diff --git a/.github/ISSUE_TEMPLATE/add-species.md b/.github/ISSUE_TEMPLATE/add-species.md new file mode 100644 index 00000000..31504d14 --- /dev/null +++ b/.github/ISSUE_TEMPLATE/add-species.md @@ -0,0 +1,228 @@ +--- +name: Add species +about: Editor's template for adding new species +title: Draft +labels: drafting, multispecies discovery, schema +assignees: brianraymor + +--- + +## Pending Issues + +1. Waiting on sscrdv to be submitted to OLS for use in references +1. [FAANG](http://www.faang.org/) is the Functional Annotation of ANimal Genomes project. _We are working to understand the genotype to phenotype link in domesticated animals._ Per their [Ontology Improver](https://data.faang.org/ontology?sortTerm=key&sortDirection=asc), *Dv terms are not referenced. Both UBERON and CL are in use. Their [schema](https://github.com/FAANG/dcc-metadata/blob/9e7c1b5304fc57a724d197384e83243562bebbf4/json_schema/type/samples/faang_samples_specimen.metadata_rules.json#L154): + +``` +"name": "developmental stage", +"description": "Ontology for Developmental stage, UBERON is preferred to EFO.", +``` + + +## Design + +This draft design reflects additions to corresponding sections in [schema 5.2.0](https://github.com/chanzuckerberg/single-cell-curation/blob/main/schema/5.2.0/schema.md). Reviewers are expected to be familiar with the CELLxGENE schema. + +**Editorial Notes** that are inlined in the design below will not be surfaced in the schema. + +--- + +### Required Ontologies + + +| Ontology | OBO Prefix | Release | Download | +|:--|:--|:--|:--| +| [Unavailable](https://github.com/OBOFoundry/OBOFoundry.github.io/tree/master/ontology) | SscrDv | [Releases](https://github.com/obophenotype/developmental-stage-ontologies/releases) | TBD | +||||| + + +#### Editorial Notes + +This ontology is under active development. CELLxGENE pins ontology releases in each version of the schema. A specific release of the ontology above must be selected in the future. + + +--- + +### Required Gene Annotations + +| Organism | Source | Required version | Download | +|:--|:--|:--|:--| +| "NCBITaxon:9823"
for Sus scrofa domesticus | [ENSEMBL (Sus scrofa domesticus)] | Sscrofa11.1 (GCA_000003025.6) | [Sus_scrofa.Sscrofa11.1.113.gtf] | + + +[ENSEMBL (Sus scrofa domesticus)]: https://useast.ensembl.org/Sus_scrofa/Info/Index +[Sus_scrofa.Sscrofa11.1.113.gtf]: https://ftp.ensembl.org/pub/release-113/gtf/sus_scrofa/Sus_scrofa.Sscrofa11.1.113.gtf.gz + +#### Editorial Notes + + +--- + +## `obs` (Cell Metadata) + +### cell_type_ontology_term_id + +No schema changes are required. + +#### Editorial Notes + +--- + +### development_stage_ontology_term_id + + + + + + + + + + + + + + +
Keydevelopment_stage_ontology_term_id
AnnotatorCurator MUST annotate.
Value + categorical with str categories. If unavailable, this MUST be "unknown".

+ If organism_ontolology_term_id is "NCBITaxon:9823" for Sus scrofa domesticus, this MUST be the most accurate descendant of SscrDv:0000000 for life cycle stage. +
+
+ +#### Editorial Notes + +This may be outdated, but [potential recommendations](https://github.com/obophenotype/developmental-stage-ontologies/blob/master/external/bgee/report.md#sus-scrofa): + +``` +UBERON:0000104 life cycle + UBERON:0000068 embryo stage + UBERON:0000106 zygote stage + UBERON:0000107 cleavage stage + UBERON:0007232 2 cell stage + UBERON:0007233 4 cell stage + UBERON:0007236 8 cell stage + UBERON:0000108 blastula stage + UBERON:0000109 gastrula stage + UBERON:0000110 neurula stage + UBERON:0000111 organogenesis stage + SscrDv:0000081 ridge limb stage (pig) + SscrDv:0000082 bud limb stage (pig) + SscrDv:0000083 paddle limb stage (pig) + UBERON:0007220 late embryonic stage + UBERON:0000092 post-embryonic stage + UBERON:0000066 fully formed stage + UBERON:0000112 sexually immature stage + UBERON:0018685 nursing stage + UBERON:0007221 neonate stage + SscrDv:0000072 0-day-old stage (pig) + SscrDv:0000073 1-day-old stage (pig) + SscrDv:0000074 2-day-old stage (pig) + SscrDv:0000075 3-day-old stage (pig) + SscrDv:0000076 4-day-old stage (pig) + SscrDv:0000077 5-day-old stage (pig) + SscrDv:0000078 6-day-old stage (pig) + UBERON:0034920 infant stage + SscrDv:0000010 1-week-old stage (pig) + SscrDv:0000011 2-week-old stage (pig) + SscrDv:0000012 3-week-old stage (pig) + SscrDv:0000018 21-day-old stage (pig) + SscrDv:0000019 22-day-old stage (pig) + SscrDv:0000020 23-day-old stage (pig) + SscrDv:0000021 24-day-old stage (pig) + SscrDv:0000022 25-day-old stage (pig) + SscrDv:0000023 26-day-old stage (pig) + SscrDv:0000024 27-day-old stage (pig) + SscrDv:0000013 4-week-old stage (pig) + SscrDv:0000025 28-day-old stage (pig) + SscrDv:0000026 29-day-old stage (pig) + SscrDv:0000027 30-day-old stage (pig) + SscrDv:0000028 31-day-old stage (pig) + SscrDv:0000029 32-day-old stage (pig) + SscrDv:0000030 33-day-old stage (pig) + SscrDv:0000031 34-day-old stage (pig) + SscrDv:0000014 5-week-old stage (pig) + SscrDv:0000032 35-day-old stage (pig) + SscrDv:0000033 36-day-old stage (pig) + SscrDv:0000034 37-day-old stage (pig) + SscrDv:0000035 38-day-old stage (pig) + SscrDv:0000036 39-day-old stage (pig) + SscrDv:0000037 40-day-old stage (pig) + SscrDv:0000038 41-day-old stage (pig) + SscrDv:0000015 6-week-old stage (pig) + SscrDv:0000016 7-week-old stage (pig) + UBERON:0034919 juvenile stage + SscrDv:0000039 2-month-old stage (pig) + SscrDv:0000017 8-week-old stage (pig) + SscrDv:0000040 9-week-old stage (pig) + SscrDv:0000041 10-week-old stage (pig) + SscrDv:0000042 11-week-old stage (pig) + SscrDv:0000043 3-month-old stage (pig) + SscrDv:0000044 12-week-old stage (pig) + SscrDv:0000045 13-week-old stage (pig) + SscrDv:0000046 14-week-old stage (pig) + SscrDv:0000047 15-week-old stage (pig) + SscrDv:0000048 4-month-old stage (pig) + SscrDv:0000049 16-week-old stage (pig) + SscrDv:0000050 17-week-old stage (pig) + SscrDv:0000051 18-week-old stage (pig) + SscrDv:0000052 19-week-old stage (pig) + SscrDv:0000053 20-week-old stage (pig) + SscrDv:0000054 5-month-old stage (pig) + SscrDv:0000055 21-week-old stage (pig) + SscrDv:0000056 22-week-old stage (pig) + SscrDv:0000057 23-week-old stage (pig) + SscrDv:0000058 24-week-old stage (pig) + SscrDv:0000059 6-month-old stage (pig) + SscrDv:0000060 7-month-old stage (pig) + SscrDv:0000061 8-month-old stage (pig) + SscrDv:0000062 9-month-old stage (pig) + SscrDv:0000063 10-month-old stage (pig) + UBERON:0000113 post-juvenile + UBERON:0018241 prime adult stage + SscrDv:0000064 11-month-old stage (pig) + SscrDv:0000065 1-year-old stage (pig) + SscrDv:0000066 2-year-old stage (pig) + SscrDv:0000067 3-year-old stage (pig) + SscrDv:0000068 4-year-old stage (pig) + SscrDv:0000069 5-year-old stage (pig) + SscrDv:0000070 6-year-old stage (pig) + SscrDv:0000071 7-year-old stage (pig) + UBERON:0007222 late adult stage +``` + +--- + +### disease_ontology_term_id + +No schema changes are required. + +#### Editorial Notes + +--- + +### organism_ontolology_term_id + +organism_ontolology_term_id is "NCBITaxon:9823" for Sus scrofa domesticus + +--- + +### sex_ontology_term_id + +No schema changes are required. + +#### Editorial Notes + +--- + +### tissue_ontology_term_id + +No schema changes are required. + + +#### Editorial Notes + +--- + +## Reference + + +[BGEE](https://www.bgee.org/species/9823) diff --git a/.github/ISSUE_TEMPLATE/tech-issue.md b/.github/ISSUE_TEMPLATE/tech-issue.md index 4965be8c..7b75dbb8 100644 --- a/.github/ISSUE_TEMPLATE/tech-issue.md +++ b/.github/ISSUE_TEMPLATE/tech-issue.md @@ -1,9 +1,11 @@ --- name: Tech Issue -about: Engineering-specific technical work that is not product-specific. Engineering team "owns" these issues. -title: "" +about: Engineering-specific technical work that is not product-specific. Engineering + team "owns" these issues. +title: '' labels: tech -assignees: "" +assignees: '' + --- ## Motivation