin term synonyms. + + + 2023-10-12 + latin term + + + + + + + + + NASA is an word acronym for the US National Aeronautics and Space Administration because the acronym is pronounced. FBI is an initialism (also known as alphabetism) for the US Federal Bureau of Investigation since the letters are pronounced one at a time. JPEG is an acronym for Joint Photographic Experts Group but does not count as a word acronym nor an initialism since it is mixed how it is pronounced. + A synonym type for describing abbreviations that are a part of the full name's words, such as initialisms or alphabetisms. + + + 2023-11-01 + acronym + @@ -1055,9 +1147,9 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - + - + @@ -1286,7 +1378,7 @@ A continuant cannot be part of an occurrent: use 'participates in'. An - + @@ -1295,6 +1387,7 @@ A continuant cannot be part of an occurrent: use 'participates in'. An http://www.obofoundry.org/ro/#OBO_REL:part_of + https://wiki.geneontology.org/Part_of @@ -1316,7 +1409,7 @@ A continuant cannot be part of an occurrent: use 'participates in'. An A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. has_part - + @@ -1338,7 +1431,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. is realized by realized_in [copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) - + Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process realized in @@ -1356,7 +1449,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. this investigation realizes this investigator role this shattering realizes this fragility to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) - + Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process realizes @@ -1381,7 +1474,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. is preceded by preceded_by - http://www.obofoundry.org/ro/#OBO_REL:preceded_by + http://www.obofoundry.org/ro/#OBO_REL:preceded_by preceded by @@ -1429,7 +1522,7 @@ We will try to build it back up by elaborating the various subproperties that ar Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic. person:Alan Ruttenberg Smith, Ceusters, Ruttenberg, 2000 years of philosophy - + is about @@ -1521,7 +1614,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which PERSON: Larry Hunter PERSON: Melanie Coutot - + has_specified_input @@ -1537,7 +1630,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of. Alan Ruttenberg PERSON:Bjoern Peters - + is_specified_input_of @@ -1561,7 +1654,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which PERSON: Larry Hunter PERSON: Melanie Courtot - + has_specified_output @@ -1578,7 +1671,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which Alan Ruttenberg PERSON:Bjoern Peters - + is_specified_output_of @@ -1594,7 +1687,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which BP, AR, PPPB branch PPPB branch derived modified according to email thread from 1/23/09 in accordince with DT and PPPB branch - + achieves_planned_objective @@ -1608,7 +1701,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which This relation obtains between an objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process. OBI OBI - + objective_achieved_by @@ -1623,7 +1716,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which A relation between a planned process and a continuant where the continuant can be a person, organization or device (such as a robot controlled by software workflow management system) that performs the planned process. OBI OBI - + The 'has performer' relation covers the need to report on who performed a planned processed. It has to cover processes done by People or Devices (such as a robot controlled by software WF management system). has performer @@ -1642,7 +1735,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence. inheres_in - + Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. characteristic of @@ -1662,7 +1755,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which bearer_of is bearer of - + has characteristic @@ -1706,7 +1799,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which a relation between a process and a continuant, in which the continuant is somehow involved in the process Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. has_participant - http://www.obofoundry.org/ro/#OBO_REL:has_participant + http://www.obofoundry.org/ro/#OBO_REL:has_participant has participant @@ -1734,7 +1827,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant. - + concretizes @@ -1751,7 +1844,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists. function_of is function of - + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. function of @@ -1800,7 +1893,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists. has_function - + has function @@ -1830,7 +1923,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. has_role - + has role @@ -1867,7 +1960,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. - dos + 2017-05-24T09:30:46Z has regulatory component activity @@ -1880,7 +1973,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. - dos + 2017-05-24T09:31:01Z By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. has negative regulatory component activity @@ -1894,7 +1987,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. - dos + 2017-05-24T09:31:17Z By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. has positive regulatory component activity @@ -1906,7 +1999,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which - dos + 2017-05-24T09:44:33Z A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. has component activity @@ -1921,7 +2014,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. - dos + 2017-05-24T09:49:21Z has component process @@ -1933,7 +2026,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which - dos + 2017-09-17T13:52:24Z Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. directly regulated by @@ -1942,7 +2035,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. - GOC:dos + @@ -1953,7 +2046,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. - dos + 2017-09-17T13:52:38Z directly negatively regulated by @@ -1961,7 +2054,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. - GOC:dos + @@ -1972,7 +2065,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. - dos + 2017-09-17T13:52:47Z directly positively regulated by @@ -1980,7 +2073,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. - GOC:dos + @@ -1991,7 +2084,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. - dos + 2017-09-22T14:14:36Z This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. has effector activity @@ -2000,7 +2093,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. - GOC:dos + @@ -2260,6 +2353,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which has input + https://wiki.geneontology.org/Has_input @@ -2294,7 +2388,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which affects acts upstream of or within - + https://wiki.geneontology.org/Acts_upstream_of_or_within @@ -2311,6 +2405,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y causally upstream of, positive effect + @@ -2326,6 +2421,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which causally upstream of, negative effect + @@ -2399,6 +2495,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized. enables + https://wiki.geneontology.org/Enables @@ -2457,7 +2554,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which actively involved in enables part of involved in - + https://wiki.geneontology.org/Involved_in @@ -2471,6 +2568,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which enabled by + https://wiki.geneontology.org/Enabled_by @@ -2583,6 +2681,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which indirectly activates indirectly positively regulates + https://wiki.geneontology.org/Indirectly_positively_regulates @@ -2610,6 +2709,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which indirectly inhibits indirectly negatively regulates + https://wiki.geneontology.org/Indirectly_negatively_regulates @@ -3148,6 +3248,7 @@ For example, A and B may be gene products and binding of B by A positively regul directly positively regulates + https://wiki.geneontology.org/Directly_positively_regulates @@ -3165,6 +3266,7 @@ For example, A and B may be gene products and binding of B by A positively regul directly negatively regulates + https://wiki.geneontology.org/Directly_negatively_regulates @@ -3216,7 +3318,7 @@ For example, A and B may be gene products and binding of B by A positively regul 2018-01-26T23:49:30Z acts upstream of or within, positive effect - + https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect @@ -3234,6 +3336,7 @@ For example, A and B may be gene products and binding of B by A positively regul 2018-01-26T23:49:51Z acts upstream of or within, negative effect + https://wiki.geneontology.org/Acts_upstream_of_or_within,_negative_effect @@ -3253,7 +3356,7 @@ For example, A and B may be gene products and binding of B by A positively regul 2018-01-26T23:53:14Z acts upstream of, positive effect - + https://wiki.geneontology.org/Acts_upstream_of,_positive_effect @@ -3273,7 +3376,7 @@ For example, A and B may be gene products and binding of B by A positively regul 2018-01-26T23:53:22Z acts upstream of, negative effect - + https://wiki.geneontology.org/Acts_upstream_of,_negative_effect @@ -3286,6 +3389,7 @@ For example, A and B may be gene products and binding of B by A positively regul 2018-03-13T23:55:05Z causally upstream of or within, negative effect + https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect @@ -3298,6 +3402,7 @@ For example, A and B may be gene products and binding of B by A positively regul 2018-03-13T23:55:19Z causally upstream of or within, positive effect + @@ -3328,7 +3433,7 @@ For example, A and B may be gene products and binding of B by A positively regul triggered by process - RO:cjm + @@ -3393,7 +3498,7 @@ For example, A and B may be gene products and binding of B by A positively regul p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q. - pg + 2022-09-26T06:07:17Z indirectly causally upstream of @@ -3406,7 +3511,7 @@ For example, A and B may be gene products and binding of B by A positively regul p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q. - pg + 2022-09-26T06:08:01Z indirectly regulates @@ -3426,7 +3531,7 @@ For example, A and B may be gene products and binding of B by A positively regul A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input. See github ticket https://github.com/oborel/obo-relations/issues/497 - 2021-11-08T12:00:00Z + 2021-11-08T12:00:00Z utilizes device utilizes material @@ -3738,13 +3843,13 @@ For example, A and B may be gene products and binding of B by A positively regul an organism the bottom right portion of a human torso the interior of your mouth - A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] + A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. independent continuant @@ -4031,10 +4136,10 @@ For example, A and B may be gene products and binding of B by A positively regul the flight of a bird the life of an organism your process of aging. - An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war) (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] + An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. process @@ -4255,10 +4360,10 @@ For example, A and B may be gene products and binding of B by A positively regul the role of being a doctor the shape of this hole. the smell of this portion of mozzarella - A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] + A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. specifically dependent continuant @@ -4560,9 +4665,9 @@ For example, A and B may be gene products and binding of B by A positively regul The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity. the pdf file on your laptop, the pdf file that is a copy thereof on my laptop the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule. - A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] + A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. generically dependent continuant @@ -4593,7 +4698,7 @@ For example, A and B may be gene products and binding of B by A positively regul BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc. A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] - + function @@ -7577,7 +7682,7 @@ JAR: A data item is an approximately justified approximately true approximate be PERSON: Chris Stoeckert PERSON: Jonathan Rees data - + data item @@ -7692,7 +7797,7 @@ this case we explicitly refer to the singular form PlanAndPlannedProcess Branch OBI_0000270 adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg) - + algorithm @@ -7741,7 +7846,7 @@ this case we explicitly refer to the singular form person:Chris Stoeckert OBI_0000030 group:OBI - + image @@ -7812,7 +7917,7 @@ Request that IAO either clarify these or change definitions not to use themperson:Chris Stoeckert OBI_0000305 group:OBI - + measurement datum @@ -8437,7 +8542,7 @@ No imports - + person @@ -8482,7 +8587,7 @@ objectives is a planned process. 6/11/9: Edited at workshop. Used to include: is initiated by an agent This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call) - + planned process @@ -8514,7 +8619,7 @@ objectives is a planned process. Is a material entity that is created or changed during material processing. PERSON: Alan Ruttenberg - + processed material @@ -8551,7 +8656,7 @@ objectives is a planned process. editor = PRS study - + investigation @@ -8582,7 +8687,7 @@ editor = PRS GROUP: Role Branch OBI Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. - + evaluant role @@ -8657,15 +8762,16 @@ editor = PRS assay Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house. - A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies. + A planned process that has the objective to produce information about a material entity (the evaluant) by examining it. 12/3/12: BP: the reference to the 'physical examination' is included to point out that a prediction is not an assay, as that does not require physical examiniation. + Discussion on OBI call 2023-05-01 resulted in an agreement to revise the textual definition of 'assay'. https://github.com/obi-ontology/obi/issues/1683. PlanAndPlannedProcess Branch measuring scientific observation OBI branch derived study assay any method - + assay @@ -8681,7 +8787,7 @@ editor = PRS PlanAndPlannedProcess Branch study OBI branch derived - + sample preparation for assay @@ -8701,7 +8807,7 @@ editor = PRS Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. May 28 2013. Updated definition taken from ReO based on discussions initiated in Philly 2011 workshop. Former defnition described a narrower view of reagents in chemistry that restricts bearers of the role to be chemical entities ("a role played by a molecular entity used to produce a chemical reaction to detect, measure, or produce other substances"). Updated definition allows for broader view of reagents in the domain of biomedical research to include larger materials that have parts that participate chemically in a molecular reaction or interaction. - + (copied from ReO) Reagents are distinguished from instruments or devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in or have parts that participate in some chemical interaction or reaction during their intended participation in some technique. By contrast, instruments do not participate in a chemical reaction/interaction during the technique. @@ -8752,7 +8858,7 @@ In regard to the statement that reagents are 'distinct' from the speci PERSON: Philippe Rocca Serra material transformation OBI branch derived - + material processing @@ -8793,7 +8899,7 @@ specimen can later be subject. GROUP: Role Branch OBI - + specimen role @@ -8877,7 +8983,7 @@ specimen can later be subject. OBI Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. study person role - + Philly2013: Historically, this role would have been borne only by humans or organizations. However, we now also want to enable investigations run by robot scientists such as ADAM (King et al, Science, 2009) investigation agent role @@ -8924,7 +9030,7 @@ for now. PERSON: Philippe Rocca-Serra PERSON: Susanna Sansone GROUP: OBI - + organization @@ -8941,7 +9047,7 @@ for now. PlanAndPlannedProcess Branch OBI branch derived + wikipedia (http://en.wikipedia.org/wiki/Protocol_%28natural_sciences%29) study protocol - + protocol @@ -8969,7 +9075,7 @@ for now. Bjoern Peters Bjoern Peters Plans and Planned Processes Branch - + planning @@ -8986,7 +9092,7 @@ for now. Daniel Schober Frank Gibson Melanie Courtot - + magnify function @@ -9012,7 +9118,7 @@ for now. An image acquisition function is a function to acquire an image of a material Frank Gibson - + image acquisition function @@ -9045,7 +9151,7 @@ for now. Frank Gibson image acquisition device sep:00096 - + image creation device @@ -9062,7 +9168,7 @@ for now. Daniel Schober Frank Gibson Melanie Courtot - + solid support function @@ -9078,7 +9184,7 @@ for now. an objective specification to determine a specified type of information about an evaluated entity (the material entity bearing evaluant role) PPPB branch PPPB branch - + assay objective @@ -9113,7 +9219,7 @@ for now. PERSON: Helen Parkinson PERSON: Melanie Courtot PERSON:Frank Gibson - + measure function @@ -9134,7 +9240,7 @@ for now. PERSON: Philippe Rocca-Serra artifact creation objective GROUP: OBI PlanAndPlannedProcess Branch - + material transformation objective @@ -9163,7 +9269,7 @@ for now. Manufacturer role is a role which inheres in a person or organization and which is realized by a manufacturing process. GROUP: Role Branch OBI - + manufacturer role @@ -9185,7 +9291,7 @@ for now. a quality inheres_in some device and is concretization of some (device_setting_specification and is_about a quality of the device There is some question of whether 'device setting' is really best modelled as a quality. To be revisited after assay terms have been worked through. See https://github.com/obi-ontology/obi/issues/133 PERSON: Frank Gibson - + device setting @@ -9237,7 +9343,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ specimen collection 5/31/2012: This process is not necessarily an acquisition, as specimens may be collected from materials already in posession 6/9/09: used at workshop - + specimen collection process @@ -9253,7 +9359,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ A objective specification to obtain a material entity for potential use as an input during an investigation. Bjoern Peters Bjoern Peters - + specimen collection objective @@ -9269,7 +9375,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ A material sample role is a specimen role borne by a material entity that is the output of a material sampling process. 7/13/09: Note that this is a relational role: between the sample taken and the 'sampled' material of which the sample is thought to be representative off. - + material sample role @@ -9304,7 +9410,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ sample population sample - + material sample @@ -9337,7 +9443,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ A device in which a measure function inheres. GROUP:OBI Philly workshop OBI - + measurement device @@ -9371,8 +9477,8 @@ http://sourceforge.net/p/obi/obi-terms/716/ manufacturer - A person or organization that has a manufacturer role - + A person or organization that has a manufacturer role. + manufacturer @@ -9407,7 +9513,7 @@ In the examples above, a reagent is an operational component of a device, but th PERSON: Helen Parkinson instrument OBI development call 2012-12-17. - + device @@ -9435,7 +9541,7 @@ In the examples above, a reagent is an operational component of a device, but th A planned process that captures an image of an object. PERSON: Jie Zheng image acquisition - + image creation @@ -9452,7 +9558,7 @@ In the examples above, a reagent is an operational component of a device, but th specimen ID NIAID GSCID-BRC metadata working group Specimen ID - + NIAID GSCID-BRC specimen identifier @@ -9470,7 +9576,7 @@ In the examples above, a reagent is an operational component of a device, but th NIAID GSCID-BRC metadata working group study title project title - + NIAID GSCID-BRC investigation title @@ -9532,7 +9638,7 @@ In the examples above, a reagent is an operational component of a device, but th PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Comments - + NIAID GSCID-BRC comment on investigation @@ -9556,7 +9662,7 @@ OBI doesn't take position as to when an organism starts or ends being an o This issue is outside the scope of OBI. GROUP: OBI Biomaterial Branch WEB: http://en.wikipedia.org/wiki/Organism - + organism @@ -9592,7 +9698,7 @@ This issue is outside the scope of OBI. PERSON: Philippe Rocca-Serra GROUP: OBI Biomaterial Branch - + specimen @@ -9657,7 +9763,7 @@ This issue is outside the scope of OBI. data processing Branch editors - + data transformation @@ -9674,7 +9780,7 @@ This issue is outside the scope of OBI. Modified definition in 2013 Philly OBI workshop James Malone PERSON: James Malone - + data transformation objective @@ -9690,7 +9796,7 @@ This issue is outside the scope of OBI. solvent role is a role which inheres in a molecular entity capable of ensuring the dissolution of another chemical entity and realized by the process of solvation Philippe Rocca-Serra adpated from wikipedia (http://en.wikipedia.org/wiki/Solvatation) - + solvent role @@ -9712,7 +9818,7 @@ This issue is outside the scope of OBI. A microscope is an instrument which magnifies the view on objects (too small to be viewed by the naked eye) under increased resolution. A microscope can be an optical instrument but also and electronic instrument. There are various kind of optical microscopes, e.g confocal microscope, epifluoresence microscope) PERSON: Phillippe Rocca-Serra wikipedia - + microscope @@ -9734,7 +9840,7 @@ This issue is outside the scope of OBI. A microscope slide is a device usually made of glass which is used as a solid matrix for (biological) material deposited on its surface and which is compatible for use with a microscope instrument PERSON: Phillippe Rocca-Serra OBI biomaterial branch - + microscope slide @@ -9759,7 +9865,7 @@ This issue is outside the scope of OBI. experimental design rediscussed at length (MC/JF/BP). 12/9/08). The definition was clarified to differentiate it from protocol. - + study design @@ -10144,6 +10250,7 @@ https://www.wolframalpha.com/share/clip?f=d41d8cd98f00b204e9800998ecf8427efdcsig A setting datum that specifies the length of time that a photo detector is allowed to collect photons before passing the accumulated charge to the A/D converter for processing. The minimum integration time is the shortest integration time the device supports and is dependent on how fast the detector can read out all of the pixel information. Integration time should not be confused with data transfer speed. This class should better be defined in a more general device ontology or a domain ontology with the scope of optical devices. integration period setting + integration time integration time setting @@ -10263,6 +10370,8 @@ https://www.wolframalpha.com/share/clip?f=d41d8cd98f00b204e9800998ecf8427efdcsig A setting datum that specifies the number of grooves in a diffraction grating device. This class should better be defined in a more general device ontology or a domain ontology with the scope of optical devices. + grating + grating setting groove density setting @@ -10326,6 +10435,8 @@ https://www.wolframalpha.com/share/clip?f=d41d8cd98f00b204e9800998ecf8427efdcsig example:objective_magnification_factor_setting_for_RamanSpectrometerX rdf:type obo:VIBSO_0000014 ; obo:OBI_0002815 (has representation) '100 x' . A setting datum that specifies the magnification factor of the objective collecting the scattered light. + magnification + magnification setting @@ -10810,6 +10921,20 @@ Together with the focal point distance, this setting defines the region of inter + + + + + The term was added to the ontology on the assumption it was a valid domain entity, but it turns out the entity does not exist in reality. + This obsolesence reason should be used conservatively. For example: Obsoleting class that describes a breed of cow based on a record in an existing database, that was later retracted as faulty (breed does not exist). Do not use this term to obsolete a historic concept (that was once valid, but not anymore). + + https://github.com/information-artifact-ontology/ontology-metadata/issues/136 + https://orcid.org/0000-0002-4142-7153 + domain entity does not exist + + + + @@ -10973,7 +11098,7 @@ Together with the focal point distance, this setting defines the region of inter Person:Alan Ruttenberg Person:Helen Parkinson 2009/09/28 Alan Ruttenberg. Fucoidan-use-case - + is member of organization @@ -11109,7 +11234,7 @@ Together with the focal point distance, this setting defines the region of inter See tracker: https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_id=177891&atid=886178 Person: Jie Zheng - + has organization member @@ -11314,15 +11439,15 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - + + + @@ -11332,15 +11457,15 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - + + + @@ -12013,9 +12138,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -12024,9 +12149,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -12058,9 +12183,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -12069,9 +12194,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -12103,9 +12228,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -12114,9 +12239,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -12148,9 +12273,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -12159,9 +12284,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -12193,9 +12318,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -12204,9 +12329,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -12238,7 +12363,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -12249,7 +12374,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -12266,7 +12391,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -12276,7 +12401,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -12294,7 +12419,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -12305,7 +12430,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -12322,7 +12447,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -12332,7 +12457,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -12349,7 +12474,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -12360,7 +12485,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -12393,9 +12518,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -12404,9 +12529,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -12437,9 +12562,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -12448,9 +12573,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -12481,9 +12606,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -12492,9 +12617,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -12525,9 +12650,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -12536,9 +12661,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -12570,8 +12695,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -12581,8 +12706,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -12609,5 +12734,5 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + diff --git a/vibso.obo b/vibso.obo index 65f627e..a3af6bf 100644 --- a/vibso.obo +++ b/vibso.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: releases/2023-06-21 +data-version: releases/2023-11-27 subsetdef: attribute_slim "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_gp2term "" @@ -10,6 +10,19 @@ subsetdef: ro-eco "" subsetdef: RO:0002259 "" subsetdef: scalar_slim "" subsetdef: value_slim "" +synonymtypedef: OMO:0003000 "abbreviation" +synonymtypedef: OMO:0003001 "ambiguous synonym" +synonymtypedef: OMO:0003002 "dubious synonym" +synonymtypedef: OMO:0003003 "layperson synonym" +synonymtypedef: OMO:0003004 "plural form" +synonymtypedef: OMO:0003005 "UK spelling synonym" +synonymtypedef: OMO:0003006 "misspelling" +synonymtypedef: OMO:0003007 "misnomer" +synonymtypedef: OMO:0003008 "previous name" +synonymtypedef: OMO:0003009 "legal name" +synonymtypedef: OMO:0003010 "International Nonproprietary Name" +synonymtypedef: OMO:0003011 "latin term" +synonymtypedef: OMO:0003012 "acronym" ontology: vibso property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-1595-3213 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2239-3955 @@ -19,7 +32,7 @@ property_value: http://purl.org/dc/terms/creator "VIBSO Workgroup" xsd:string property_value: http://purl.org/dc/terms/description "_WIP - NOT READY FOR PRODUCTION_ The Vibration Spectroscopy Ontology (VIBSO) is used to represent information regarding the excution and analysis of vibrational spectroscopy assays." xsd:string property_value: http://purl.org/dc/terms/license https://creativecommons.org/licenses/by/4.0/ property_value: http://purl.org/dc/terms/title "Vibrational Spectroscopy Ontology" xsd:string -property_value: owl:versionInfo "2023-06-21" xsd:string +property_value: owl:versionInfo "2023-11-27" xsd:string [Term] id: BFO:0000001 @@ -31,8 +44,8 @@ property_value: IAO:0000112 "the Second World War" xsd:string property_value: IAO:0000112 "Verdi’s Requiem" xsd:string property_value: IAO:0000112 "your body mass index" xsd:string property_value: IAO:0000116 "BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81" xsd:string -property_value: IAO:0000116 "Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000004", comment="per discussion with Barry Smith", http://www.w3.org/2000/01/rdf-schema#seeAlso="http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf"} -property_value: IAO:0000600 "An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/001-001"} +property_value: IAO:0000116 "Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000004", comment="per discussion with Barry Smith", seeAlso="http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf"} +property_value: IAO:0000600 "An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/001-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] @@ -45,15 +58,15 @@ relationship: BFO:0000050 BFO:0000002 {all_only="true"} ! part of continuant property_value: BFO:0000179 "continuant" xsd:string property_value: BFO:0000180 "Continuant" xsd:string property_value: IAO:0000116 "BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240" xsd:string -property_value: IAO:0000116 "Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000007"} -property_value: IAO:0000600 "A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/008-002"} -property_value: IAO:0000601 "if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/126-001"} -property_value: IAO:0000601 "if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/009-002"} -property_value: IAO:0000601 "if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/011-002"} -property_value: IAO:0000602 "(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/009-002"} -property_value: IAO:0000602 "(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/126-001"} -property_value: IAO:0000602 "(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/008-002"} -property_value: IAO:0000602 "(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/011-002"} +property_value: IAO:0000116 "Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000007"} +property_value: IAO:0000600 "A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/008-002"} +property_value: IAO:0000601 "if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/126-001"} +property_value: IAO:0000601 "if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/009-002"} +property_value: IAO:0000601 "if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/011-002"} +property_value: IAO:0000602 "(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/009-002"} +property_value: IAO:0000602 "(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/126-001"} +property_value: IAO:0000602 "(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/008-002"} +property_value: IAO:0000602 "(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/011-002"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] @@ -66,20 +79,20 @@ property_value: BFO:0000179 "occurrent" xsd:string property_value: BFO:0000180 "Occurrent" xsd:string property_value: IAO:0000116 "BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region" xsd:string property_value: IAO:0000116 "BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players." xsd:string -property_value: IAO:0000116 "Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000006", comment="per discussion with Barry Smith"} -property_value: IAO:0000116 "Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000012"} -property_value: IAO:0000600 "An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/077-002"} -property_value: IAO:0000601 "b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/079-001"} -property_value: IAO:0000601 "Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/108-001"} -property_value: IAO:0000602 "(forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/108-001"} -property_value: IAO:0000602 "(forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/079-001"} +property_value: IAO:0000116 "Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process." xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000006", comment="per discussion with Barry Smith"} +property_value: IAO:0000116 "Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame." xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000012"} +property_value: IAO:0000600 "An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/077-002"} +property_value: IAO:0000601 "b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/079-001"} +property_value: IAO:0000601 "Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/108-001"} +property_value: IAO:0000602 "(forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/108-001"} +property_value: IAO:0000602 "(forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/079-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000004 name: independent continuant -def: "A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything." [] -def: "b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/017-002"} +def: "b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])" [] {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/017-002"} +comment: A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. is_a: BFO:0000002 ! continuant disjoint_from: BFO:0000020 ! specifically dependent continuant disjoint_from: BFO:0000031 ! generically dependent continuant @@ -96,11 +109,11 @@ property_value: IAO:0000112 "an orchestra." xsd:string property_value: IAO:0000112 "an organism" xsd:string property_value: IAO:0000112 "the bottom right portion of a human torso" xsd:string property_value: IAO:0000112 "the interior of your mouth" xsd:string -property_value: IAO:0000601 "For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/134-001"} -property_value: IAO:0000601 "For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/018-002"} -property_value: IAO:0000602 "(forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/018-002"} -property_value: IAO:0000602 "(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/134-001"} -property_value: IAO:0000602 "(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/017-002"} +property_value: IAO:0000601 "For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/134-001"} +property_value: IAO:0000601 "For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/018-002"} +property_value: IAO:0000602 "(forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/018-002"} +property_value: IAO:0000602 "(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/134-001"} +property_value: IAO:0000602 "(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/017-002"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] @@ -112,11 +125,11 @@ disjoint_from: BFO:0000140 ! continuant fiat boundary property_value: BFO:0000179 "s-region" xsd:string property_value: BFO:0000180 "SpatialRegion" xsd:string property_value: IAO:0000116 "BFO 2 Reference: Spatial regions do not participate in processes." xsd:string -property_value: IAO:0000116 "Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000002", comment="per discussion with Barry Smith"} -property_value: IAO:0000600 "A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/035-001"} -property_value: IAO:0000601 "All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/036-001"} -property_value: IAO:0000602 "(forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/036-001"} -property_value: IAO:0000602 "(forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/035-001"} +property_value: IAO:0000116 "Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional." xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000002", comment="per discussion with Barry Smith"} +property_value: IAO:0000600 "A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/035-001"} +property_value: IAO:0000601 "All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/036-001"} +property_value: IAO:0000602 "(forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/036-001"} +property_value: IAO:0000602 "(forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/035-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] @@ -128,13 +141,13 @@ disjoint_from: BFO:0000015 ! process disjoint_from: BFO:0000035 ! process boundary property_value: BFO:0000179 "t-region" xsd:string property_value: BFO:0000180 "TemporalRegion" xsd:string -property_value: IAO:0000116 "Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000003", comment="per discussion with Barry Smith"} -property_value: IAO:0000600 "A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/100-001"} -property_value: IAO:0000601 "All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/101-001"} -property_value: IAO:0000601 "Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/119-002"} -property_value: IAO:0000602 "(forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/119-002"} -property_value: IAO:0000602 "(forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/101-001"} -property_value: IAO:0000602 "(forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/100-001"} +property_value: IAO:0000116 "Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000003", comment="per discussion with Barry Smith"} +property_value: IAO:0000600 "A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/100-001"} +property_value: IAO:0000601 "All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/101-001"} +property_value: IAO:0000601 "Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/119-002"} +property_value: IAO:0000602 "(forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/119-002"} +property_value: IAO:0000602 "(forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/101-001"} +property_value: IAO:0000602 "(forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/100-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] @@ -146,8 +159,8 @@ property_value: BFO:0000179 "2d-s-region" xsd:string property_value: BFO:0000180 "TwoDimensionalSpatialRegion" xsd:string property_value: IAO:0000112 "an infinitely thin plane in space." xsd:string property_value: IAO:0000112 "the surface of a sphere-shaped part of space" xsd:string -property_value: IAO:0000600 "A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/039-001"} -property_value: IAO:0000602 "(forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/039-001"} +property_value: IAO:0000600 "A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/039-001"} +property_value: IAO:0000602 "(forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/039-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] @@ -159,24 +172,24 @@ property_value: BFO:0000180 "SpatiotemporalRegion" xsd:string property_value: IAO:0000112 "the spatiotemporal region occupied by a human life" xsd:string property_value: IAO:0000112 "the spatiotemporal region occupied by a process of cellular meiosis." xsd:string property_value: IAO:0000112 "the spatiotemporal region occupied by the development of a cancer tumor" xsd:string -property_value: IAO:0000600 "A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/095-001"} -property_value: IAO:0000601 "All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/096-001"} -property_value: IAO:0000601 "Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/099-001"} -property_value: IAO:0000601 "Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/098-001"} +property_value: IAO:0000600 "A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/095-001"} +property_value: IAO:0000601 "All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/096-001"} +property_value: IAO:0000601 "Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/099-001"} +property_value: IAO:0000601 "Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/098-001"} property_value: IAO:0000601 "Every spatiotemporal region occupies_spatiotemporal_region itself." xsd:string -property_value: IAO:0000601 "Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/107-002"} -property_value: IAO:0000602 "(forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/107-002"} -property_value: IAO:0000602 "(forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/099-001"} -property_value: IAO:0000602 "(forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/096-001"} -property_value: IAO:0000602 "(forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/098-001"} -property_value: IAO:0000602 "(forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/095-001"} +property_value: IAO:0000601 "Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/107-002"} +property_value: IAO:0000602 "(forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/107-002"} +property_value: IAO:0000602 "(forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/099-001"} +property_value: IAO:0000602 "(forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/096-001"} +property_value: IAO:0000602 "(forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/098-001"} +property_value: IAO:0000602 "(forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/095-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000015 name: process -def: "An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t." [] -def: "p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/083-003"} +def: "p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])" [] {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/083-003"} +comment: An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. is_a: BFO:0000003 ! occurrent property_value: BFO:0000179 "process" xsd:string property_value: BFO:0000180 "Process" xsd:string @@ -188,7 +201,7 @@ property_value: IAO:0000112 "the flight of a bird" xsd:string property_value: IAO:0000112 "the life of an organism" xsd:string property_value: IAO:0000112 "your process of aging." xsd:string property_value: IAO:0000116 "BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war)" xsd:string -property_value: IAO:0000602 "(iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/083-003"} +property_value: IAO:0000602 "(iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/083-003"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] @@ -203,10 +216,10 @@ property_value: IAO:0000112 "certain people have a predisposition to colon cance property_value: IAO:0000112 "children are innately disposed to categorize objects in certain ways." xsd:string property_value: IAO:0000112 "the cell wall is disposed to filter chemicals in endocytosis and exocytosis" xsd:string property_value: IAO:0000116 "BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type." xsd:string -property_value: IAO:0000600 "b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/062-002"} -property_value: IAO:0000601 "If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/063-002"} -property_value: IAO:0000602 "(forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/063-002"} -property_value: IAO:0000602 "(forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/062-002"} +property_value: IAO:0000600 "b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/062-002"} +property_value: IAO:0000601 "If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/063-002"} +property_value: IAO:0000602 "(forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/063-002"} +property_value: IAO:0000602 "(forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/062-002"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] @@ -223,10 +236,10 @@ property_value: IAO:0000112 "the disposition of your blood to coagulate" xsd:str property_value: IAO:0000112 "the function of your reproductive organs" xsd:string property_value: IAO:0000112 "the role of being a doctor" xsd:string property_value: IAO:0000112 "the role of this boundary to delineate where Utah and Colorado meet" xsd:string -property_value: IAO:0000600 "To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/058-002"} -property_value: IAO:0000601 "All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/060-002"} -property_value: IAO:0000602 "(forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/060-002"} -property_value: IAO:0000602 "(forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/058-002"} +property_value: IAO:0000600 "To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/058-002"} +property_value: IAO:0000601 "All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/060-002"} +property_value: IAO:0000602 "(forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/060-002"} +property_value: IAO:0000602 "(forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/058-002"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] @@ -236,8 +249,8 @@ is_a: BFO:0000006 ! spatial region disjoint_from: BFO:0000028 ! three-dimensional spatial region property_value: BFO:0000179 "0d-s-region" xsd:string property_value: BFO:0000180 "ZeroDimensionalSpatialRegion" xsd:string -property_value: IAO:0000600 "A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/037-001"} -property_value: IAO:0000602 "(forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/037-001"} +property_value: IAO:0000600 "A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/037-001"} +property_value: IAO:0000602 "(forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/037-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] @@ -253,17 +266,17 @@ property_value: IAO:0000112 "the length of the circumference of your waist" xsd: property_value: IAO:0000112 "the mass of this piece of gold." xsd:string property_value: IAO:0000112 "the shape of your nose" xsd:string property_value: IAO:0000112 "the shape of your nostril" xsd:string -property_value: IAO:0000600 "a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/055-001"} -property_value: IAO:0000601 "If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/105-001"} -property_value: IAO:0000602 "(forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/105-001"} -property_value: IAO:0000602 "(forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/055-001"} +property_value: IAO:0000600 "a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/055-001"} +property_value: IAO:0000601 "If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/105-001"} +property_value: IAO:0000602 "(forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/105-001"} +property_value: IAO:0000602 "(forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/055-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000020 name: specifically dependent continuant -def: "A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same." [] -def: "b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/050-003"} +def: "b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])" [] {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/050-003"} +comment: A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. is_a: BFO:0000002 ! continuant disjoint_from: BFO:0000031 ! generically dependent continuant relationship: BFO:0000050 BFO:0000020 {all_only="true"} ! part of specifically dependent continuant @@ -280,8 +293,8 @@ property_value: IAO:0000112 "the pink color of a medium rare piece of grilled fi property_value: IAO:0000112 "the role of being a doctor" xsd:string property_value: IAO:0000112 "the shape of this hole." xsd:string property_value: IAO:0000112 "the smell of this portion of mozzarella" xsd:string -property_value: IAO:0000116 "Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000005", comment="per discussion with Barry Smith"} -property_value: IAO:0000602 "(iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/050-003"} +property_value: IAO:0000116 "Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc." xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000005", comment="per discussion with Barry Smith"} +property_value: IAO:0000602 "(iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/050-003"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] @@ -299,8 +312,8 @@ property_value: IAO:0000112 "the role of a stone in marking a property boundary" property_value: IAO:0000112 "the role of subject in a clinical trial" xsd:string property_value: IAO:0000112 "the student role" xsd:string property_value: IAO:0000116 "BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives." xsd:string -property_value: IAO:0000600 "b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/061-001"} -property_value: IAO:0000602 "(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/061-001"} +property_value: IAO:0000600 "b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/061-001"} +property_value: IAO:0000602 "(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/061-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] @@ -317,8 +330,8 @@ property_value: IAO:0000112 "the FMA:regional parts of an intact human body." xs property_value: IAO:0000112 "the upper and lower lobes of the left lung" xsd:string property_value: IAO:0000112 "the Western hemisphere of the Earth" xsd:string property_value: IAO:0000116 "BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisions" xsd:string -property_value: IAO:0000600 "b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/027-004"} -property_value: IAO:0000602 "(forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/027-004"} +property_value: IAO:0000600 "b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/027-004"} +property_value: IAO:0000602 "(forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/027-004"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] @@ -329,8 +342,8 @@ disjoint_from: BFO:0000028 ! three-dimensional spatial region property_value: BFO:0000179 "1d-s-region" xsd:string property_value: BFO:0000180 "OneDimensionalSpatialRegion" xsd:string property_value: IAO:0000112 "an edge of a cube-shaped portion of space." xsd:string -property_value: IAO:0000600 "A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/038-001"} -property_value: IAO:0000602 "(forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/038-001"} +property_value: IAO:0000600 "A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/038-001"} +property_value: IAO:0000602 "(forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/038-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] @@ -352,12 +365,12 @@ property_value: IAO:0000112 "the aggregate of blood cells in your body" xsd:stri property_value: IAO:0000112 "the nitrogen atoms in the atmosphere" xsd:string property_value: IAO:0000112 "the restaurants in Palo Alto" xsd:string property_value: IAO:0000112 "your collection of Meissen ceramic plates." xsd:string -property_value: IAO:0000116 "An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000301"} -property_value: IAO:0000116 "An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000011"} +property_value: IAO:0000116 "An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000301"} +property_value: IAO:0000116 "An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000011"} property_value: IAO:0000116 "BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee)." xsd:string -property_value: IAO:0000119 "ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000300"} -property_value: IAO:0000600 "b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/025-004"} -property_value: IAO:0000602 "(forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/025-004"} +property_value: IAO:0000119 "ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158." xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000300"} +property_value: IAO:0000600 "b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/025-004"} +property_value: IAO:0000602 "(forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/025-004"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] @@ -368,8 +381,8 @@ property_value: BFO:0000179 "3d-s-region" xsd:string property_value: BFO:0000180 "ThreeDimensionalSpatialRegion" xsd:string property_value: IAO:0000112 "a cube-shaped region of space" xsd:string property_value: IAO:0000112 "a sphere-shaped region of space," xsd:string -property_value: IAO:0000600 "A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/040-001"} -property_value: IAO:0000602 "(forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/040-001"} +property_value: IAO:0000600 "A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/040-001"} +property_value: IAO:0000602 "(forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/040-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] @@ -393,8 +406,8 @@ property_value: IAO:0000112 "the interior of your refrigerator" xsd:string property_value: IAO:0000112 "the lumen of your gut" xsd:string property_value: IAO:0000112 "the Piazza San Marco" xsd:string property_value: IAO:0000112 "your left nostril (a fiat part – the opening – of your left nasal cavity)" xsd:string -property_value: IAO:0000600 "b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/034-002"} -property_value: IAO:0000602 "(forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/034-002"} +property_value: IAO:0000600 "b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/034-002"} +property_value: IAO:0000602 "(forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/034-002"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] @@ -419,14 +432,14 @@ property_value: IAO:0000116 "BFO 2 Reference: BFO rests on the presupposition th property_value: IAO:0000116 "BFO 2 Reference: Each object is such that there are entities of which we can assert unproblematically that they lie in its interior, and other entities of which we can assert unproblematically that they lie in its exterior. This may not be so for entities lying at or near the boundary between the interior and exterior. This means that two objects – for example the two cells depicted in Figure 3 – may be such that there are material entities crossing their boundaries which belong determinately to neither cell. Something similar obtains in certain cases of conjoined twins (see below)." xsd:string property_value: IAO:0000116 "BFO 2 Reference: To say that b is causally unified means: b is a material entity which is such that its material parts are tied together in such a way that, in environments typical for entities of the type in question,if c, a continuant part of b that is in the interior of b at t, is larger than a certain threshold size (which will be determined differently from case to case, depending on factors such as porosity of external cover) and is moved in space to be at t at a location on the exterior of the spatial region that had been occupied by b at t, then either b’s other parts will be moved in coordinated fashion or b will be damaged (be affected, for example, by breakage or tearing) in the interval between t and t.causal changes in one part of b can have consequences for other parts of b without the mediation of any entity that lies on the exterior of b. Material entities with no proper material parts would satisfy these conditions trivially. Candidate examples of types of causal unity for material entities of more complex sorts are as follows (this is not intended to be an exhaustive list):CU1: Causal unity via physical coveringHere the parts in the interior of the unified entity are combined together causally through a common membrane or other physical covering\\. The latter points outwards toward and may serve a protective function in relation to what lies on the exterior of the entity [13, 47" xsd:string property_value: IAO:0000116 "BFO 2 Reference: ‘objects’ are sometimes referred to as ‘grains’ [74" xsd:string -property_value: IAO:0000600 "b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/024-001"} +property_value: IAO:0000600 "b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/024-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000031 name: generically dependent continuant -def: "A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time." [] -def: "b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/074-001"} +def: "b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])" [] {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/074-001"} +comment: A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. is_a: BFO:0000002 ! continuant relationship: BFO:0000050 BFO:0000031 {all_only="true"} ! part of generically dependent continuant property_value: BFO:0000179 "gdc" xsd:string @@ -434,7 +447,7 @@ property_value: BFO:0000180 "GenericallyDependentContinuant" xsd:string property_value: IAO:0000112 "The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity." xsd:string property_value: IAO:0000112 "the pdf file on your laptop, the pdf file that is a copy thereof on my laptop" xsd:string property_value: IAO:0000112 "the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule." xsd:string -property_value: IAO:0000602 "(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/074-001"} +property_value: IAO:0000602 "(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/074-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] @@ -443,26 +456,26 @@ name: function is_a: BFO:0000016 ! disposition property_value: BFO:0000179 "function" xsd:string property_value: BFO:0000180 "Function" xsd:string -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000112 "the function of a hammer to drive in nails" xsd:string property_value: IAO:0000112 "the function of a heart pacemaker to regulate the beating of a heart through electricity" xsd:string property_value: IAO:0000112 "the function of amylase in saliva to break down starch into sugar" xsd:string property_value: IAO:0000116 "BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc." xsd:string -property_value: IAO:0000600 "A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/064-001"} -property_value: IAO:0000602 "(forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/064-001"} +property_value: IAO:0000600 "A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/064-001"} +property_value: IAO:0000602 "(forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/064-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000035 name: process boundary -def: "p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/084-001"} +def: "p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001])" [] {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/084-001"} is_a: BFO:0000003 ! occurrent property_value: BFO:0000179 "p-boundary" xsd:string property_value: BFO:0000180 "ProcessBoundary" xsd:string property_value: IAO:0000112 "the boundary between the 2nd and 3rd year of your life." xsd:string -property_value: IAO:0000601 "Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/085-002"} -property_value: IAO:0000602 "(forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/085-002"} -property_value: IAO:0000602 "(iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/084-001"} +property_value: IAO:0000601 "Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/085-002"} +property_value: IAO:0000602 "(forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/085-002"} +property_value: IAO:0000602 "(iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/084-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] @@ -474,8 +487,8 @@ property_value: BFO:0000179 "1d-t-region" xsd:string property_value: BFO:0000180 "OneDimensionalTemporalRegion" xsd:string property_value: IAO:0000112 "the temporal region during which a process occurs." xsd:string property_value: IAO:0000116 "BFO 2 Reference: A temporal interval is a special kind of one-dimensional temporal region, namely one that is self-connected (is without gaps or breaks)." xsd:string -property_value: IAO:0000600 "A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/103-001"} -property_value: IAO:0000602 "(forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/103-001"} +property_value: IAO:0000600 "A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/103-001"} +property_value: IAO:0000602 "(forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/103-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] @@ -501,26 +514,26 @@ property_value: IAO:0000112 "the undetached arm of a human being" xsd:string property_value: IAO:0000116 "BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60" xsd:string property_value: IAO:0000116 "BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity." xsd:string property_value: IAO:0000116 "BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here." xsd:string -property_value: IAO:0000600 "A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/019-002"} -property_value: IAO:0000601 "every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/021-002"} -property_value: IAO:0000601 "Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/020-002"} -property_value: IAO:0000602 "(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/021-002"} -property_value: IAO:0000602 "(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/020-002"} -property_value: IAO:0000602 "(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/019-002"} +property_value: IAO:0000600 "A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/019-002"} +property_value: IAO:0000601 "every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/021-002"} +property_value: IAO:0000601 "Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/020-002"} +property_value: IAO:0000602 "(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/021-002"} +property_value: IAO:0000602 "(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/020-002"} +property_value: IAO:0000602 "(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/019-002"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000140 name: continuant fiat boundary -def: "b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/029-001"} +def: "b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001])" [] {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/029-001"} is_a: BFO:0000141 ! immaterial entity property_value: BFO:0000179 "cf-boundary" xsd:string property_value: BFO:0000180 "ContinuantFiatBoundary" xsd:string property_value: IAO:0000116 "BFO 2 Reference: a continuant fiat boundary is a boundary of some material entity (for example: the plane separating the Northern and Southern hemispheres; the North Pole), or it is a boundary of some immaterial entity (for example of some portion of airspace). Three basic kinds of continuant fiat boundary can be distinguished (together with various combination kinds [29" xsd:string property_value: IAO:0000116 "BFO 2 Reference: In BFO 1.1 the assumption was made that the external surface of a material entity such as a cell could be treated as if it were a boundary in the mathematical sense. The new document propounds the view that when we talk about external surfaces of material objects in this way then we are talking about something fiat. To be dealt with in a future version: fiat boundaries at different levels of granularity.More generally, the focus in discussion of boundaries in BFO 2.0 is now on fiat boundaries, which means: boundaries for which there is no assumption that they coincide with physical discontinuities. The ontology of boundaries becomes more closely allied with the ontology of regions." xsd:string -property_value: IAO:0000116 "Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000008"} +property_value: IAO:0000116 "Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions." xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000008"} property_value: IAO:0000601 "Every continuant fiat boundary is located at some spatial region at every time at which it exists" xsd:string -property_value: IAO:0000602 "(iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/029-001"} +property_value: IAO:0000602 "(iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/029-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] @@ -545,14 +558,14 @@ property_value: IAO:0000112 "all lines of latitude and longitude" xsd:string property_value: IAO:0000112 "The Equator" xsd:string property_value: IAO:0000112 "the line separating the outer surface of the mucosa of the lower lip from the outer surface of the skin of the chin." xsd:string property_value: IAO:0000112 "the median sulcus of your tongue" xsd:string -property_value: IAO:0000600 "a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/032-001"} -property_value: IAO:0000602 "(iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/032-001"} +property_value: IAO:0000600 "a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/032-001"} +property_value: IAO:0000602 "(iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/032-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000144 name: process profile -def: "b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/093-002"} +def: "b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002])" [] {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/093-002"} is_a: BFO:0000015 ! process disjoint_from: BFO:0000182 ! history property_value: BFO:0000179 "process-profile" xsd:string @@ -560,21 +573,21 @@ property_value: BFO:0000180 "ProcessProfile" xsd:string property_value: IAO:0000112 "On a somewhat higher level of complexity are what we shall call rate process profiles, which are the targets of selective abstraction focused not on determinate quality magnitudes plotted over time, but rather on certain ratios between these magnitudes and elapsed times. A speed process profile, for example, is represented by a graph plotting against time the ratio of distance covered per unit of time. Since rates may change, and since such changes, too, may have rates of change, we have to deal here with a hierarchy of process profile universals at successive levels" xsd:string property_value: IAO:0000112 "One important sub-family of rate process profiles is illustrated by the beat or frequency profiles of cyclical processes, illustrated by the 60 beats per minute beating process of John’s heart, or the 120 beats per minute drumming process involved in one of John’s performances in a rock band, and so on. Each such process includes what we shall call a beat process profile instance as part, a subtype of rate process profile in which the salient ratio is not distance covered but rather number of beat cycles per unit of time. Each beat process profile instance instantiates the determinable universal beat process profile. But it also instantiates multiple more specialized universals at lower levels of generality, selected from rate process profilebeat process profileregular beat process profile3 bpm beat process profile4 bpm beat process profileirregular beat process profileincreasing beat process profileand so on.In the case of a regular beat process profile, a rate can be assigned in the simplest possible fashion by dividing the number of cycles by the length of the temporal region occupied by the beating process profile as a whole. Irregular process profiles of this sort, for example as identified in the clinic, or in the readings on an aircraft instrument panel, are often of diagnostic significance." xsd:string property_value: IAO:0000112 "The simplest type of process profiles are what we shall call ‘quality process profiles’, which are the process profiles which serve as the foci of the sort of selective abstraction that is involved when measurements are made of changes in single qualities, as illustrated, for example, by process profiles of mass, temperature, aortic pressure, and so on." xsd:string -property_value: IAO:0000600 "b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/094-005"} -property_value: IAO:0000602 "(forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/094-005"} -property_value: IAO:0000602 "(iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/093-002"} +property_value: IAO:0000600 "b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/094-005"} +property_value: IAO:0000602 "(forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/094-005"} +property_value: IAO:0000602 "(iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/093-002"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000145 name: relational quality -def: "b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/057-001"} +def: "b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001])" [] {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/057-001"} is_a: BFO:0000019 ! quality property_value: BFO:0000179 "r-quality" xsd:string property_value: BFO:0000180 "RelationalQuality" xsd:string property_value: IAO:0000112 "a marriage bond, an instance of requited love, an obligation between one person and another." xsd:string property_value: IAO:0000112 "John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married." xsd:string -property_value: IAO:0000602 "(iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/057-001"} +property_value: IAO:0000602 "(iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/057-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] @@ -583,8 +596,8 @@ name: two-dimensional continuant fiat boundary is_a: BFO:0000140 ! continuant fiat boundary property_value: BFO:0000179 "2d-cf-boundary" xsd:string property_value: BFO:0000180 "TwoDimensionalContinuantFiatBoundary" xsd:string -property_value: IAO:0000600 "a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/033-001"} -property_value: IAO:0000602 "(iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/033-001"} +property_value: IAO:0000600 "a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/033-001"} +property_value: IAO:0000602 "(iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/033-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] @@ -596,9 +609,9 @@ property_value: BFO:0000180 "ZeroDimensionalContinuantFiatBoundary" xsd:string property_value: IAO:0000112 "the geographic North Pole" xsd:string property_value: IAO:0000112 "the point of origin of some spatial coordinate system." xsd:string property_value: IAO:0000112 "the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet" xsd:string -property_value: IAO:0000116 "zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000001", comment="requested by Melanie Courtot", http://www.w3.org/2000/01/rdf-schema#seeAlso="ZDRnpiIi:TUJ"} -property_value: IAO:0000600 "a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/031-001"} -property_value: IAO:0000602 "(iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/031-001"} +property_value: IAO:0000116 "zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona." xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000001", comment="requested by Melanie Courtot", seeAlso="ZDRnpiIi:TUJ"} +property_value: IAO:0000600 "a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/031-001"} +property_value: IAO:0000602 "(iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/031-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] @@ -613,8 +626,8 @@ property_value: IAO:0000112 "the moment at which a child is born" xsd:string property_value: IAO:0000112 "the moment at which a finger is detached in an industrial accident" xsd:string property_value: IAO:0000112 "the moment of death." xsd:string property_value: IAO:0000118 "temporal instant." xsd:string -property_value: IAO:0000600 "A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/102-001"} -property_value: IAO:0000602 "(forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/102-001"} +property_value: IAO:0000600 "A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/102-001"} +property_value: IAO:0000602 "(forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] " xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/102-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] @@ -623,7 +636,7 @@ name: history is_a: BFO:0000015 ! process property_value: BFO:0000179 "history" xsd:string property_value: BFO:0000180 "History" xsd:string -property_value: IAO:0000600 "A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/138-001"} +property_value: IAO:0000600 "A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001])" xsd:string {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/138-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] @@ -1976,7 +1989,7 @@ id: IAO:0000027 name: data item def: "An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements." [] is_a: IAO:0000030 ! information content entity -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "data item" xsd:string property_value: IAO:0000112 "Data items include counts of things, analyte concentrations, and statistical summaries." xsd:string property_value: IAO:0000114 IAO:0000125 @@ -2051,7 +2064,7 @@ id: IAO:0000064 name: algorithm def: "A plan specification which describes the inputs and output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata." [] is_a: IAO:0000104 ! plan specification -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "algorithm" xsd:string property_value: IAO:0000112 "PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies." xsd:string property_value: IAO:0000114 IAO:0000120 @@ -2077,7 +2090,7 @@ id: IAO:0000101 name: image def: "An image is an affine projection to a two dimensional surface, of measurements of some quality of an entity or entities repeated at regular intervals across a spatial range, where the measurements are represented as color and luminosity on the projected on surface." [] is_a: IAO:0000308 ! figure -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "image" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "person:Alan Ruttenberg" xsd:string @@ -2120,7 +2133,7 @@ id: IAO:0000109 name: measurement datum def: "A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device." [] is_a: IAO:0000027 ! data item -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "measurement datum" xsd:string property_value: IAO:0000112 "Examples of measurement data are the recoding of the weight of a mouse as {40,mass,\"grams\"}, the recording of an observation of the behavior of the mouse {,process,\"agitated\"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}." xsd:string property_value: IAO:0000114 IAO:0000125 @@ -2485,14 +2498,14 @@ property_value: IAO:0000111 "EL++ ontology module" xsd:string id: NCBITaxon:9606 name: person is_a: OBI:0100026 ! organism -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl [Term] id: OBI:0000011 name: planned process def: "A process that realizes a plan which is the concretization of a plan specification." [] is_a: BFO:0000015 ! process -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "planned process" xsd:string property_value: IAO:0000111 "planned process" xsd:string property_value: IAO:0000112 "Injecting mice with a vaccine in order to test its efficacy" xsd:string @@ -2513,7 +2526,7 @@ is_a: BFO:0000040 ! material entity intersection_of: BFO:0000040 ! material entity intersection_of: OBI:0000312 OBI:0000094 ! is_specified_output_of material processing relationship: OBI:0000312 OBI:0000094 ! is_specified_output_of material processing -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "processed material" xsd:string property_value: IAO:0000112 "Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples" xsd:string property_value: IAO:0000114 IAO:0000122 @@ -2524,7 +2537,7 @@ id: OBI:0000066 name: investigation def: "a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s)." [] is_a: OBI:0000011 ! planned process -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "investigation" xsd:string property_value: IAO:0000112 "Lung cancer investigation using expression profiling, a stem cell transplant investigation, biobanking is not an investigation, though it may be part of an investigation" xsd:string property_value: IAO:0000114 IAO:0000122 @@ -2542,7 +2555,7 @@ def: "a role that inheres in a material entity that is realized in an assay in w is_a: BFO:0000023 ! role relationship: BFO:0000054 OBI:0000070 {all_only="true"} ! realized in assay relationship: RO:0000052 BFO:0000040 ! characteristic of material entity -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "evaluant role" xsd:string property_value: IAO:0000112 "When a specimen of blood is assayed for glucose concentration, the blood has the evaluant role. When measuring the mass of a mouse, the evaluant is the mouse. When measuring the time of DNA replication, the evaluant is the DNA. When measuring the intensity of light on a surface, the evaluant is the light source." xsd:string property_value: IAO:0000114 IAO:0000122 @@ -2555,17 +2568,18 @@ property_value: IAO:0000232 "Feb 10, 2009. changes after discussion at OBI Cons [Term] id: OBI:0000070 name: assay -def: "A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies." [] +def: "A planned process that has the objective to produce information about a material entity (the evaluant) by examining it." [] is_a: OBI:0000011 ! planned process disjoint_from: OBI:0000339 ! planning disjoint_from: OBI:0200000 ! data transformation relationship: BFO:0000055 OBI:0000067 ! realizes evaluant role relationship: OBI:0000417 OBI:0000441 ! achieves_planned_objective assay objective -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "assay" xsd:string property_value: IAO:0000112 "Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house." xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000116 "12/3/12: BP: the reference to the 'physical examination' is included to point out that a prediction is not an assay, as that does not require physical examiniation." xsd:string +property_value: IAO:0000116 "Discussion on OBI call 2023-05-01 resulted in an agreement to revise the textual definition of 'assay'. https://github.com/obi-ontology/obi/issues/1683." xsd:string property_value: IAO:0000117 "PlanAndPlannedProcess Branch" xsd:string property_value: IAO:0000118 "measuring" xsd:string property_value: IAO:0000118 "scientific observation" xsd:string @@ -2578,7 +2592,7 @@ id: OBI:0000073 name: sample preparation for assay def: "A sample_preparation_for_assay is a protocol_application including material_enrollments and biomaterial_transformations. definition_source: OBI." [] is_a: OBI:0000094 ! material processing -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "sample preparation for assay" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "PlanAndPlannedProcess Branch" xsd:string @@ -2591,7 +2605,7 @@ name: reagent role def: "A role inhering in a biological or chemical entity that is intended to be applied in a scientific technique to participate (or have molecular components that participate) in a chemical reaction that facilitates the generation of data about some entity distinct from the bearer, or the generation of some specified material output distinct from the bearer." [] comment: (copied from ReO)\nReagents are distinguished from instruments or devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in or have parts that participate in some chemical interaction or reaction during their intended participation in some technique. By contrast, instruments do not participate in a chemical reaction/interaction during the technique.\n\nReagents are distinguished from study subjects/evaluants in that study subjects and evaluants are that about which conclusions are drawn and knowledge is sought in an investigation - while reagents, by definition, are not. It should be noted, however, that reagent and study subject/evaluant roles can be borne by instances of the same type of material entity - but a given instance will realize only one of these roles in the execution of a given assay or technique. For example, taq polymerase can bear a reagent role or an evaluant role. In a DNA sequencing assay aimed at generating sequence data about some plasmid, the reagent role of the taq polymerase is realized. In an assay to evaluate the quality of the taq polymerase itself, the evaluant/study subject role of the taq is realized, but not the reagent role since the taq is the subject about which data is generated.\n\nIn regard to the statement that reagents are 'distinct' from the specified outputs of a technique, note that a reagent may be incorporated into a material output of a technique, as long as the IDENTITY of this output is distinct from that of the bearer of the reagent role. For example, dNTPs input into a PCR are reagents that become part of the material output of this technique, but this output has a new identity (ie that of a 'nucleic acid molecule') that is distinct from the identity of the dNTPs that comprise it. Similarly, a biotin molecule input into a cell labeling technique are reagents that become part of the specified output, but the identity of the output is that of some modified cell specimen which shares identity with the input unmodified cell specimen, and not with the biotin label. Thus, we see that an important criteria of 'reagent-ness' is that it is a facilitator, and not the primary focus of an investigation or material processing technique (ie not the specified subject/evaluant about which knowledge is sought, or the specified output material of the technique). is_a: BFO:0000023 ! role -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "reagent role" xsd:string property_value: IAO:0000112 "Buffer, dye, a catalyst, a solvating agent." xsd:string property_value: IAO:0000114 IAO:0000120 @@ -2608,7 +2622,7 @@ is_a: OBI:0000011 ! planned process relationship: OBI:0000293 BFO:0000040 {all_only="true"} ! has_specified_input material entity relationship: OBI:0000299 OBI:0000047 ! has_specified_output processed material relationship: OBI:0000417 OBI:0000456 ! achieves_planned_objective material transformation objective -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "material processing" xsd:string property_value: IAO:0000112 "A cell lysis, production of a cloning vector, creating a buffer." xsd:string property_value: IAO:0000114 IAO:0000122 @@ -2625,7 +2639,7 @@ id: OBI:0000112 name: specimen role def: "a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation" [] is_a: BFO:0000023 ! role -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "specimen role" xsd:string property_value: IAO:0000112 "liver section; a portion of a culture of cells; a nemotode or other animal once no longer a subject (generally killed); portion of blood from a patient." xsd:string property_value: IAO:0000114 IAO:0000122 @@ -2644,7 +2658,7 @@ def: "A role borne by an entity and that is realized in a process that is part o comment: Philly2013: Historically, this role would have been borne only by humans or organizations. However, we now also want to enable investigations run by robot scientists such as ADAM (King et al, Science, 2009) is_a: BFO:0000023 ! role relationship: BFO:0000054 OBI:0000066 {all_only="true"} ! realized in investigation -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "investigation agent role" xsd:string property_value: IAO:0000112 "The person perform microarray experiments and submit microarray results (including raw data, processed data) with experiment description to ArrayExpress." xsd:string property_value: IAO:0000114 IAO:0000122 @@ -2661,7 +2675,7 @@ id: OBI:0000245 name: organization def: "An entity that can bear roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members." [] is_a: BFO:0000040 ! material entity -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "organization" xsd:string property_value: IAO:0000112 "PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods." xsd:string property_value: IAO:0000114 IAO:0000122 @@ -2677,7 +2691,7 @@ id: OBI:0000272 name: protocol def: "A plan specification which has sufficient level of detail and quantitative information to communicate it between investigation agents, so that different investigation agents will reliably be able to independently reproduce the process." [] is_a: IAO:0000104 ! plan specification -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "protocol" xsd:string property_value: IAO:0000112 "PCR protocol, has objective specification, amplify DNA fragment of interest, and has action specification describes the amounts of experimental reagents used (e..g. buffers, dNTPS, enzyme), and the temperature and cycle time settings for running the PCR." xsd:string property_value: IAO:0000114 IAO:0000122 @@ -2689,7 +2703,7 @@ property_value: OBI:0001847 "study protocol" xsd:string id: OBI:0000339 name: planning def: "a process of creating or modifying a plan specification" [] -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "planning" xsd:string property_value: IAO:0000112 "The process of a scientist thinking about and deciding what reagents to use as part of a protocol for an experiment. Note that the scientist could be human or a \"robot scientist\" executing software." xsd:string property_value: IAO:0000114 IAO:0000122 @@ -2703,7 +2717,7 @@ id: OBI:0000369 name: magnify function def: "A magnify function is a function to increase the size of a transmitted object image through the precise arrangement of energy diffraction elements along an imaging path." [] is_a: BFO:0000034 ! function -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "magnify function" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "Bill Bug" xsd:string @@ -2718,7 +2732,7 @@ def: "An image acquisition function is a function to acquire an image of a mater is_a: OBI:0000453 ! measure function relationship: BFO:0000054 OBI:0001007 {all_only="true"} ! realized in image creation relationship: RO:0000052 OBI:0000398 ! characteristic of image creation device -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "image acquisition function" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "Frank Gibson" xsd:string @@ -2731,7 +2745,7 @@ is_a: OBI:0000832 ! measurement device intersection_of: OBI:0000968 ! device intersection_of: RO:0000085 OBI:0000397 ! has function image acquisition function relationship: RO:0000085 OBI:0000397 ! has function image acquisition function -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "image acquisition device" xsd:string property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000117 "Frank Gibson" xsd:string @@ -2743,7 +2757,7 @@ id: OBI:0000399 name: solid support function def: "A solid support function is a function of a device on which an entity is kept in a defined position and prevented in its movement" [] is_a: BFO:0000034 ! function -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "solid support function" xsd:string property_value: IAO:0000112 "Taped, glued, pinned, dried or molecularly bonded to a solid support" xsd:string property_value: IAO:0000114 IAO:0000122 @@ -2756,7 +2770,7 @@ id: OBI:0000441 name: assay objective def: "an objective specification to determine a specified type of information about an evaluated entity (the material entity bearing evaluant role)" [] is_a: IAO:0000005 ! objective specification -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "assay objective" xsd:string property_value: IAO:0000112 "the objective to determine the weight of a mouse." xsd:string property_value: IAO:0000114 IAO:0000122 @@ -2769,7 +2783,7 @@ name: measure function def: "Measure function is a function that is borne by a processed material and realized in a process in which information about some entity is expressed relative to some reference." [] is_a: BFO:0000034 ! function relationship: RO:0000079 OBI:0000047 ! function of processed material -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "measure function" xsd:string property_value: IAO:0000112 "A glucometer measures blood glucose concentration, the glucometer has a measure function." xsd:string property_value: IAO:0000114 IAO:0000122 @@ -2783,7 +2797,7 @@ id: OBI:0000456 name: material transformation objective def: "an objective specifiction that creates an specific output object from input materials." [] is_a: IAO:0000005 ! objective specification -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "material transformation objective" xsd:string property_value: IAO:0000112 "The objective to create a mouse infected with LCM virus. The objective to create a defined solution of PBS." xsd:string property_value: IAO:0000114 IAO:0000122 @@ -2800,7 +2814,7 @@ id: OBI:0000571 name: manufacturer role def: "Manufacturer role is a role which inheres in a person or organization and which is realized by a manufacturing process." [] is_a: BFO:0000023 ! role -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "manufacturer role" xsd:string property_value: IAO:0000112 "With respect to The Accuri C6 Flow Cytometer System, the organization Accuri bears the role manufacturer role. With respect to a transformed line of tissue culture cells derived by a specific lab, the lab whose personnel isolated the cll line bears the role manufacturer role. With respect to a specific antibody produced by an individual scientist, the scientist who purifies, characterizes and distributes the anitbody bears the role manufacturer role." xsd:string property_value: IAO:0000114 IAO:0000123 @@ -2813,7 +2827,7 @@ name: device setting def: "a quality inheres_in some device and is concretization of some (device_setting_specification and is_about a quality of the device" [] is_a: BFO:0000019 ! quality relationship: RO:0000052 OBI:0000047 ! characteristic of processed material -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "device setting" xsd:string property_value: IAO:0000112 "Examples, 300V for 4 hours, 200mvolts, 37degrees.A knob set a 300 V is the device setting, the protocol stating to set the instrument to 300V is a device setting specification" xsd:string property_value: IAO:0000114 IAO:0000123 @@ -2830,7 +2844,7 @@ intersection_of: OBI:0000417 OBI:0000684 ! achieves_planned_objective specimen c relationship: OBI:0000293 BFO:0000040 ! has_specified_input material entity relationship: OBI:0000299 OBI:0100051 ! has_specified_output specimen relationship: OBI:0000417 OBI:0000684 ! achieves_planned_objective specimen collection objective -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "specimen collection process" xsd:string property_value: IAO:0000112 "drawing blood from a patient for analysis, collecting a piece of a plant for depositing in a herbarium, buying meat from a butcher in order to measure its protein content in an investigation" xsd:string property_value: IAO:0000114 IAO:0000122 @@ -2848,7 +2862,7 @@ id: OBI:0000684 name: specimen collection objective def: "A objective specification to obtain a material entity for potential use as an input during an investigation." [] is_a: IAO:0000005 ! objective specification -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "specimen collection objective" xsd:string property_value: IAO:0000112 "The objective to collect bits of excrement in the rainforest. The objective to obtain a blood sample from a patient." xsd:string property_value: IAO:0000114 IAO:0000122 @@ -2860,7 +2874,7 @@ id: OBI:0000740 name: material sample role def: "A material sample role is a specimen role borne by a material entity that is the output of a material sampling process." [] is_a: OBI:0000112 ! specimen role -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "material sample role" xsd:string property_value: IAO:0000112 "a role borne by a portion of blood taken to represent all the blood in an organism; the role borne by a population of humans with HIV enrolled in a study taken to represent patients with HIV in general." xsd:string property_value: IAO:0000114 IAO:0000125 @@ -2875,7 +2889,7 @@ is_a: OBI:0100051 ! specimen intersection_of: BFO:0000040 ! material entity intersection_of: RO:0000087 OBI:0000740 ! has role material sample role relationship: RO:0000087 OBI:0000740 ! has role material sample role -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "material sample" xsd:string property_value: IAO:0000112 "blood drawn from patient to measure his systemic glucose level. A population of humans with HIV enrolled in a study taken to represent patients with HIV in general." xsd:string property_value: IAO:0000114 IAO:0000123 @@ -2892,7 +2906,7 @@ is_a: OBI:0000968 ! device intersection_of: OBI:0000968 ! device intersection_of: RO:0000085 OBI:0000453 ! has function measure function relationship: RO:0000085 OBI:0000453 ! has function measure function -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "measurement device" xsd:string property_value: IAO:0000112 "A ruler, a microarray scanner, a Geiger counter." xsd:string property_value: IAO:0000114 IAO:0000122 @@ -2902,10 +2916,10 @@ property_value: IAO:0000119 "OBI" xsd:string [Term] id: OBI:0000835 name: manufacturer -def: "A person or organization that has a manufacturer role" [] +def: "A person or organization that has a manufacturer role." [] is_a: BFO:0000040 ! material entity relationship: RO:0000087 OBI:0000571 ! has role manufacturer role -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "manufacturer" xsd:string property_value: IAO:0000114 IAO:0000123 @@ -2915,7 +2929,7 @@ name: device def: "A material entity that is designed to perform a function in a scientific investigation, but is not a reagent." [] is_a: OBI:0000047 ! processed material relationship: RO:0000085 BFO:0000034 ! has function function -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "device" xsd:string property_value: IAO:0000112 "A voltmeter is a measurement device which is intended to perform some measure function." xsd:string property_value: IAO:0000112 "An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure." xsd:string @@ -2932,7 +2946,7 @@ def: "A planned process that captures an image of an object." [] is_a: OBI:0000011 ! planned process relationship: OBI:0000293 BFO:0000040 ! has_specified_input material entity relationship: OBI:0000299 IAO:0000101 ! has_specified_output image -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "image acquisition" xsd:string property_value: IAO:0000112 "Taking a polaroid picture of a patients skin lesion; Using a digital camera to take a picture of a gel" xsd:string property_value: IAO:0000114 IAO:0000123 @@ -2944,7 +2958,7 @@ id: OBI:0001616 name: specimen identifier def: "A CRID symbol denotes a specimen and used to distinguish one specimen from another in an investigation." [] is_a: IAO:0000577 ! centrally registered identifier symbol -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: http://purl.org/dc/elements/1.1/source "NIAID GSCID-BRC" xsd:string property_value: IAO:0000111 "specimen identifier" xsd:string property_value: IAO:0000114 IAO:0000120 @@ -2958,7 +2972,7 @@ id: OBI:0001622 name: investigation title def: "A textual entity that denotes an investigation." [] is_a: OBI:0001898 ! comment on investigation -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: http://purl.org/dc/elements/1.1/source "NIAID GSCID-BRC" xsd:string property_value: IAO:0000111 "investigation title" xsd:string property_value: IAO:0000114 IAO:0000120 @@ -2972,7 +2986,7 @@ id: OBI:0001898 name: comment on investigation def: "A textual entity that is about any of the aspects of an investigation worth noting" [] is_a: IAO:0000300 ! textual entity -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: http://purl.org/dc/elements/1.1/source "NIAID GSCID-BRC" xsd:string property_value: IAO:0000111 "comment on investigation" xsd:string property_value: IAO:0000114 IAO:0000120 @@ -2985,7 +2999,7 @@ id: OBI:0100026 name: organism def: "A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs." [] is_a: BFO:0000040 ! material entity -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "organism" xsd:string property_value: IAO:0000112 "animal" xsd:string property_value: IAO:0000112 "fungus" xsd:string @@ -3005,7 +3019,7 @@ is_a: BFO:0000040 ! material entity intersection_of: BFO:0000040 ! material entity intersection_of: RO:0000087 OBI:0000112 ! has role specimen role relationship: RO:0000087 OBI:0000112 ! has role specimen role -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "specimen" xsd:string property_value: IAO:0000112 "Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen." xsd:string property_value: IAO:0000114 IAO:0000122 @@ -3022,7 +3036,7 @@ def: "A planned process that produces output data from input data." [] is_a: OBI:0000011 ! planned process relationship: OBI:0000293 IAO:0000027 {all_only="true"} ! has_specified_input data item relationship: OBI:0000417 OBI:0200166 ! achieves_planned_objective data transformation objective -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "data transformation" xsd:string property_value: IAO:0000112 "The application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value." xsd:string property_value: IAO:0000114 IAO:0000122 @@ -3044,7 +3058,7 @@ id: OBI:0200166 name: data transformation objective def: "An objective specification to transformation input data into output data" [] is_a: IAO:0000005 ! objective specification -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "data transformation objective" xsd:string property_value: IAO:0000112 "normalize objective" xsd:string property_value: IAO:0000114 IAO:0000122 @@ -3057,7 +3071,7 @@ id: OBI:0302732 name: solvent role def: "solvent role is a role which inheres in a molecular entity capable of ensuring the dissolution of another chemical entity and realized by the process of solvation" [] is_a: BFO:0000023 ! role -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "solvent role" xsd:string property_value: IAO:0000112 "PMID: 18373502.Transfusion. 2008 Mar 25. Solvent/detergent treatment of platelet concentrates enhances the release of growth factors." xsd:string property_value: IAO:0000114 IAO:0000125 @@ -3070,7 +3084,7 @@ name: microscope def: "A microscope is an instrument which magnifies the view on objects (too small to be viewed by the naked eye) under increased resolution. A microscope can be an optical instrument but also and electronic instrument. There are various kind of optical microscopes, e.g confocal microscope, epifluoresence microscope)" [] is_a: OBI:0000398 ! image creation device relationship: RO:0000085 OBI:0000369 ! has function magnify function -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "microscope" xsd:string property_value: IAO:0000112 "PMID:18466942. A light and transmission electron microscope study of hepatic portal tracts in the rhesus monkey (Macacus rhesus). Tissue Cell. 2008 May 6" xsd:string property_value: IAO:0000114 IAO:0000123 @@ -3083,7 +3097,7 @@ name: microscope slide def: "A microscope slide is a device usually made of glass which is used as a solid matrix for (biological) material deposited on its surface and which is compatible for use with a microscope instrument" [] is_a: OBI:0000968 ! device relationship: RO:0000085 OBI:0000399 ! has function solid support function -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "microscope slide" xsd:string property_value: IAO:0000112 "PMID: 9668975.Microscope slide for enhanced analysis of DNA damage using the comet assay." xsd:string property_value: IAO:0000114 IAO:0000123 @@ -3096,7 +3110,7 @@ name: study design def: "A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution." [] is_a: IAO:0000104 ! plan specification relationship: BFO:0000051 OBI:0000272 ! has part protocol -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "study design" xsd:string property_value: IAO:0000112 "a matched pairs study design describes criteria by which subjects are identified as pairs which then undergo the same protocols, and the data generated is analyzed by comparing the differences between the paired subjects, which constitute the results of the executed study design." xsd:string property_value: IAO:0000114 IAO:0000122 @@ -3305,6 +3319,7 @@ is_a: IAO:0000140 ! setting datum property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-1595-3213 property_value: IAO:0000116 "This class should better be defined in a more general device ontology or a domain ontology with the scope of optical devices." xsd:string property_value: IAO:0000118 "integration period setting" xsd:string +property_value: IAO:0000118 "integration time" xsd:string property_value: seeAlso https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/40 [Term] @@ -3379,6 +3394,8 @@ def: "A setting datum that specifies the number of grooves in a diffraction grat is_a: IAO:0000140 ! setting datum property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-1595-3213 property_value: IAO:0000116 "This class should better be defined in a more general device ontology or a domain ontology with the scope of optical devices." xsd:string +property_value: IAO:0000118 "grating" xsd:string +property_value: IAO:0000118 "grating setting" xsd:string property_value: seeAlso https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/45 [Term] @@ -3419,6 +3436,8 @@ property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/000 property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-1595-3213 property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-2239-3955 property_value: IAO:0000112 "example:RamanSpectrometerX rdf:type obo:CHMO_0001235 (Raman spectrometer) ;\n obo:OBI_0000293 (has_specified_input) example:objective_magnification_factor_setting_for_RamanSpectrometerX .\nexample:objective_magnification_factor_setting_for_RamanSpectrometerX rdf:type obo:VIBSO_0000014 ;\n obo:OBI_0002815 (has representation) '100 x' ." xsd:string +property_value: IAO:0000118 "magnification" xsd:string +property_value: IAO:0000118 "magnification setting" xsd:string property_value: seeAlso https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/24%20 [Term] @@ -3601,7 +3620,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "is part of" xsd:string property_value: IAO:0000112 "my brain is part of my body (continuant parthood, two material entities)" xsd:string property_value: IAO:0000112 "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" xsd:string @@ -3621,6 +3640,7 @@ property_value: RO:0040042 BFO:0000031 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:PartOf property_value: seeAlso "http://www.obofoundry.org/ro/#OBO_REL:part_of" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Part_of" xsd:anyURI is_transitive: true is_a: RO:0002131 ! overlaps inverse_of: BFO:0000051 ! has part @@ -3632,7 +3652,7 @@ def: "a core relation that holds between a whole and its part" [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "has part" xsd:string property_value: IAO:0000112 "my body has part my brain (continuant parthood, two material entities)" xsd:string property_value: IAO:0000112 "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" xsd:string @@ -3649,7 +3669,7 @@ is_a: RO:0002131 ! overlaps id: BFO:0000054 name: realized in comment: Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "realized in" xsd:string property_value: IAO:0000112 "this disease is realized in this disease course" xsd:string property_value: IAO:0000112 "this fragility is realized in this shattering" xsd:string @@ -3666,7 +3686,7 @@ inverse_of: BFO:0000055 ! realizes id: BFO:0000055 name: realizes comment: Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "realizes" xsd:string property_value: IAO:0000112 "this disease course realizes this disease" xsd:string property_value: IAO:0000112 "this investigation realizes this investigator role" xsd:string @@ -3681,7 +3701,7 @@ id: BFO:0000062 name: preceded by def: "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco -property_value: http://purl.org/dc/elements/1.1/source "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" xsd:string +property_value: http://purl.org/dc/terms/source "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" xsd:string property_value: IAO:0000111 "preceded by" xsd:string property_value: IAO:0000116 "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." xsd:string property_value: IAO:0000118 "is preceded by" xsd:string @@ -3714,7 +3734,7 @@ is_a: BFO:0000051 ! has part id: IAO:0000136 name: is about def: "A (currently) primitive relation that relates an information artifact to an entity." [] -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000112 "This document is about information artifacts and their representations" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of \"mentions\" relation. Weaken the is_about relationship to be primitive. \n\nWe will try to build it back up by elaborating the various subproperties that are more precisely defined.\n\nSome currently missing phenomena that should be considered \"about\" are predications - \"The only person who knows the answer is sitting beside me\" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic." xsd:string @@ -3747,7 +3767,7 @@ is_a: IAO:0000136 ! is about id: OBI:0000293 name: has_specified_input def: "The inverse property of is_specified_input_of" [] -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "has_specified_input" xsd:string property_value: IAO:0000111 "has_specified_input" xsd:string property_value: IAO:0000112 "see is_input_of example_of_usage" xsd:string @@ -3764,7 +3784,7 @@ is_a: RO:0000057 ! has participant id: OBI:0000295 name: is_specified_input_of def: "A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of." [] -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "is_specified_input_of" xsd:string property_value: IAO:0000112 "some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay" xsd:string property_value: IAO:0000114 IAO:0000122 @@ -3776,7 +3796,7 @@ is_a: RO:0000056 ! participates in id: OBI:0000299 name: has_specified_output def: "The inverse property of is_specified_output_of" [] -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "has_specified_output" xsd:string property_value: IAO:0000111 "has_specified_output" xsd:string property_value: IAO:0000114 IAO:0000122 @@ -3791,7 +3811,7 @@ is_a: RO:0000057 ! has participant id: OBI:0000312 name: is_specified_output_of def: "A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of." [] -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "is_specified_output_of" xsd:string property_value: IAO:0000111 "is_specified_output_of" xsd:string property_value: IAO:0000114 IAO:0000122 @@ -3804,7 +3824,7 @@ is_a: RO:0000056 ! participates in id: OBI:0000417 name: achieves_planned_objective def: "This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process." [] -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "achieves_planned_objective" xsd:string property_value: IAO:0000112 "A cell sorting process achieves the objective specification 'material separation objective'" xsd:string property_value: IAO:0000114 IAO:0000120 @@ -3816,7 +3836,7 @@ property_value: IAO:0000232 "modified according to email thread from 1/23/09 in id: OBI:0000833 name: objective_achieved_by def: "This relation obtains between an objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process." [] -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "objective_achieved_by" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "OBI" xsd:string @@ -3827,7 +3847,7 @@ id: OBI:0001950 name: has performer def: "A relation between a planned process and a continuant where the continuant can be a person, organization or device (such as a robot controlled by software workflow management system) that performs the planned process." [] comment: The 'has performer' relation covers the need to report on who performed a planned processed. It has to cover processes done by People or Devices (such as a robot controlled by software WF management system). -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "has performer" xsd:string property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "OBI" xsd:string @@ -3839,7 +3859,7 @@ id: RO:0000052 name: characteristic of def: "a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence." [] comment: Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "inheres in" xsd:string property_value: IAO:0000112 "this fragility is a characteristic of this vase" xsd:string property_value: IAO:0000112 "this red color is a characteristic of this apple" xsd:string @@ -3853,7 +3873,7 @@ inverse_of: RO:0000053 ! has characteristic id: RO:0000053 name: has characteristic def: "Inverse of characteristic_of" [] -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000111 "bearer of" xsd:string property_value: IAO:0000112 "this apple is bearer of this red color" xsd:string property_value: IAO:0000112 "this vase is bearer of this fragility" xsd:string @@ -3881,7 +3901,7 @@ inverse_of: RO:0000057 ! has participant id: RO:0000057 name: has participant def: "a relation between a process and a continuant, in which the continuant is somehow involved in the process" [] -property_value: http://purl.org/dc/elements/1.1/source "http://www.obofoundry.org/ro/#OBO_REL:has_participant" xsd:string +property_value: http://purl.org/dc/terms/source "http://www.obofoundry.org/ro/#OBO_REL:has_participant" xsd:string property_value: IAO:0000111 "has participant" xsd:string property_value: IAO:0000112 "this blood coagulation has participant this blood clot" xsd:string property_value: IAO:0000112 "this investigation has participant this investigator" xsd:string @@ -3906,7 +3926,7 @@ inverse_of: RO:0000059 ! concretizes id: RO:0000059 name: concretizes def: "A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant." [] -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000112 "A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant)." xsd:string property_value: IAO:0000112 "An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process)." xsd:string domain: BFO:0000020 ! specifically dependent continuant @@ -3917,7 +3937,7 @@ id: RO:0000079 name: function of def: "a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence" [] comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000112 "this catalysis function is a function of this enzyme" xsd:string property_value: IAO:0000116 "A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists." xsd:string property_value: IAO:0000118 "function_of" xsd:string @@ -3954,7 +3974,7 @@ inverse_of: RO:0000087 ! has role id: RO:0000085 name: has function def: "a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence" [] -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000112 "this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)" xsd:string property_value: IAO:0000116 "A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists." xsd:string property_value: IAO:0000118 "has_function" xsd:string @@ -3976,7 +3996,7 @@ is_a: RO:0000053 ! has characteristic id: RO:0000087 name: has role def: "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence" [] -property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-03-10/obi.owl +property_value: http://purl.org/dc/elements/1.1/source http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl property_value: IAO:0000112 "this person has role this investigator role (more colloquially: this person has this role of investigator)" xsd:string property_value: IAO:0000116 "A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists." xsd:string property_value: IAO:0000118 "has_role" xsd:string @@ -4007,7 +4027,7 @@ name: has regulatory component activity def: "A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B." [] is_a: RO:0002017 ! has component activity is_a: RO:0002334 ! regulated by -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:30:46Z [Typedef] @@ -4017,7 +4037,7 @@ def: "A relationship that holds between a GO molecular function and a component comment: By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. is_a: RO:0002013 ! has regulatory component activity is_a: RO:0002335 ! negatively regulated by -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:31:01Z [Typedef] @@ -4027,7 +4047,7 @@ def: "A relationship that holds between a GO molecular function and a component comment: By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. is_a: RO:0002013 ! has regulatory component activity is_a: RO:0002336 ! positively regulated by -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:31:17Z [Typedef] @@ -4035,7 +4055,7 @@ id: RO:0002017 name: has component activity comment: A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. is_a: RO:0002018 ! has component process -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:44:33Z [Typedef] @@ -4045,44 +4065,44 @@ def: "w 'has process component' p if p and w are processes, w 'has part' p and domain: BFO:0000015 ! process range: BFO:0000015 ! process is_a: RO:0002180 ! has component -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:49:21Z [Typedef] id: RO:0002022 name: directly regulated by -comment: Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. {xref="GOC:dos"} +comment: Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. {xref="https://orcid.org/0000-0002-7073-9172"} is_a: RO:0002334 ! regulated by inverse_of: RO:0002578 ! directly regulates -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-09-17T13:52:24Z [Typedef] id: RO:0002023 name: directly negatively regulated by -def: "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1." [GOC:dos] +def: "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1." [https://orcid.org/0000-0002-7073-9172] is_a: RO:0002022 ! directly regulated by inverse_of: RO:0002630 ! directly negatively regulates -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-09-17T13:52:38Z [Typedef] id: RO:0002024 name: directly positively regulated by -def: "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1." [GOC:dos] +def: "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1." [https://orcid.org/0000-0002-7073-9172] is_a: RO:0002022 ! directly regulated by inverse_of: RO:0002629 ! directly positively regulates -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-09-17T13:52:47Z [Typedef] id: RO:0002025 name: has effector activity -def: "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity." [GOC:dos] +def: "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity." [https://orcid.org/0000-0002-7073-9172] comment: This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. is_functional: true is_a: RO:0002017 ! has component activity -created_by: dos +created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-09-22T14:14:36Z [Typedef] @@ -4125,7 +4145,7 @@ subset: ro-eco property_value: IAO:0000114 IAO:0000125 property_value: RO:0001900 RO:0001901 holds_over_chain: BFO:0000050 BFO:0000050 -holds_over_chain: BFO:0000051 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} +holds_over_chain: BFO:0000051 BFO:0000050 {RO:0002582="true"} holds_over_chain: BFO:0000051 RO:0002131 is_symmetric: true is_a: RO:0002323 ! mereotopologically related to @@ -4222,7 +4242,7 @@ def: "c stands in this relationship to p if and only if there exists some p' suc property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has function in" xsd:string property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/reflexivity/ -holds_over_chain: RO:0002215 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} +holds_over_chain: RO:0002215 BFO:0000050 {RO:0002582="true"} is_a: RO:0002328 ! functionally related to is_a: RO:0002500 ! causal agent in process @@ -4250,6 +4270,7 @@ subset: ro-eco property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "consumes" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Has_input" xsd:anyURI domain: BFO:0000015 ! process is_a: RO:0000057 ! has participant inverse_of: RO:0002352 ! input of @@ -4271,7 +4292,7 @@ def: "c acts upstream of or within p if c is enables f, and f is causally upstre subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term synonym: "affects" RELATED [] property_value: IAO:0000112 "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway." xsd:string -property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within +property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within" xsd:anyURI holds_over_chain: RO:0002327 RO:0002418 is_a: RO:0002500 ! causal agent in process @@ -4284,6 +4305,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: RO:0004049 RO:0002411 +property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of,_positive_effect is_a: RO:0002411 ! causally upstream of is_a: RO:0004047 ! causally upstream of or within, positive effect @@ -4295,6 +4317,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: RO:0004050 RO:0002411 +property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of,_negative_effect is_a: RO:0002411 ! causally upstream of is_a: RO:0004046 ! causally upstream of or within, negative effect @@ -4308,7 +4331,7 @@ property_value: IAO:0000118 "inheres in part of" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 property_value: RO:0001900 RO:0001901 property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/reflexivity/ -holds_over_chain: RO:0000052 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} +holds_over_chain: RO:0000052 BFO:0000050 {RO:0002582="true"} is_a: RO:0002502 ! depends on transitive_over: BFO:0000050 ! part of @@ -4333,6 +4356,7 @@ property_value: IAO:0000118 "has" xsd:string property_value: IAO:0000118 "is catalyzing" xsd:string property_value: IAO:0000118 "is executing" xsd:string property_value: IAO:0000232 "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized." xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Enables" xsd:anyURI is_a: RO:0002215 ! capable of inverse_of: RO:0002333 ! enabled by transitive_over: BFO:0000051 ! has part @@ -4351,7 +4375,7 @@ name: part of structure that is capable of def: "this relation holds between c and p when c is part of some c', and c' is capable of p." [] property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "false" xsd:boolean -holds_over_chain: BFO:0000050 RO:0002215 {http://purl.obolibrary.org/obo/RO_0002581="true"} +holds_over_chain: BFO:0000050 RO:0002215 {RO:0002581="true"} is_a: RO:0002328 ! functionally related to [Typedef] @@ -4361,7 +4385,7 @@ def: "c involved_in p if and only if c enables some process p', and p' is part o property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "actively involved in" xsd:string property_value: IAO:0000118 "enables part of" xsd:string -property_value: seeAlso Involved:in +property_value: seeAlso "https://wiki.geneontology.org/Involved_in" xsd:anyURI holds_over_chain: RO:0002327 BFO:0000050 is_a: RO:0000056 ! participates in is_a: RO:0002431 ! involved in or involved in regulation of @@ -4373,6 +4397,7 @@ name: enabled by def: "inverse of enables" [] subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: seeAlso "https://wiki.geneontology.org/Enabled_by" xsd:anyURI is_a: RO:0000057 ! has participant is_a: RO:0002328 ! functionally related to @@ -4440,6 +4465,7 @@ def: "p indirectly positively regulates q iff p is indirectly causally upstream property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "indirectly activates" xsd:string property_value: RO:0002579 RO:0002213 +property_value: seeAlso "https://wiki.geneontology.org/Indirectly_positively_regulates" xsd:anyURI holds_over_chain: RO:0002409 RO:0002409 holds_over_chain: RO:0002629 RO:0002407 holds_over_chain: RO:0002629 RO:0002629 @@ -4455,6 +4481,7 @@ def: "p indirectly negatively regulates q iff p is indirectly causally upstream property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "indirectly inhibits" xsd:string property_value: RO:0002579 RO:0002212 +property_value: seeAlso "https://wiki.geneontology.org/Indirectly_negatively_regulates" xsd:anyURI holds_over_chain: RO:0002630 RO:0002409 holds_over_chain: RO:0002630 RO:0002630 is_transitive: true @@ -4786,6 +4813,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly positively regulates (process to process)" xsd:string property_value: RO:0004049 RO:0002578 +property_value: seeAlso "https://wiki.geneontology.org/Directly_positively_regulates" xsd:anyURI is_a: RO:0002213 ! positively regulates is_a: RO:0002578 ! directly regulates @@ -4799,6 +4827,7 @@ subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly negatively regulates (process to process)" xsd:string property_value: RO:0004050 RO:0002578 +property_value: seeAlso "https://wiki.geneontology.org/Directly_negatively_regulates" xsd:anyURI is_a: RO:0002212 ! negatively regulates is_a: RO:0002578 ! directly regulates @@ -4827,7 +4856,7 @@ id: RO:0004032 name: acts upstream of or within, positive effect subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: RO:0004049 RO:0002264 -property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within,_positive_effect +property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect" xsd:anyURI holds_over_chain: RO:0002327 RO:0004047 is_a: RO:0002264 ! acts upstream of or within created_by: https://orcid.org/0000-0002-6601-2165 @@ -4838,6 +4867,7 @@ id: RO:0004033 name: acts upstream of or within, negative effect subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: RO:0004050 RO:0002264 +property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within,_negative_effect" xsd:anyURI holds_over_chain: RO:0002327 RO:0004046 is_a: RO:0002264 ! acts upstream of or within created_by: https://orcid.org/0000-0002-6601-2165 @@ -4849,7 +4879,7 @@ name: acts upstream of, positive effect def: "c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive" [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: RO:0004049 RO:0002263 -property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_positive_effect +property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of,_positive_effect" xsd:anyURI holds_over_chain: RO:0002327 RO:0002304 is_a: RO:0002263 ! acts upstream of is_a: RO:0004032 ! acts upstream of or within, positive effect @@ -4862,7 +4892,7 @@ name: acts upstream of, negative effect def: "c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative" [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: RO:0004050 RO:0002263 -property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_negative_effect +property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of,_negative_effect" xsd:anyURI holds_over_chain: RO:0002327 RO:0002305 is_a: RO:0002263 ! acts upstream of is_a: RO:0004033 ! acts upstream of or within, negative effect @@ -4873,6 +4903,7 @@ creation_date: 2018-01-26T23:53:22Z id: RO:0004046 name: causally upstream of or within, negative effect property_value: RO:0004050 RO:0002418 +property_value: seeAlso "https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect" xsd:anyURI is_a: RO:0002418 ! causally upstream of or within created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-03-13T23:55:05Z @@ -4881,6 +4912,7 @@ creation_date: 2018-03-13T23:55:05Z id: RO:0004047 name: causally upstream of or within, positive effect property_value: RO:0004049 RO:0002418 +property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of_or_within,_positive_effect is_a: RO:0002418 ! causally upstream of or within created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-03-13T23:55:19Z @@ -4889,7 +4921,7 @@ creation_date: 2018-03-13T23:55:19Z id: RO:0009501 name: realized in response to def: "r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r." [] -synonym: "triggered by process" EXACT [RO:cjm] +synonym: "triggered by process" EXACT [https://orcid.org/0000-0002-6601-2165] property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6996-0040 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6601-2165 property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7073-9172 @@ -4945,7 +4977,7 @@ id: RO:0012011 name: indirectly causally upstream of def: "p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q." [] is_a: RO:0002411 ! causally upstream of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2022-09-26T06:07:17Z [Typedef] @@ -4954,7 +4986,7 @@ name: indirectly regulates def: "p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q." [] is_a: RO:0002211 ! regulates is_a: RO:0012011 ! indirectly causally upstream of -created_by: pg +created_by: https://orcid.org/0000-0003-1813-6857 creation_date: 2022-09-26T06:08:01Z [Typedef] diff --git a/vibso.owl b/vibso.owl index 693682b..dbc0ffd 100644 --- a/vibso.owl +++ b/vibso.owl @@ -27,7 +27,7 @@ xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#" xmlns:wikipedia="https://en.wikipedia.org/wiki/"> - + @@ -36,7 +36,7 @@ _WIP - NOT READY FOR PRODUCTION_ The Vibration Spectroscopy Ontology (VIBSO) is used to represent information regarding the excution and analysis of vibrational spectroscopy assays. Vibrational Spectroscopy Ontology - 2023-06-21 + 2023-11-27 @@ -104,6 +104,7 @@ PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + example of usage example of usage @@ -158,6 +159,26 @@ We don't have definitions of 'meaning' or 'expression' Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. +We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. + 2012-04-05: +Barry Smith + +The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. + +Can you fix to something like: + +A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. + +Alan Ruttenberg + +Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. + +On the specifics of the proposed definition: + +We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. + +Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. + We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> @@ -632,7 +653,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] 2023-03-03 abbreviation - + @@ -645,7 +666,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] 2023-03-03 ambiguous synonym - + @@ -658,7 +679,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] 2023-03-03 dubious synonym - + @@ -672,7 +693,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] 2023-03-03 layperson synonym - + @@ -686,7 +707,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] 2023-03-03 plural form - + @@ -700,7 +721,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] 2023-03-03 UK spelling synonym - + @@ -713,7 +734,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] 2023-03-03 misspelling - + @@ -726,7 +747,78 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] 2023-03-03 misnomer - + + + + + + + + + MAPT, the gene that encodes the Tau protein, has a previous name DDPAC. Note: in this case, the name type is more specifically the gene symbol. + A synonym type for names that have been used as primary labels in the past. + + + 2023-07-25 + previous name + + + + + + + + + The legal name for Harvard University (https://ror.org/03vek6s52) is President and Fellows of Harvard College + A synonym type for the legal entity name + + + 2023-07-27 + legal name + + + + + + + + + CHEBI:46195 has been assigned the english International Nonproproprietary Name (INN) "paracetamol". In some cases such as this one, the INN might be the same as the ontology's primary label + The International Nonproprietary Name (INN) is a standardize name for a pharmaceutical drug or active ingredient issued by the World Health Organization (WHO) meant to address the issues with country- or language-specific brand names. These are issued in several languages, including English, Latin, French, Russian, Spanish, Arabic, and Chinese. + + + 2023-09-30 + INN + International Nonproprietary Name + + + + + + + + + nasopharynx (UBERON:0001728) has the latin name "pars nasalis pharyngis + A synonym type for describing Latin term synonyms. + + + 2023-10-12 + latin term + + + + + + + + + NASA is an word acronym for the US National Aeronautics and Space Administration because the acronym is pronounced. FBI is an initialism (also known as alphabetism) for the US Federal Bureau of Investigation since the letters are pronounced one at a time. JPEG is an acronym for Joint Photographic Experts Group but does not count as a word acronym nor an initialism since it is mixed how it is pronounced. + A synonym type for describing abbreviations that are a part of the full name's words, such as initialisms or alphabetisms. + + + 2023-11-01 + acronym + @@ -1055,9 +1147,9 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - + - + @@ -1286,7 +1378,7 @@ A continuant cannot be part of an occurrent: use 'participates in'. An - + @@ -1295,6 +1387,7 @@ A continuant cannot be part of an occurrent: use 'participates in'. An http://www.obofoundry.org/ro/#OBO_REL:part_of + https://wiki.geneontology.org/Part_of @@ -1316,7 +1409,7 @@ A continuant cannot be part of an occurrent: use 'participates in'. An A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. has_part - + @@ -1338,7 +1431,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. is realized by realized_in [copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) - + Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process realized in @@ -1356,7 +1449,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. this investigation realizes this investigator role this shattering realizes this fragility to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) - + Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process realizes @@ -1381,7 +1474,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. is preceded by preceded_by - http://www.obofoundry.org/ro/#OBO_REL:preceded_by + http://www.obofoundry.org/ro/#OBO_REL:preceded_by preceded by @@ -1429,7 +1522,7 @@ We will try to build it back up by elaborating the various subproperties that ar Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic. person:Alan Ruttenberg Smith, Ceusters, Ruttenberg, 2000 years of philosophy - + is about @@ -1521,7 +1614,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which PERSON: Larry Hunter PERSON: Melanie Coutot - + has_specified_input @@ -1537,7 +1630,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of. Alan Ruttenberg PERSON:Bjoern Peters - + is_specified_input_of @@ -1561,7 +1654,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which PERSON: Larry Hunter PERSON: Melanie Courtot - + has_specified_output @@ -1578,7 +1671,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which Alan Ruttenberg PERSON:Bjoern Peters - + is_specified_output_of @@ -1594,7 +1687,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which BP, AR, PPPB branch PPPB branch derived modified according to email thread from 1/23/09 in accordince with DT and PPPB branch - + achieves_planned_objective @@ -1608,7 +1701,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which This relation obtains between an objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process. OBI OBI - + objective_achieved_by @@ -1623,7 +1716,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which A relation between a planned process and a continuant where the continuant can be a person, organization or device (such as a robot controlled by software workflow management system) that performs the planned process. OBI OBI - + The 'has performer' relation covers the need to report on who performed a planned processed. It has to cover processes done by People or Devices (such as a robot controlled by software WF management system). has performer @@ -1642,7 +1735,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence. inheres_in - + Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. characteristic of @@ -1662,7 +1755,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which bearer_of is bearer of - + has characteristic @@ -1706,7 +1799,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which a relation between a process and a continuant, in which the continuant is somehow involved in the process Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. has_participant - http://www.obofoundry.org/ro/#OBO_REL:has_participant + http://www.obofoundry.org/ro/#OBO_REL:has_participant has participant @@ -1734,7 +1827,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant. - + concretizes @@ -1751,7 +1844,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists. function_of is function of - + This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. function of @@ -1800,7 +1893,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists. has_function - + has function @@ -1830,7 +1923,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. has_role - + has role @@ -1867,7 +1960,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. - dos + 2017-05-24T09:30:46Z has regulatory component activity @@ -1880,7 +1973,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. - dos + 2017-05-24T09:31:01Z By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. has negative regulatory component activity @@ -1894,7 +1987,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. - dos + 2017-05-24T09:31:17Z By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. has positive regulatory component activity @@ -1906,7 +1999,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which - dos + 2017-05-24T09:44:33Z A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. has component activity @@ -1921,7 +2014,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. - dos + 2017-05-24T09:49:21Z has component process @@ -1933,7 +2026,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which - dos + 2017-09-17T13:52:24Z Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. directly regulated by @@ -1942,7 +2035,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. - GOC:dos + @@ -1953,7 +2046,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. - dos + 2017-09-17T13:52:38Z directly negatively regulated by @@ -1961,7 +2054,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. - GOC:dos + @@ -1972,7 +2065,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. - dos + 2017-09-17T13:52:47Z directly positively regulated by @@ -1980,7 +2073,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. - GOC:dos + @@ -1991,7 +2084,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. - dos + 2017-09-22T14:14:36Z This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. has effector activity @@ -2000,7 +2093,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. - GOC:dos + @@ -2260,6 +2353,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which has input + https://wiki.geneontology.org/Has_input @@ -2294,7 +2388,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which affects acts upstream of or within - + https://wiki.geneontology.org/Acts_upstream_of_or_within @@ -2311,6 +2405,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y causally upstream of, positive effect + @@ -2326,6 +2421,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which causally upstream of, negative effect + @@ -2399,6 +2495,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized. enables + https://wiki.geneontology.org/Enables @@ -2457,7 +2554,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which actively involved in enables part of involved in - + https://wiki.geneontology.org/Involved_in @@ -2471,6 +2568,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which enabled by + https://wiki.geneontology.org/Enabled_by @@ -2583,6 +2681,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which indirectly activates indirectly positively regulates + https://wiki.geneontology.org/Indirectly_positively_regulates @@ -2610,6 +2709,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which indirectly inhibits indirectly negatively regulates + https://wiki.geneontology.org/Indirectly_negatively_regulates @@ -3148,6 +3248,7 @@ For example, A and B may be gene products and binding of B by A positively regul directly positively regulates + https://wiki.geneontology.org/Directly_positively_regulates @@ -3165,6 +3266,7 @@ For example, A and B may be gene products and binding of B by A positively regul directly negatively regulates + https://wiki.geneontology.org/Directly_negatively_regulates @@ -3216,7 +3318,7 @@ For example, A and B may be gene products and binding of B by A positively regul 2018-01-26T23:49:30Z acts upstream of or within, positive effect - + https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect @@ -3234,6 +3336,7 @@ For example, A and B may be gene products and binding of B by A positively regul 2018-01-26T23:49:51Z acts upstream of or within, negative effect + https://wiki.geneontology.org/Acts_upstream_of_or_within,_negative_effect @@ -3253,7 +3356,7 @@ For example, A and B may be gene products and binding of B by A positively regul 2018-01-26T23:53:14Z acts upstream of, positive effect - + https://wiki.geneontology.org/Acts_upstream_of,_positive_effect @@ -3273,7 +3376,7 @@ For example, A and B may be gene products and binding of B by A positively regul 2018-01-26T23:53:22Z acts upstream of, negative effect - + https://wiki.geneontology.org/Acts_upstream_of,_negative_effect @@ -3286,6 +3389,7 @@ For example, A and B may be gene products and binding of B by A positively regul 2018-03-13T23:55:05Z causally upstream of or within, negative effect + https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect @@ -3298,6 +3402,7 @@ For example, A and B may be gene products and binding of B by A positively regul 2018-03-13T23:55:19Z causally upstream of or within, positive effect + @@ -3328,7 +3433,7 @@ For example, A and B may be gene products and binding of B by A positively regul triggered by process - RO:cjm + @@ -3393,7 +3498,7 @@ For example, A and B may be gene products and binding of B by A positively regul p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q. - pg + 2022-09-26T06:07:17Z indirectly causally upstream of @@ -3406,7 +3511,7 @@ For example, A and B may be gene products and binding of B by A positively regul p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q. - pg + 2022-09-26T06:08:01Z indirectly regulates @@ -3426,7 +3531,7 @@ For example, A and B may be gene products and binding of B by A positively regul A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input. See github ticket https://github.com/oborel/obo-relations/issues/497 - 2021-11-08T12:00:00Z + 2021-11-08T12:00:00Z utilizes device utilizes material @@ -3738,13 +3843,13 @@ For example, A and B may be gene products and binding of B by A positively regul an organism the bottom right portion of a human torso the interior of your mouth - A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] + A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. independent continuant @@ -4031,10 +4136,10 @@ For example, A and B may be gene products and binding of B by A positively regul the flight of a bird the life of an organism your process of aging. - An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war) (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] + An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. process @@ -4255,10 +4360,10 @@ For example, A and B may be gene products and binding of B by A positively regul the role of being a doctor the shape of this hole. the smell of this portion of mozzarella - A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] + A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. specifically dependent continuant @@ -4560,9 +4665,9 @@ For example, A and B may be gene products and binding of B by A positively regul The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity. the pdf file on your laptop, the pdf file that is a copy thereof on my laptop the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule. - A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] + A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. generically dependent continuant @@ -4593,7 +4698,7 @@ For example, A and B may be gene products and binding of B by A positively regul BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc. A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] - + function @@ -7577,7 +7682,7 @@ JAR: A data item is an approximately justified approximately true approximate be PERSON: Chris Stoeckert PERSON: Jonathan Rees data - + data item @@ -7692,7 +7797,7 @@ this case we explicitly refer to the singular form PlanAndPlannedProcess Branch OBI_0000270 adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg) - + algorithm @@ -7741,7 +7846,7 @@ this case we explicitly refer to the singular form person:Chris Stoeckert OBI_0000030 group:OBI - + image @@ -7812,7 +7917,7 @@ Request that IAO either clarify these or change definitions not to use themperson:Chris Stoeckert OBI_0000305 group:OBI - + measurement datum @@ -8437,7 +8542,7 @@ No imports - + person @@ -8482,7 +8587,7 @@ objectives is a planned process. 6/11/9: Edited at workshop. Used to include: is initiated by an agent This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call) - + planned process @@ -8514,7 +8619,7 @@ objectives is a planned process. Is a material entity that is created or changed during material processing. PERSON: Alan Ruttenberg - + processed material @@ -8551,7 +8656,7 @@ objectives is a planned process. editor = PRS study - + investigation @@ -8582,7 +8687,7 @@ editor = PRS GROUP: Role Branch OBI Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. - + evaluant role @@ -8657,15 +8762,16 @@ editor = PRS assay Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house. - A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies. + A planned process that has the objective to produce information about a material entity (the evaluant) by examining it. 12/3/12: BP: the reference to the 'physical examination' is included to point out that a prediction is not an assay, as that does not require physical examiniation. + Discussion on OBI call 2023-05-01 resulted in an agreement to revise the textual definition of 'assay'. https://github.com/obi-ontology/obi/issues/1683. PlanAndPlannedProcess Branch measuring scientific observation OBI branch derived study assay any method - + assay @@ -8681,7 +8787,7 @@ editor = PRS PlanAndPlannedProcess Branch study OBI branch derived - + sample preparation for assay @@ -8701,7 +8807,7 @@ editor = PRS Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. May 28 2013. Updated definition taken from ReO based on discussions initiated in Philly 2011 workshop. Former defnition described a narrower view of reagents in chemistry that restricts bearers of the role to be chemical entities ("a role played by a molecular entity used to produce a chemical reaction to detect, measure, or produce other substances"). Updated definition allows for broader view of reagents in the domain of biomedical research to include larger materials that have parts that participate chemically in a molecular reaction or interaction. - + (copied from ReO) Reagents are distinguished from instruments or devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in or have parts that participate in some chemical interaction or reaction during their intended participation in some technique. By contrast, instruments do not participate in a chemical reaction/interaction during the technique. @@ -8752,7 +8858,7 @@ In regard to the statement that reagents are 'distinct' from the speci PERSON: Philippe Rocca Serra material transformation OBI branch derived - + material processing @@ -8793,7 +8899,7 @@ specimen can later be subject. GROUP: Role Branch OBI - + specimen role @@ -8877,7 +8983,7 @@ specimen can later be subject. OBI Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. study person role - + Philly2013: Historically, this role would have been borne only by humans or organizations. However, we now also want to enable investigations run by robot scientists such as ADAM (King et al, Science, 2009) investigation agent role @@ -8924,7 +9030,7 @@ for now. PERSON: Philippe Rocca-Serra PERSON: Susanna Sansone GROUP: OBI - + organization @@ -8941,7 +9047,7 @@ for now. PlanAndPlannedProcess Branch OBI branch derived + wikipedia (http://en.wikipedia.org/wiki/Protocol_%28natural_sciences%29) study protocol - + protocol @@ -8969,7 +9075,7 @@ for now. Bjoern Peters Bjoern Peters Plans and Planned Processes Branch - + planning @@ -8986,7 +9092,7 @@ for now. Daniel Schober Frank Gibson Melanie Courtot - + magnify function @@ -9012,7 +9118,7 @@ for now. An image acquisition function is a function to acquire an image of a material Frank Gibson - + image acquisition function @@ -9045,7 +9151,7 @@ for now. Frank Gibson image acquisition device sep:00096 - + image creation device @@ -9062,7 +9168,7 @@ for now. Daniel Schober Frank Gibson Melanie Courtot - + solid support function @@ -9078,7 +9184,7 @@ for now. an objective specification to determine a specified type of information about an evaluated entity (the material entity bearing evaluant role) PPPB branch PPPB branch - + assay objective @@ -9113,7 +9219,7 @@ for now. PERSON: Helen Parkinson PERSON: Melanie Courtot PERSON:Frank Gibson - + measure function @@ -9134,7 +9240,7 @@ for now. PERSON: Philippe Rocca-Serra artifact creation objective GROUP: OBI PlanAndPlannedProcess Branch - + material transformation objective @@ -9163,7 +9269,7 @@ for now. Manufacturer role is a role which inheres in a person or organization and which is realized by a manufacturing process. GROUP: Role Branch OBI - + manufacturer role @@ -9185,7 +9291,7 @@ for now. a quality inheres_in some device and is concretization of some (device_setting_specification and is_about a quality of the device There is some question of whether 'device setting' is really best modelled as a quality. To be revisited after assay terms have been worked through. See https://github.com/obi-ontology/obi/issues/133 PERSON: Frank Gibson - + device setting @@ -9237,7 +9343,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ specimen collection 5/31/2012: This process is not necessarily an acquisition, as specimens may be collected from materials already in posession 6/9/09: used at workshop - + specimen collection process @@ -9253,7 +9359,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ A objective specification to obtain a material entity for potential use as an input during an investigation. Bjoern Peters Bjoern Peters - + specimen collection objective @@ -9269,7 +9375,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ A material sample role is a specimen role borne by a material entity that is the output of a material sampling process. 7/13/09: Note that this is a relational role: between the sample taken and the 'sampled' material of which the sample is thought to be representative off. - + material sample role @@ -9304,7 +9410,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ sample population sample - + material sample @@ -9337,7 +9443,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ A device in which a measure function inheres. GROUP:OBI Philly workshop OBI - + measurement device @@ -9371,8 +9477,8 @@ http://sourceforge.net/p/obi/obi-terms/716/ manufacturer - A person or organization that has a manufacturer role - + A person or organization that has a manufacturer role. + manufacturer @@ -9407,7 +9513,7 @@ In the examples above, a reagent is an operational component of a device, but th PERSON: Helen Parkinson instrument OBI development call 2012-12-17. - + device @@ -9435,7 +9541,7 @@ In the examples above, a reagent is an operational component of a device, but th A planned process that captures an image of an object. PERSON: Jie Zheng image acquisition - + image creation @@ -9452,7 +9558,7 @@ In the examples above, a reagent is an operational component of a device, but th specimen ID NIAID GSCID-BRC metadata working group Specimen ID - + NIAID GSCID-BRC specimen identifier @@ -9470,7 +9576,7 @@ In the examples above, a reagent is an operational component of a device, but th NIAID GSCID-BRC metadata working group study title project title - + NIAID GSCID-BRC investigation title @@ -9532,7 +9638,7 @@ In the examples above, a reagent is an operational component of a device, but th PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Comments - + NIAID GSCID-BRC comment on investigation @@ -9556,7 +9662,7 @@ OBI doesn't take position as to when an organism starts or ends being an o This issue is outside the scope of OBI. GROUP: OBI Biomaterial Branch WEB: http://en.wikipedia.org/wiki/Organism - + organism @@ -9592,7 +9698,7 @@ This issue is outside the scope of OBI. PERSON: Philippe Rocca-Serra GROUP: OBI Biomaterial Branch - + specimen @@ -9657,7 +9763,7 @@ This issue is outside the scope of OBI. data processing Branch editors - + data transformation @@ -9674,7 +9780,7 @@ This issue is outside the scope of OBI. Modified definition in 2013 Philly OBI workshop James Malone PERSON: James Malone - + data transformation objective @@ -9690,7 +9796,7 @@ This issue is outside the scope of OBI. solvent role is a role which inheres in a molecular entity capable of ensuring the dissolution of another chemical entity and realized by the process of solvation Philippe Rocca-Serra adpated from wikipedia (http://en.wikipedia.org/wiki/Solvatation) - + solvent role @@ -9712,7 +9818,7 @@ This issue is outside the scope of OBI. A microscope is an instrument which magnifies the view on objects (too small to be viewed by the naked eye) under increased resolution. A microscope can be an optical instrument but also and electronic instrument. There are various kind of optical microscopes, e.g confocal microscope, epifluoresence microscope) PERSON: Phillippe Rocca-Serra wikipedia - + microscope @@ -9734,7 +9840,7 @@ This issue is outside the scope of OBI. A microscope slide is a device usually made of glass which is used as a solid matrix for (biological) material deposited on its surface and which is compatible for use with a microscope instrument PERSON: Phillippe Rocca-Serra OBI biomaterial branch - + microscope slide @@ -9759,7 +9865,7 @@ This issue is outside the scope of OBI. experimental design rediscussed at length (MC/JF/BP). 12/9/08). The definition was clarified to differentiate it from protocol. - + study design @@ -10144,6 +10250,7 @@ https://www.wolframalpha.com/share/clip?f=d41d8cd98f00b204e9800998ecf8427efdcsig A setting datum that specifies the length of time that a photo detector is allowed to collect photons before passing the accumulated charge to the A/D converter for processing. The minimum integration time is the shortest integration time the device supports and is dependent on how fast the detector can read out all of the pixel information. Integration time should not be confused with data transfer speed. This class should better be defined in a more general device ontology or a domain ontology with the scope of optical devices. integration period setting + integration time integration time setting @@ -10263,6 +10370,8 @@ https://www.wolframalpha.com/share/clip?f=d41d8cd98f00b204e9800998ecf8427efdcsig A setting datum that specifies the number of grooves in a diffraction grating device. This class should better be defined in a more general device ontology or a domain ontology with the scope of optical devices. + grating + grating setting groove density setting @@ -10326,6 +10435,8 @@ https://www.wolframalpha.com/share/clip?f=d41d8cd98f00b204e9800998ecf8427efdcsig example:objective_magnification_factor_setting_for_RamanSpectrometerX rdf:type obo:VIBSO_0000014 ; obo:OBI_0002815 (has representation) '100 x' . A setting datum that specifies the magnification factor of the objective collecting the scattered light. + magnification + magnification setting @@ -10810,6 +10921,20 @@ Together with the focal point distance, this setting defines the region of inter + + + + + The term was added to the ontology on the assumption it was a valid domain entity, but it turns out the entity does not exist in reality. + This obsolesence reason should be used conservatively. For example: Obsoleting class that describes a breed of cow based on a record in an existing database, that was later retracted as faulty (breed does not exist). Do not use this term to obsolete a historic concept (that was once valid, but not anymore). + + https://github.com/information-artifact-ontology/ontology-metadata/issues/136 + https://orcid.org/0000-0002-4142-7153 + domain entity does not exist + + + + @@ -10973,7 +11098,7 @@ Together with the focal point distance, this setting defines the region of inter Person:Alan Ruttenberg Person:Helen Parkinson 2009/09/28 Alan Ruttenberg. Fucoidan-use-case - + is member of organization @@ -11109,7 +11234,7 @@ Together with the focal point distance, this setting defines the region of inter See tracker: https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_id=177891&atid=886178 Person: Jie Zheng - + has organization member @@ -11314,15 +11439,15 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - + + + @@ -11332,15 +11457,15 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - + + + @@ -12013,9 +12138,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -12024,9 +12149,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -12058,9 +12183,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -12069,9 +12194,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -12103,9 +12228,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -12114,9 +12239,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -12148,9 +12273,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -12159,9 +12284,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -12193,9 +12318,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -12204,9 +12329,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + - + @@ -12238,7 +12363,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -12249,7 +12374,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -12266,7 +12391,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -12276,7 +12401,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -12294,7 +12419,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -12305,7 +12430,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -12322,7 +12447,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -12332,7 +12457,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -12349,7 +12474,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -12360,7 +12485,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -12393,9 +12518,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -12404,9 +12529,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -12437,9 +12562,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -12448,9 +12573,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -12481,9 +12606,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -12492,9 +12617,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -12525,9 +12650,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -12536,9 +12661,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -12570,8 +12695,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -12581,8 +12706,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -12609,5 +12734,5 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - +