From 4976b504801be77faa44fbf129d9741182111982 Mon Sep 17 00:00:00 2001 From: cmaumet Date: Fri, 24 Oct 2014 17:17:04 +0100 Subject: [PATCH 01/14] Noise -> Error --- nidm/nidm-results/terms/nidm-results.owl | 97 +++++++++++++++++------- 1 file changed, 70 insertions(+), 27 deletions(-) diff --git a/nidm/nidm-results/terms/nidm-results.owl b/nidm/nidm-results/terms/nidm-results.owl index ef8d2af02..c6ca225b8 100644 --- a/nidm/nidm-results/terms/nidm-results.owl +++ b/nidm/nidm-results/terms/nidm-results.owl @@ -160,6 +160,20 @@ nidm:hasErrorDependence rdf:type owl:ObjectProperty ; +### http://www.incf.org/ns/nidash/nidm#hasErrorDistribution + +nidm:hasErrorDistribution rdf:type owl:ObjectProperty ; + + prov:definition "FIXME" ; + + obo:IAO_0000114 obo:IAO_0000124 ; + + rdfs:range nidm:ErrorDistribution ; + + rdfs:domain nidm:ErrorModel . + + + ### http://www.incf.org/ns/nidash/nidm#hasMapHeader nidm:hasMapHeader rdf:type owl:ObjectProperty ; @@ -172,18 +186,6 @@ nidm:hasMapHeader rdf:type owl:ObjectProperty ; -### http://www.incf.org/ns/nidash/nidm#hasNoiseDistribution - -nidm:hasNoiseDistribution rdf:type owl:ObjectProperty ; - - prov:definition "FIXME" ; - - rdfs:domain nidm:ErrorModel ; - - rdfs:range nidm:NoiseDistribution . - - - ### http://www.incf.org/ns/nidash/nidm#inCoordinateSpace nidm:inCoordinateSpace rdf:type owl:ObjectProperty ; @@ -1517,7 +1519,7 @@ spm:softwareRevision rdf:type owl:DatatypeProperty ; fsl:BinomialDistribution rdf:type owl:Class ; - rdfs:subClassOf nidm:NoiseDistribution ; + rdfs:subClassOf nidm:ErrorDistribution ; owl:sameAs "http://purl.obolibrary.org/obo/STATO_0000276"^^xsd:anyURI . @@ -1566,9 +1568,11 @@ fsl:ContrastVarianceMap rdf:type owl:Class ; fsl:NonParametricSymmetricDistribution rdf:type owl:Class ; - rdfs:subClassOf nidm:NoiseDistribution ; + rdfs:subClassOf nidm:ErrorDistribution ; - prov:definition "FIXME" . + prov:definition "FIXME" ; + + obo:IAO_0000114 obo:IAO_0000124 . @@ -1669,6 +1673,41 @@ nidm:ConnectivityCriterion rdf:type owl:Class ; obo:IAO_0000114 obo:IAO_0000122 . +### http://www.incf.org/ns/nidash/nidm#ConnectivityCriterion2D + +nidm:ConnectivityCriterion2D rdf:type owl:Class ; + + owl:equivalentClass [ rdf:type owl:Class ; + owl:oneOf ( nidm:connected4In2D + nidm:connected6In2D + nidm:connected8In2D + ) + ] ; + + rdfs:subClassOf nidm:ConnectivityCriterion ; + + prov:definition """The order of neighbourhood used to determine whether two pixels + are neighbours in 2D. Possible values are: 4 (pixels share an edge), 8 (voxels share an edge or a corner).""" . + + + +### http://www.incf.org/ns/nidash/nidm#ConnectivityCriterion3D + +nidm:ConnectivityCriterion3D rdf:type owl:Class ; + + owl:equivalentClass [ rdf:type owl:Class ; + owl:oneOf ( nidm:connected6In3D + nidm:connected18In3D + nidm:connected26In3D + ) + ] ; + + rdfs:subClassOf nidm:ConnectivityCriterion ; + + prov:definition "The order of neighbourhood used to determine whether two voxels are neighbours in 3D. Possible values are: 6 (voxels share a face), 18 (voxels share a face or edge), 26 (voxels share a face, edge or corner)." . +>>>>>>> Noise -> Error + + ### http://www.incf.org/ns/nidash/nidm#ContrastEstimation @@ -1896,6 +1935,16 @@ nidm:ErrorDependence rdf:type owl:Class ; +### http://www.incf.org/ns/nidash/nidm#ErrorDistribution + +nidm:ErrorDistribution rdf:type owl:Class ; + + rdfs:subClassOf prov:Entity ; + + obo:IAO_0000114 obo:IAO_0000124 . + + + ### http://www.incf.org/ns/nidash/nidm#ErrorModel nidm:ErrorModel rdf:type owl:Class ; @@ -2015,7 +2064,7 @@ nidm:FStatistic rdf:type owl:Class ; nidm:GaussianDistribution rdf:type owl:Class ; - rdfs:subClassOf nidm:NoiseDistribution ; + rdfs:subClassOf nidm:ErrorDistribution ; owl:sameAs "http://purl.obolibrary.org/obo/STATO_0000227"^^xsd:anyURI . @@ -2217,21 +2266,15 @@ nidm:NIDMObjectModel rdf:type owl:Class ; -### http://www.incf.org/ns/nidash/nidm#NoiseDistribution - -nidm:NoiseDistribution rdf:type owl:Class ; - - rdfs:subClassOf prov:Entity . - - - ### http://www.incf.org/ns/nidash/nidm#NonParametricDistribution nidm:NonParametricDistribution rdf:type owl:Class ; - rdfs:subClassOf nidm:NoiseDistribution ; + rdfs:subClassOf nidm:ErrorDistribution ; - prov:definition "FIXME" . + prov:definition "FIXME" ; + + obo:IAO_0000114 obo:IAO_0000124 . @@ -2337,7 +2380,7 @@ nidm:PixelConnectivityCriterion rdf:type owl:Class ; nidm:PoissonDistribution rdf:type owl:Class ; - rdfs:subClassOf nidm:NoiseDistribution ; + rdfs:subClassOf nidm:ErrorDistribution ; owl:sameAs "http://purl.obolibrary.org/obo/STATO_0000051"^^xsd:anyURI . From ee0a8540607b7a9104590fe4e53554e7c3cb9223 Mon Sep 17 00:00:00 2001 From: cmaumet Date: Fri, 24 Oct 2014 17:19:31 +0100 Subject: [PATCH 02/14] Definition of Error Distribution terms --- nidm/nidm-results/terms/nidm-results.owl | 16 +++++++++------- 1 file changed, 9 insertions(+), 7 deletions(-) diff --git a/nidm/nidm-results/terms/nidm-results.owl b/nidm/nidm-results/terms/nidm-results.owl index c6ca225b8..ae7e54aea 100644 --- a/nidm/nidm-results/terms/nidm-results.owl +++ b/nidm/nidm-results/terms/nidm-results.owl @@ -164,9 +164,9 @@ nidm:hasErrorDependence rdf:type owl:ObjectProperty ; nidm:hasErrorDistribution rdf:type owl:ObjectProperty ; - prov:definition "FIXME" ; + prov:definition "Property that associates a NoiseDistribution with a NoiseModel." ; - obo:IAO_0000114 obo:IAO_0000124 ; + obo:IAO_0000114 obo:IAO_0000125 ; rdfs:range nidm:ErrorDistribution ; @@ -1570,9 +1570,9 @@ fsl:NonParametricSymmetricDistribution rdf:type owl:Class ; rdfs:subClassOf nidm:ErrorDistribution ; - prov:definition "FIXME" ; + prov:definition "Probability distribution defined empirically on the data assuming a symmetric probability distribution. Non-parametric distribution are usually defined using permutation of the class labels or sign-flipping." ; - obo:IAO_0000114 obo:IAO_0000124 . + obo:IAO_0000114 obo:IAO_0000125 . @@ -1941,7 +1941,9 @@ nidm:ErrorDistribution rdf:type owl:Class ; rdfs:subClassOf prov:Entity ; - obo:IAO_0000114 obo:IAO_0000124 . + obo:IAO_0000115 "Probability distribution used to model the noise." ; + + obo:IAO_0000114 obo:IAO_0000125 . @@ -2272,9 +2274,9 @@ nidm:NonParametricDistribution rdf:type owl:Class ; rdfs:subClassOf nidm:ErrorDistribution ; - prov:definition "FIXME" ; + prov:definition "Probability distribution defined empirically on the data without assumption on the shape of the probability distribution. Non-parametric distribution are usually defined using permutation of the class labels or sign-flipping." ; - obo:IAO_0000114 obo:IAO_0000124 . + obo:IAO_0000114 obo:IAO_0000125 . From fcf667a24f0e72a3f3d9a8310509456fc1d0b9b0 Mon Sep 17 00:00:00 2001 From: cmaumet Date: Fri, 24 Oct 2014 17:21:42 +0100 Subject: [PATCH 03/14] Update terms README --- nidm/nidm-results/terms/README.md | 14 ++++++++++++++ 1 file changed, 14 insertions(+) diff --git a/nidm/nidm-results/terms/README.md b/nidm/nidm-results/terms/README.md index 234233fe7..30259b675 100644 --- a/nidm/nidm-results/terms/README.md +++ b/nidm/nidm-results/terms/README.md @@ -6,6 +6,10 @@

Classes

+ + + + @@ -35,6 +39,10 @@ + + + + @@ -141,6 +149,12 @@ + + + + + + From e55429eb0ea78fe169f9d1cde1428c70536e4697 Mon Sep 17 00:00:00 2001 From: cmaumet Date: Fri, 24 Oct 2014 17:28:40 +0100 Subject: [PATCH 04/14] hasNoiseDistribution -> hasErrorDistribution (examples) --- nidm/nidm-results/fsl/example001/fsl_nidm.provn | 2 +- nidm/nidm-results/fsl/fsl_results.provn | 2 +- nidm/nidm-results/spm/example001/example001_spm_results.provn | 2 +- nidm/nidm-results/spm/example002/spm_results_2contrasts.provn | 3 ++- nidm/nidm-results/spm/example003/spm_results_conjunction.provn | 2 +- nidm/nidm-results/spm/spm_results.provn | 2 +- 6 files changed, 7 insertions(+), 6 deletions(-) diff --git a/nidm/nidm-results/fsl/example001/fsl_nidm.provn b/nidm/nidm-results/fsl/example001/fsl_nidm.provn index 919a24413..2268f1fa6 100644 --- a/nidm/nidm-results/fsl/example001/fsl_nidm.provn +++ b/nidm/nidm-results/fsl/example001/fsl_nidm.provn @@ -96,7 +96,7 @@ entity(niiri:fsl_results_id,[prov:type = 'prov:Bundle', prov:label = "FSL Result entity(niiri:coordinate_0004_5,[prov:type = 'nidm:Coordinate', prov:label = "Coordinate 0004_5", fsl:coordinate1InVoxels = "39" %% xsd:float, fsl:coordinate2InVoxels = "13" %% xsd:float, fsl:coordinate3InVoxels = "12" %% xsd:float, nidm:coordinate1 = "-25.5" %% xsd:float, nidm:coordinate2 = "-80.4" %% xsd:float, nidm:coordinate3 = "-15.3" %% xsd:float]) entity(niiri:coordinate_0004_4,[prov:type = 'nidm:Coordinate', prov:label = "Coordinate 0004_4", fsl:coordinate1InVoxels = "45" %% xsd:float, fsl:coordinate2InVoxels = "15" %% xsd:float, fsl:coordinate3InVoxels = "14" %% xsd:float, nidm:coordinate1 = "-48.1" %% xsd:float, nidm:coordinate2 = "-73.7" %% xsd:float, nidm:coordinate3 = "-9.24" %% xsd:float]) entity(niiri:coordinate_0004_6,[prov:type = 'nidm:Coordinate', prov:label = "Coordinate 0004_6", fsl:coordinate1InVoxels = "32" %% xsd:float, fsl:coordinate2InVoxels = "10" %% xsd:float, fsl:coordinate3InVoxels = "16" %% xsd:float, nidm:coordinate1 = "0.791" %% xsd:float, nidm:coordinate2 = "-87.2" %% xsd:float, nidm:coordinate3 = "3.23" %% xsd:float]) -entity(niiri:error_model_id,[prov:type = 'nidm:ErrorModel', nidm:hasNoiseDistribution = 'nidm:GaussianDistribution', nidm:errorVarianceHomogeneous = "true" %% xsd:boolean, nidm:varianceSpatialModel = 'nidm:SpatiallyLocal', nidm:hasErrorDependence = 'nidm:SeriallyCorrelatedError', nidm:dependenceSpatialModel = 'nidm:SpatiallyRegularized']) +entity(niiri:error_model_id,[prov:type = 'nidm:ErrorModel', nidm:hasErrorDistribution = 'nidm:GaussianDistribution', nidm:errorVarianceHomogeneous = "true" %% xsd:boolean, nidm:varianceSpatialModel = 'nidm:SpatiallyLocal', nidm:hasErrorDependence = 'nidm:SeriallyCorrelatedError', nidm:dependenceSpatialModel = 'nidm:SpatiallyRegularized']) entity(niiri:z_statistic_map_id_1,[prov:type = 'nidm:StatisticMap', prov:label = "Z-Statistic Map: Generation", prov:location = "file://./ZStatistic.nii.gz" %% xsd:anyURI, nidm:statisticType = 'nidm:ZStatistic', dct:format = "image/nifti" %% xsd:string, nidm:contrastName = "Generation" %% xsd:string, nidm:filename = "zstat1.nii.gz" %% xsd:string, nidm:filename = "ZStatistic.nii.gz" %% xsd:string, nidm:errorDegreesOfFreedom = "INF" %% xsd:float, nidm:effectDegreesOfFreedom = "1" %% xsd:float, nidm:inCoordinateSpace = 'niiri:coordinate_space_id_12', crypto:sha512 = "3a68a4e5963766af86d22a871a4dbca9568a46441a567855b3a84dbd47ea01acea11ed77b37ce85078a219adaa92264296a4548c1ba39b11ff028e8fefd95d03" %% xsd:string]) entity(niiri:cluster_0003,[prov:type = 'nidm:Cluster', prov:label = "Cluster 0003", nidm:clusterSizeInVoxels = "499" %% xsd:int, nidm:pValueFWER = "1.26e-12" %% xsd:float, nidm:clusterLabelId = "3" %% xsd:int]) entity(niiri:cluster_0004,[prov:type = 'nidm:Cluster', prov:label = "Cluster 0004", nidm:clusterSizeInVoxels = "1203" %% xsd:int, nidm:clusterLabelId = "4" %% xsd:int, nidm:pValueFWER = "8.02e-24" %% xsd:float]) diff --git a/nidm/nidm-results/fsl/fsl_results.provn b/nidm/nidm-results/fsl/fsl_results.provn index 62905e21a..55d9d3255 100644 --- a/nidm/nidm-results/fsl/fsl_results.provn +++ b/nidm/nidm-results/fsl/fsl_results.provn @@ -52,7 +52,7 @@ entity(niiri:peak_0006,[prov:type = 'nidm:Peak', prov:label = "Peak 6", prov:loc entity(niiri:peak_definition_criteria_id,[prov:type = 'nidm:PeakDefinitionCriteria', prov:label = "Peak Definition Criteria", nidm:maxNumberOfPeaksPerCluster = "3" %% xsd:int, nidm:minDistanceBetweenPeaks = "8.0" %% xsd:float]) entity(niiri:fsl_results_id,[prov:type = 'prov:Bundle', prov:label = "FSL Results", nidm:objectModel = 'nidm:FSLResults', nidm:version = "0.2.0" %% xsd:string]) entity(niiri:contrast_map_id,[prov:type = 'nidm:ContrastMap', prov:label = "Contrast Map: listening > rest", prov:location = "file:///path/to/Contrast.nii.gz" %% xsd:anyURI, dct:format = "image/nifti" %% xsd:string, nidm:contrastName = "listening > rest" %% xsd:string, nidm:filename = "cope1.nii.gz" %% xsd:string, nidm:filename = "Contrast.nii.gz" %% xsd:string, nidm:inCoordinateSpace = 'niiri:coordinate_space_id_1', crypto:sha512 = "400a2f07d99ed9be06577e6ecc89222cf4b688c654bc89067da558e88b73b97dd1b25e6c98f2a735fa0a1409598cff7e6025bda55abb6b9f5ef65d8d307eeba8" %% xsd:string]) -entity(niiri:error_model_id,[prov:type = 'nidm:ErrorModel', nidm:hasNoiseDistribution = 'nidm:GaussianDistribution', nidm:errorVarianceHomogeneous = "true" %% xsd:boolean, nidm:varianceSpatialModel = 'nidm:SpatiallyLocal', nidm:hasErrorDependence = 'nidm:IndependentError', nidm:dependenceSpatialModel = 'nidm:SpatiallyLocal']) +entity(niiri:error_model_id,[prov:type = 'nidm:ErrorModel', nidm:hasErrorDistribution = 'nidm:GaussianDistribution', nidm:errorVarianceHomogeneous = "true" %% xsd:boolean, nidm:varianceSpatialModel = 'nidm:SpatiallyLocal', nidm:hasErrorDependence = 'nidm:IndependentError', nidm:dependenceSpatialModel = 'nidm:SpatiallyLocal']) entity(niiri:cluster_definition_criteria_id,[prov:type = 'nidm:ClusterDefinitionCriteria', prov:label = "Cluster Connectivity Criterion: 18", nidm:hasConnectivityCriterion = 'nidm:voxel18Connected']) entity(niiri:cluster_0001,[prov:type = 'nidm:Cluster', prov:label = "Cluster 0001", nidm:clusterSizeInVoxels = "530" %% xsd:int, nidm:pValueFWER = "0.000000" %% xsd:float]) entity(niiri:cluster_0002,[prov:type = 'nidm:Cluster', prov:label = "Cluster 0002", nidm:clusterSizeInVoxels = "445" %% xsd:int, nidm:pValueFWER = "0.000000" %% xsd:float]) diff --git a/nidm/nidm-results/spm/example001/example001_spm_results.provn b/nidm/nidm-results/spm/example001/example001_spm_results.provn index 4489a85e8..a0a135460 100644 --- a/nidm/nidm-results/spm/example001/example001_spm_results.provn +++ b/nidm/nidm-results/spm/example001/example001_spm_results.provn @@ -173,7 +173,7 @@ document entity(niiri:error_model_id, [prov:type = 'nidm:ErrorModel', - nidm:hasNoiseDistribution = 'nidm:GaussianDistribution', + nidm:hasErrorDistribution = 'nidm:GaussianDistribution', nidm:errorVarianceHomogeneous = "true" %%xsd:boolean, nidm:varianceSpatialModel = 'nidm:SpatiallyLocal', nidm:hasErrorDependence = 'nidm:SeriallyCorrelatedError', diff --git a/nidm/nidm-results/spm/example002/spm_results_2contrasts.provn b/nidm/nidm-results/spm/example002/spm_results_2contrasts.provn index a25c10667..7fde97a5a 100644 --- a/nidm/nidm-results/spm/example002/spm_results_2contrasts.provn +++ b/nidm/nidm-results/spm/example002/spm_results_2contrasts.provn @@ -1,3 +1,4 @@ + document prefix crypto prefix neurolex @@ -55,7 +56,7 @@ entity(niiri:resels_per_voxel_map_id_der,[prov:type = 'spm:ReselsPerVoxelMap', n entity(niiri:beta_map_id_3_der,[prov:type = 'nidm:ParameterEstimateMap', nidm:filename = "beta_0003.nii" %% xsd:string, dct:format = "image/nifti" %% xsd:string, crypto:sha512 = "e43b6e01b0463fe7d40782137867a..." %% xsd:string]) entity(niiri:peak_definition_criteria_id,[prov:type = 'nidm:PeakDefinitionCriteria', prov:label = "Peak Definition Criteria", nidm:maxNumberOfPeaksPerCluster = "3" %% xsd:int, nidm:minDistanceBetweenPeaks = "8.0" %% xsd:float]) entity(niiri:contrast_map_id,[prov:type = 'nidm:ContrastMap', prov:label = "Contrast Map: listening > reading", prov:location = "file:///path/to/Contrast_0001.nii.gz" %% xsd:anyURI, nidm:filename = "Contrast_0001.nii.gz" %% xsd:string, dct:format = "image/nifti" %% xsd:string, nidm:contrastName = "listening > reading" %% xsd:string, nidm:inCoordinateSpace = 'niiri:coordinate_space_id_1', crypto:sha512 = "e43b6e01b0463fe7d40782137867a..." %% xsd:string]) -entity(niiri:error_model_id,[prov:type = 'nidm:ErrorModel', nidm:hasNoiseDistribution = 'nidm:GaussianDistribution', nidm:errorVarianceHomogeneous = "true" %% xsd:boolean, nidm:varianceSpatialModel = 'nidm:SpatiallyLocal', nidm:hasErrorDependence = 'nidm:IndependentError', nidm:dependenceSpatialModel = 'nidm:SpatiallyLocal']) +entity(niiri:error_model_id,[prov:type = 'nidm:ErrorModel', nidm:hasErrorDistribution = 'nidm:GaussianDistribution', nidm:errorVarianceHomogeneous = "true" %% xsd:boolean, nidm:varianceSpatialModel = 'nidm:SpatiallyLocal', nidm:hasErrorDependence = 'nidm:IndependentError', nidm:dependenceSpatialModel = 'nidm:SpatiallyLocal']) entity(niiri:cluster_definition_criteria_id,[prov:type = 'nidm:ClusterDefinitionCriteria', prov:label = "Cluster Connectivity Criterion: 18", nidm:hasConnectivityCriterion = 'nidm:voxel18Connected']) entity(niiri:beta_map_id_2_der,[prov:type = 'nidm:ParameterEstimateMap', nidm:filename = "beta_0002.nii" %% xsd:string, dct:format = "image/nifti" %% xsd:string, crypto:sha512 = "e43b6e01b0463fe7d40782137867a..." %% xsd:string]) entity(niiri:spm_results_id,[prov:type = 'prov:Bundle', prov:label = "SPM Results", nidm:objectModel = 'nidm:SPMResults', nidm:version = "0.2.0" %% xsd:string]) diff --git a/nidm/nidm-results/spm/example003/spm_results_conjunction.provn b/nidm/nidm-results/spm/example003/spm_results_conjunction.provn index 6c5544be6..93856b342 100644 --- a/nidm/nidm-results/spm/example003/spm_results_conjunction.provn +++ b/nidm/nidm-results/spm/example003/spm_results_conjunction.provn @@ -162,7 +162,7 @@ document entity(niiri:error_model_id, [prov:type = 'nidm:ErrorModel', - nidm:hasNoiseDistribution = 'nidm:GaussianDistribution', + nidm:hasErrorDistribution = 'nidm:GaussianDistribution', nidm:errorVarianceHomogeneous = "true" %%xsd:boolean, nidm:varianceSpatialModel = 'nidm:SpatiallyLocal', nidm:hasErrorDependence = 'nidm:IndependentError', diff --git a/nidm/nidm-results/spm/spm_results.provn b/nidm/nidm-results/spm/spm_results.provn index 29fbfca28..c9f188bdf 100644 --- a/nidm/nidm-results/spm/spm_results.provn +++ b/nidm/nidm-results/spm/spm_results.provn @@ -232,7 +232,7 @@ document entity(niiri:error_model_id, [prov:type = 'nidm:ErrorModel', - nidm:hasNoiseDistribution = 'nidm:GaussianDistribution', + nidm:hasErrorDistribution = 'nidm:GaussianDistribution', nidm:errorVarianceHomogeneous = "true" %%xsd:boolean, nidm:varianceSpatialModel = 'nidm:SpatiallyLocal', nidm:hasErrorDependence = 'nidm:IndependentError', From b530131f7228f659b028fcb5bc65cd87aa880176 Mon Sep 17 00:00:00 2001 From: cmaumet Date: Mon, 27 Oct 2014 08:19:04 +0000 Subject: [PATCH 05/14] defined -> estimated --- nidm/nidm-results/terms/README.md | 4 ++-- nidm/nidm-results/terms/nidm-results.owl | 6 +++--- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/nidm/nidm-results/terms/README.md b/nidm/nidm-results/terms/README.md index 30259b675..2751e19ce 100644 --- a/nidm/nidm-results/terms/README.md +++ b/nidm/nidm-results/terms/README.md @@ -8,7 +8,7 @@ - + @@ -41,7 +41,7 @@ - + diff --git a/nidm/nidm-results/terms/nidm-results.owl b/nidm/nidm-results/terms/nidm-results.owl index ae7e54aea..cad95b501 100644 --- a/nidm/nidm-results/terms/nidm-results.owl +++ b/nidm/nidm-results/terms/nidm-results.owl @@ -1570,7 +1570,7 @@ fsl:NonParametricSymmetricDistribution rdf:type owl:Class ; rdfs:subClassOf nidm:ErrorDistribution ; - prov:definition "Probability distribution defined empirically on the data assuming a symmetric probability distribution. Non-parametric distribution are usually defined using permutation of the class labels or sign-flipping." ; + prov:definition "Probability distribution estimated empirically on the data assuming a symmetric probability distribution. Non-parametric distribution are usually estimated using permutation of the class labels or sign-flipping." ; obo:IAO_0000114 obo:IAO_0000125 . @@ -1697,8 +1697,8 @@ nidm:ConnectivityCriterion3D rdf:type owl:Class ; owl:equivalentClass [ rdf:type owl:Class ; owl:oneOf ( nidm:connected6In3D - nidm:connected18In3D nidm:connected26In3D + nidm:connected18In3D ) ] ; @@ -2274,7 +2274,7 @@ nidm:NonParametricDistribution rdf:type owl:Class ; rdfs:subClassOf nidm:ErrorDistribution ; - prov:definition "Probability distribution defined empirically on the data without assumption on the shape of the probability distribution. Non-parametric distribution are usually defined using permutation of the class labels or sign-flipping." ; + prov:definition "Probability distribution estimated empirically on the data without assumption on the shape of the probability distribution. Non-parametric distribution are usually estimated using permutation of the class labels or sign-flipping." ; obo:IAO_0000114 obo:IAO_0000125 . From 577e00ac202aa2dc0ffe40892d6ce96afb39713d Mon Sep 17 00:00:00 2001 From: cmaumet Date: Wed, 29 Oct 2014 10:23:57 +0000 Subject: [PATCH 06/14] fix: remaining conflict in owl --- nidm/nidm-results/terms/nidm-results.owl | 2 -- 1 file changed, 2 deletions(-) diff --git a/nidm/nidm-results/terms/nidm-results.owl b/nidm/nidm-results/terms/nidm-results.owl index cad95b501..56a8c63cf 100644 --- a/nidm/nidm-results/terms/nidm-results.owl +++ b/nidm/nidm-results/terms/nidm-results.owl @@ -1705,8 +1705,6 @@ nidm:ConnectivityCriterion3D rdf:type owl:Class ; rdfs:subClassOf nidm:ConnectivityCriterion ; prov:definition "The order of neighbourhood used to determine whether two voxels are neighbours in 3D. Possible values are: 6 (voxels share a face), 18 (voxels share a face or edge), 26 (voxels share a face, edge or corner)." . ->>>>>>> Noise -> Error - ### http://www.incf.org/ns/nidash/nidm#ContrastEstimation From 0255750802b7221f4775bd76dcc75d176163030d Mon Sep 17 00:00:00 2001 From: cmaumet Date: Mon, 3 Nov 2014 09:46:56 +0000 Subject: [PATCH 07/14] If document does not exist then return not identical --- nidm/nidm-results/test/TestCommons.py | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/nidm/nidm-results/test/TestCommons.py b/nidm/nidm-results/test/TestCommons.py index 71ccbfc1c..21db7387f 100644 --- a/nidm/nidm-results/test/TestCommons.py +++ b/nidm/nidm-results/test/TestCommons.py @@ -76,12 +76,14 @@ def compare_ttl_documents(ttl_doc1, ttl_doc2, prefix_uri_from_first=False): doc_graph.parse(ttl_doc1) same_doc_graph = Graph() - # This is a fix as sometimes prefixes URIs are lost on the Prov Store - # if doc_graph.parse(ttl_doc2) is called directly try: + # This is a fix as sometimes prefixes URIs are lost on the Prov Store + # if doc_graph.parse(ttl_doc2) is called directly logger.info(' Opening '+ttl_doc2) ttl_doc2_req = urllib2.urlopen(ttl_doc2) same_doc_graph.parse(data=ttl_doc2_req.read(), format='turtle') + except urllib2.HTTPError: + return False except ValueError: same_doc_graph.parse(ttl_doc2, format='turtle') From b4e8a059ed36d4485fc97869c90d0403be18daeb Mon Sep 17 00:00:00 2001 From: cmaumet Date: Mon, 3 Nov 2014 14:09:56 +0000 Subject: [PATCH 08/14] hasNoiseDistribution -> hasErrorDistribution --- nidm/nidm-results/fsl/example001/fsl_nidm.ttl | 2 +- nidm/nidm-results/fsl/fsl_results.ttl | 2 +- nidm/nidm-results/spm/example001/example001_spm_results.ttl | 2 +- nidm/nidm-results/spm/example002/spm_results_2contrasts.ttl | 2 +- nidm/nidm-results/spm/example003/spm_results_conjunction.ttl | 2 +- nidm/nidm-results/spm/spm_results.ttl | 2 +- 6 files changed, 6 insertions(+), 6 deletions(-) diff --git a/nidm/nidm-results/fsl/example001/fsl_nidm.ttl b/nidm/nidm-results/fsl/example001/fsl_nidm.ttl index db3b5fa2f..ddcf0e2d7 100644 --- a/nidm/nidm-results/fsl/example001/fsl_nidm.ttl +++ b/nidm/nidm-results/fsl/example001/fsl_nidm.ttl @@ -287,7 +287,7 @@ niiri:contrast_id_1 a prov:Entity , nidm:ContrastWeights ; nidm:contrastName "Generation"^^xsd:string . niiri:error_model_id a prov:Entity , nidm:ErrorModel ; - nidm:hasNoiseDistribution nidm:GaussianDistribution ; + nidm:hasErrorDistribution nidm:GaussianDistribution ; nidm:errorVarianceHomogeneous "true"^^xsd:boolean ; nidm:varianceSpatialModel nidm:SpatiallyLocal ; nidm:hasErrorDependence nidm:SeriallyCorrelatedError ; diff --git a/nidm/nidm-results/fsl/fsl_results.ttl b/nidm/nidm-results/fsl/fsl_results.ttl index cdc26d02e..d8241ca65 100644 --- a/nidm/nidm-results/fsl/fsl_results.ttl +++ b/nidm/nidm-results/fsl/fsl_results.ttl @@ -158,7 +158,7 @@ niiri:contrast_id a prov:Entity , nidm:ContrastWeights ; nidm:contrastName "listening > rest"^^xsd:string . niiri:error_model_id a prov:Entity , nidm:ErrorModel ; - nidm:hasNoiseDistribution nidm:GaussianDistribution ; + nidm:hasErrorDistribution nidm:GaussianDistribution ; nidm:errorVarianceHomogeneous "true"^^xsd:boolean ; nidm:varianceSpatialModel nidm:SpatiallyLocal ; nidm:hasErrorDependence nidm:IndependentError ; diff --git a/nidm/nidm-results/spm/example001/example001_spm_results.ttl b/nidm/nidm-results/spm/example001/example001_spm_results.ttl index d12292301..a9a53420c 100644 --- a/nidm/nidm-results/spm/example001/example001_spm_results.ttl +++ b/nidm/nidm-results/spm/example001/example001_spm_results.ttl @@ -178,7 +178,7 @@ niiri:contrast_id a prov:Entity , nidm:ContrastWeights ; nidm:contrastName "passive listening > rest"^^xsd:string . niiri:error_model_id a prov:Entity , nidm:ErrorModel ; - nidm:hasNoiseDistribution nidm:GaussianDistribution ; + nidm:hasErrorDistribution nidm:GaussianDistribution ; nidm:errorVarianceHomogeneous "true"^^xsd:boolean ; nidm:varianceSpatialModel nidm:SpatiallyLocal ; nidm:hasErrorDependence nidm:SeriallyCorrelatedError ; diff --git a/nidm/nidm-results/spm/example002/spm_results_2contrasts.ttl b/nidm/nidm-results/spm/example002/spm_results_2contrasts.ttl index 66a984221..39c8df737 100644 --- a/nidm/nidm-results/spm/example002/spm_results_2contrasts.ttl +++ b/nidm/nidm-results/spm/example002/spm_results_2contrasts.ttl @@ -173,7 +173,7 @@ niiri:beta_map_id_3_der a prov:Entity , nidm:ParameterEstimateMap ; niiri:beta_map_id_3 prov:wasDerivedFrom niiri:beta_map_id_3_der . niiri:error_model_id a prov:Entity , nidm:ErrorModel ; - nidm:hasNoiseDistribution nidm:GaussianDistribution ; + nidm:hasErrorDistribution nidm:GaussianDistribution ; nidm:errorVarianceHomogeneous "true"^^xsd:boolean ; nidm:varianceSpatialModel nidm:SpatiallyLocal ; nidm:hasErrorDependence nidm:IndependentError ; diff --git a/nidm/nidm-results/spm/example003/spm_results_conjunction.ttl b/nidm/nidm-results/spm/example003/spm_results_conjunction.ttl index aed9607e9..b481c8111 100644 --- a/nidm/nidm-results/spm/example003/spm_results_conjunction.ttl +++ b/nidm/nidm-results/spm/example003/spm_results_conjunction.ttl @@ -149,7 +149,7 @@ niiri:map_id_7 a prov:Entity , nidm:ParameterEstimateMap ; niiri:beta_map_id_3 prov:wasDerivedFrom niiri:map_id_7 . niiri:error_model_id a prov:Entity , nidm:ErrorModel ; - nidm:hasNoiseDistribution nidm:GaussianDistribution ; + nidm:hasErrorDistribution nidm:GaussianDistribution ; nidm:errorVarianceHomogeneous "true"^^xsd:boolean ; nidm:varianceSpatialModel nidm:SpatiallyLocal ; nidm:hasErrorDependence nidm:IndependentError ; diff --git a/nidm/nidm-results/spm/spm_results.ttl b/nidm/nidm-results/spm/spm_results.ttl index 3058c874d..fd70e51b3 100644 --- a/nidm/nidm-results/spm/spm_results.ttl +++ b/nidm/nidm-results/spm/spm_results.ttl @@ -239,7 +239,7 @@ niiri:contrast_id a prov:Entity , nidm:ContrastWeights ; nidm:contrastName "listening > rest"^^xsd:string . niiri:error_model_id a prov:Entity , nidm:ErrorModel ; - nidm:hasNoiseDistribution nidm:GaussianDistribution ; + nidm:hasErrorDistribution nidm:GaussianDistribution ; nidm:errorVarianceHomogeneous "true"^^xsd:boolean ; nidm:varianceSpatialModel nidm:SpatiallyLocal ; nidm:hasErrorDependence nidm:IndependentError ; From bb325ec263f6626e427a5782c851b217f42c9bc6 Mon Sep 17 00:00:00 2001 From: cmaumet Date: Thu, 6 Nov 2014 10:34:50 +0000 Subject: [PATCH 09/14] Noise -> Error --- nidm/nidm-results/terms/nidm-results.owl | 48 +++++++++++++++++++++--- 1 file changed, 43 insertions(+), 5 deletions(-) diff --git a/nidm/nidm-results/terms/nidm-results.owl b/nidm/nidm-results/terms/nidm-results.owl index 56a8c63cf..fad11a92b 100644 --- a/nidm/nidm-results/terms/nidm-results.owl +++ b/nidm/nidm-results/terms/nidm-results.owl @@ -164,7 +164,7 @@ nidm:hasErrorDependence rdf:type owl:ObjectProperty ; nidm:hasErrorDistribution rdf:type owl:ObjectProperty ; - prov:definition "Property that associates a NoiseDistribution with a NoiseModel." ; + prov:definition "Property that associates an ErrorDistribution with an ErrorModel." ; obo:IAO_0000114 obo:IAO_0000125 ; @@ -1673,14 +1673,15 @@ nidm:ConnectivityCriterion rdf:type owl:Class ; obo:IAO_0000114 obo:IAO_0000122 . + ### http://www.incf.org/ns/nidash/nidm#ConnectivityCriterion2D nidm:ConnectivityCriterion2D rdf:type owl:Class ; owl:equivalentClass [ rdf:type owl:Class ; owl:oneOf ( nidm:connected4In2D - nidm:connected6In2D nidm:connected8In2D + nidm:connected6In2D ) ] ; @@ -1696,9 +1697,9 @@ nidm:ConnectivityCriterion2D rdf:type owl:Class ; nidm:ConnectivityCriterion3D rdf:type owl:Class ; owl:equivalentClass [ rdf:type owl:Class ; - owl:oneOf ( nidm:connected6In3D + owl:oneOf ( nidm:connected18In3D + nidm:connected6In3D nidm:connected26In3D - nidm:connected18In3D ) ] ; @@ -1707,6 +1708,7 @@ nidm:ConnectivityCriterion3D rdf:type owl:Class ; prov:definition "The order of neighbourhood used to determine whether two voxels are neighbours in 3D. Possible values are: 6 (voxels share a face), 18 (voxels share a face or edge), 26 (voxels share a face, edge or corner)." . + ### http://www.incf.org/ns/nidash/nidm#ContrastEstimation nidm:ContrastEstimation rdf:type owl:Class ; @@ -1939,7 +1941,7 @@ nidm:ErrorDistribution rdf:type owl:Class ; rdfs:subClassOf prov:Entity ; - obo:IAO_0000115 "Probability distribution used to model the noise." ; + obo:IAO_0000115 "Probability distribution used to model the error." ; obo:IAO_0000114 obo:IAO_0000125 . @@ -2950,6 +2952,42 @@ nidm:Mni305CoordinateSystem rdf:type nidm:MNICoordinateSystem , +### http://www.incf.org/ns/nidash/nidm#connected18In3D + +nidm:connected18In3D rdf:type owl:NamedIndividual . + + + +### http://www.incf.org/ns/nidash/nidm#connected26In3D + +nidm:connected26In3D rdf:type owl:NamedIndividual . + + + +### http://www.incf.org/ns/nidash/nidm#connected4In2D + +nidm:connected4In2D rdf:type owl:NamedIndividual . + + + +### http://www.incf.org/ns/nidash/nidm#connected6In2D + +nidm:connected6In2D rdf:type owl:NamedIndividual . + + + +### http://www.incf.org/ns/nidash/nidm#connected6In3D + +nidm:connected6In3D rdf:type owl:NamedIndividual . + + + +### http://www.incf.org/ns/nidash/nidm#connected8In2D + +nidm:connected8In2D rdf:type owl:NamedIndividual . + + + ### http://www.incf.org/ns/nidash/nidm#pixel4connected nidm:pixel4connected rdf:type nidm:PixelConnectivityCriterion , From 9ff7a1e7489b91df82e116889eabbfa96bd11ecb Mon Sep 17 00:00:00 2001 From: cmaumet Date: Thu, 6 Nov 2014 10:40:59 +0000 Subject: [PATCH 10/14] Copy definitions from STATO for Distribution terms defined as sameAs --- nidm/nidm-results/terms/nidm-results.owl | 18 +++++++++++++++--- 1 file changed, 15 insertions(+), 3 deletions(-) diff --git a/nidm/nidm-results/terms/nidm-results.owl b/nidm/nidm-results/terms/nidm-results.owl index fad11a92b..f4df7fa73 100644 --- a/nidm/nidm-results/terms/nidm-results.owl +++ b/nidm/nidm-results/terms/nidm-results.owl @@ -1521,7 +1521,11 @@ fsl:BinomialDistribution rdf:type owl:Class ; rdfs:subClassOf nidm:ErrorDistribution ; - owl:sameAs "http://purl.obolibrary.org/obo/STATO_0000276"^^xsd:anyURI . + owl:sameAs "http://purl.obolibrary.org/obo/STATO_0000276"^^xsd:anyURI ; + + rdfs:isDefinedBy "The binomial distribution is a discrete probability distribution which describes the probability of k successes in n draws with replacement from a finite population of size N. The binomial distribution is frequently used to model the number of successes in a sample of size n drawn with replacement from a population of size N. The binomial distribution gives the discrete probability distribution of obtaining exactly n successes out of N Bernoulli trials (where the result of each Bernoulli trial is true with probability p and false with probability q=1-p ) notation: B(n,p) The mean is N*p The variance is N*p*q. (Definition from STATO)." ; + + obo:IAO_0000114 obo:IAO_0000122 . @@ -2068,7 +2072,11 @@ nidm:GaussianDistribution rdf:type owl:Class ; rdfs:subClassOf nidm:ErrorDistribution ; - owl:sameAs "http://purl.obolibrary.org/obo/STATO_0000227"^^xsd:anyURI . + owl:sameAs "http://purl.obolibrary.org/obo/STATO_0000227"^^xsd:anyURI ; + + rdfs:isDefinedBy "A normal distribution is a continuous probability distribution described by a probability distribution function described here: http://mathworld.wolfram.com/NormalDistribution.html (Definition from STATO)." ; + + obo:IAO_0000114 obo:IAO_0000122 . @@ -2384,7 +2392,11 @@ nidm:PoissonDistribution rdf:type owl:Class ; rdfs:subClassOf nidm:ErrorDistribution ; - owl:sameAs "http://purl.obolibrary.org/obo/STATO_0000051"^^xsd:anyURI . + owl:sameAs "http://purl.obolibrary.org/obo/STATO_0000051"^^xsd:anyURI ; + + rdfs:isDefinedBy "Poisson distribution is a probability distribution used to model the number of events occurring within a given time interval. It is defined by a real number (λ) and an integer k representing the number of events and a function. The expected value of a Poisson-distributed random variable is equal to λ and so is its variance. (Definition from STATO)." ; + + obo:IAO_0000114 obo:IAO_0000122 . From 9ab9a3c9ae8e62b12fa0222f42bcd6f3a2b395e5 Mon Sep 17 00:00:00 2001 From: cmaumet Date: Thu, 6 Nov 2014 11:03:02 +0000 Subject: [PATCH 11/14] Update terms README --- nidm/nidm-results/terms/README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nidm/nidm-results/terms/README.md b/nidm/nidm-results/terms/README.md index 2751e19ce..a58559076 100644 --- a/nidm/nidm-results/terms/README.md +++ b/nidm/nidm-results/terms/README.md @@ -151,7 +151,7 @@ - + From 9d4d942b49b8ce819fe5df7508533995e66d94ad Mon Sep 17 00:00:00 2001 From: cmaumet Date: Fri, 7 Nov 2014 14:57:17 +0000 Subject: [PATCH 12/14] Update Prov Store links --- nidm/nidm-results/fsl/README.md | 8 ++++---- nidm/nidm-results/fsl/example001/README.md | 8 ++++---- nidm/nidm-results/spm/README.md | 8 ++++---- nidm/nidm-results/spm/example001/README.md | 8 ++++---- nidm/nidm-results/spm/example002/README.md | 8 ++++---- nidm/nidm-results/spm/example003/README.md | 8 ++++---- 6 files changed, 24 insertions(+), 24 deletions(-) diff --git a/nidm/nidm-results/fsl/README.md b/nidm/nidm-results/fsl/README.md index 42c5b1293..672b40347 100644 --- a/nidm/nidm-results/fsl/README.md +++ b/nidm/nidm-results/fsl/README.md @@ -1,9 +1,9 @@ -Prov store: https://provenance.ecs.soton.ac.uk/store/documents/31569/ +Prov store: https://provenance.ecs.soton.ac.uk/store/documents/31574/ -Alternative serialisations: [json](https://provenance.ecs.soton.ac.uk/store/documents/31569.json), [turtle](https://provenance.ecs.soton.ac.uk/store/documents/31569.ttl), -Graph: [svg](https://provenance.ecs.soton.ac.uk/store/documents/31569.svg), [PDF](https://provenance.ecs.soton.ac.uk/store/documents/31569.pdf), [png](https://provenance.ecs.soton.ac.uk/store/documents/31569.png) +Alternative serialisations: [json](https://provenance.ecs.soton.ac.uk/store/documents/31574.json), [turtle](https://provenance.ecs.soton.ac.uk/store/documents/31574.ttl), +Graph: [svg](https://provenance.ecs.soton.ac.uk/store/documents/31574.svg), [PDF](https://provenance.ecs.soton.ac.uk/store/documents/31574.pdf), [png](https://provenance.ecs.soton.ac.uk/store/documents/31574.png) -![Prov Graph](https://provenance.ecs.soton.ac.uk/store/documents/31569.png) +![Prov Graph](https://provenance.ecs.soton.ac.uk/store/documents/31574.png) \ No newline at end of file diff --git a/nidm/nidm-results/fsl/example001/README.md b/nidm/nidm-results/fsl/example001/README.md index c7c5c8053..e3778af30 100644 --- a/nidm/nidm-results/fsl/example001/README.md +++ b/nidm/nidm-results/fsl/example001/README.md @@ -1,9 +1,9 @@ -Prov store: https://provenance.ecs.soton.ac.uk/store/documents/31568/ +Prov store: https://provenance.ecs.soton.ac.uk/store/documents/31572/ -Alternative serialisations: [json](https://provenance.ecs.soton.ac.uk/store/documents/31568.json), [turtle](https://provenance.ecs.soton.ac.uk/store/documents/31568.ttl), -Graph: [svg](https://provenance.ecs.soton.ac.uk/store/documents/31568.svg), [PDF](https://provenance.ecs.soton.ac.uk/store/documents/31568.pdf), [png](https://provenance.ecs.soton.ac.uk/store/documents/31568.png) +Alternative serialisations: [json](https://provenance.ecs.soton.ac.uk/store/documents/31572.json), [turtle](https://provenance.ecs.soton.ac.uk/store/documents/31572.ttl), +Graph: [svg](https://provenance.ecs.soton.ac.uk/store/documents/31572.svg), [PDF](https://provenance.ecs.soton.ac.uk/store/documents/31572.pdf), [png](https://provenance.ecs.soton.ac.uk/store/documents/31572.png) -![Prov Graph](https://provenance.ecs.soton.ac.uk/store/documents/31568.png) +![Prov Graph](https://provenance.ecs.soton.ac.uk/store/documents/31572.png) \ No newline at end of file diff --git a/nidm/nidm-results/spm/README.md b/nidm/nidm-results/spm/README.md index 34317b7ff..5295a0f3b 100644 --- a/nidm/nidm-results/spm/README.md +++ b/nidm/nidm-results/spm/README.md @@ -1,9 +1,9 @@ -Prov store: https://provenance.ecs.soton.ac.uk/store/documents/31470/ +Prov store: https://provenance.ecs.soton.ac.uk/store/documents/31570/ -Alternative serialisations: [json](https://provenance.ecs.soton.ac.uk/store/documents/31470.json), [turtle](https://provenance.ecs.soton.ac.uk/store/documents/31470.ttl), -Graph: [svg](https://provenance.ecs.soton.ac.uk/store/documents/31470.svg), [PDF](https://provenance.ecs.soton.ac.uk/store/documents/31470.pdf), [png](https://provenance.ecs.soton.ac.uk/store/documents/31470.png) +Alternative serialisations: [json](https://provenance.ecs.soton.ac.uk/store/documents/31570.json), [turtle](https://provenance.ecs.soton.ac.uk/store/documents/31570.ttl), +Graph: [svg](https://provenance.ecs.soton.ac.uk/store/documents/31570.svg), [PDF](https://provenance.ecs.soton.ac.uk/store/documents/31570.pdf), [png](https://provenance.ecs.soton.ac.uk/store/documents/31570.png) -![Prov Graph](https://provenance.ecs.soton.ac.uk/store/documents/31470.png) +![Prov Graph](https://provenance.ecs.soton.ac.uk/store/documents/31570.png) \ No newline at end of file diff --git a/nidm/nidm-results/spm/example001/README.md b/nidm/nidm-results/spm/example001/README.md index a3ed782a1..30930d095 100644 --- a/nidm/nidm-results/spm/example001/README.md +++ b/nidm/nidm-results/spm/example001/README.md @@ -1,9 +1,9 @@ -Prov store: https://provenance.ecs.soton.ac.uk/store/documents/31471/ +Prov store: https://provenance.ecs.soton.ac.uk/store/documents/31575/ -Alternative serialisations: [json](https://provenance.ecs.soton.ac.uk/store/documents/31471.json), [turtle](https://provenance.ecs.soton.ac.uk/store/documents/31471.ttl), -Graph: [svg](https://provenance.ecs.soton.ac.uk/store/documents/31471.svg), [PDF](https://provenance.ecs.soton.ac.uk/store/documents/31471.pdf), [png](https://provenance.ecs.soton.ac.uk/store/documents/31471.png) +Alternative serialisations: [json](https://provenance.ecs.soton.ac.uk/store/documents/31575.json), [turtle](https://provenance.ecs.soton.ac.uk/store/documents/31575.ttl), +Graph: [svg](https://provenance.ecs.soton.ac.uk/store/documents/31575.svg), [PDF](https://provenance.ecs.soton.ac.uk/store/documents/31575.pdf), [png](https://provenance.ecs.soton.ac.uk/store/documents/31575.png) -![Prov Graph](https://provenance.ecs.soton.ac.uk/store/documents/31471.png) +![Prov Graph](https://provenance.ecs.soton.ac.uk/store/documents/31575.png) \ No newline at end of file diff --git a/nidm/nidm-results/spm/example002/README.md b/nidm/nidm-results/spm/example002/README.md index f9e04bab6..b79933119 100644 --- a/nidm/nidm-results/spm/example002/README.md +++ b/nidm/nidm-results/spm/example002/README.md @@ -1,9 +1,9 @@ -Prov store: https://provenance.ecs.soton.ac.uk/store/documents/31482/ +Prov store: https://provenance.ecs.soton.ac.uk/store/documents/31573/ -Alternative serialisations: [json](https://provenance.ecs.soton.ac.uk/store/documents/31482.json), [turtle](https://provenance.ecs.soton.ac.uk/store/documents/31482.ttl), -Graph: [svg](https://provenance.ecs.soton.ac.uk/store/documents/31482.svg), [PDF](https://provenance.ecs.soton.ac.uk/store/documents/31482.pdf), [png](https://provenance.ecs.soton.ac.uk/store/documents/31482.png) +Alternative serialisations: [json](https://provenance.ecs.soton.ac.uk/store/documents/31573.json), [turtle](https://provenance.ecs.soton.ac.uk/store/documents/31573.ttl), +Graph: [svg](https://provenance.ecs.soton.ac.uk/store/documents/31573.svg), [PDF](https://provenance.ecs.soton.ac.uk/store/documents/31573.pdf), [png](https://provenance.ecs.soton.ac.uk/store/documents/31573.png) -![Prov Graph](https://provenance.ecs.soton.ac.uk/store/documents/31482.png) +![Prov Graph](https://provenance.ecs.soton.ac.uk/store/documents/31573.png) \ No newline at end of file diff --git a/nidm/nidm-results/spm/example003/README.md b/nidm/nidm-results/spm/example003/README.md index e343ee4b1..c3cbf4290 100644 --- a/nidm/nidm-results/spm/example003/README.md +++ b/nidm/nidm-results/spm/example003/README.md @@ -1,9 +1,9 @@ -Prov store: https://provenance.ecs.soton.ac.uk/store/documents/30690/ +Prov store: https://provenance.ecs.soton.ac.uk/store/documents/31571/ -Alternative serialisations: [json](https://provenance.ecs.soton.ac.uk/store/documents/30690.json), [turtle](https://provenance.ecs.soton.ac.uk/store/documents/30690.ttl), -Graph: [svg](https://provenance.ecs.soton.ac.uk/store/documents/30690.svg), [PDF](https://provenance.ecs.soton.ac.uk/store/documents/30690.pdf), [png](https://provenance.ecs.soton.ac.uk/store/documents/30690.png) +Alternative serialisations: [json](https://provenance.ecs.soton.ac.uk/store/documents/31571.json), [turtle](https://provenance.ecs.soton.ac.uk/store/documents/31571.ttl), +Graph: [svg](https://provenance.ecs.soton.ac.uk/store/documents/31571.svg), [PDF](https://provenance.ecs.soton.ac.uk/store/documents/31571.pdf), [png](https://provenance.ecs.soton.ac.uk/store/documents/31571.png) -![Prov Graph](https://provenance.ecs.soton.ac.uk/store/documents/30690.png) +![Prov Graph](https://provenance.ecs.soton.ac.uk/store/documents/31571.png) \ No newline at end of file From c2b92c1ab385c8cb2a8af1b60f48e74f76b82410 Mon Sep 17 00:00:00 2001 From: cmaumet Date: Fri, 7 Nov 2014 16:16:22 +0000 Subject: [PATCH 13/14] Updates suggested by @khelm and @nicholst --- nidm/nidm-results/terms/nidm-results.owl | 28 ++++++++++++------------ 1 file changed, 14 insertions(+), 14 deletions(-) diff --git a/nidm/nidm-results/terms/nidm-results.owl b/nidm/nidm-results/terms/nidm-results.owl index f4df7fa73..0ac63965b 100644 --- a/nidm/nidm-results/terms/nidm-results.owl +++ b/nidm/nidm-results/terms/nidm-results.owl @@ -166,7 +166,7 @@ nidm:hasErrorDistribution rdf:type owl:ObjectProperty ; prov:definition "Property that associates an ErrorDistribution with an ErrorModel." ; - obo:IAO_0000114 obo:IAO_0000125 ; + obo:IAO_0000114 obo:IAO_0000122 ; rdfs:range nidm:ErrorDistribution ; @@ -872,9 +872,9 @@ http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#P-Value""" ; rdfs:range [ rdf:type rdfs:Datatype ; owl:onDatatype xsd:float ; - owl:withRestrictions ( [ xsd:minInclusive "0.0"^^xsd:float + owl:withRestrictions ( [ xsd:maxInclusive "1.0"^^xsd:float ] - [ xsd:maxInclusive "1.0"^^xsd:float + [ xsd:minInclusive "0.0"^^xsd:float ] ) ] . @@ -902,9 +902,9 @@ nidm:pValueFWER rdf:type owl:DatatypeProperty ; rdfs:range [ rdf:type rdfs:Datatype ; owl:onDatatype xsd:float ; - owl:withRestrictions ( [ xsd:minInclusive "0.0"^^xsd:float + owl:withRestrictions ( [ xsd:maxInclusive "1.0"^^xsd:float ] - [ xsd:maxInclusive "1.0"^^xsd:float + [ xsd:minInclusive "0.0"^^xsd:float ] ) ] . @@ -930,9 +930,9 @@ nidm:pValueUncorrected rdf:type owl:DatatypeProperty ; rdfs:range [ rdf:type rdfs:Datatype ; owl:onDatatype xsd:float ; - owl:withRestrictions ( [ xsd:minInclusive "0.0"^^xsd:float + owl:withRestrictions ( [ xsd:maxInclusive "1.0"^^xsd:float ] - [ xsd:maxInclusive "1.0"^^xsd:float + [ xsd:minInclusive "0.0"^^xsd:float ] ) ] . @@ -958,9 +958,9 @@ nidm:qValueFDR rdf:type owl:DatatypeProperty ; rdfs:range [ rdf:type rdfs:Datatype ; owl:onDatatype xsd:float ; - owl:withRestrictions ( [ xsd:minInclusive "0.0"^^xsd:float + owl:withRestrictions ( [ xsd:maxInclusive "1.0"^^xsd:float ] - [ xsd:maxInclusive "1.0"^^xsd:float + [ xsd:minInclusive "0.0"^^xsd:float ] ) ] . @@ -1574,9 +1574,9 @@ fsl:NonParametricSymmetricDistribution rdf:type owl:Class ; rdfs:subClassOf nidm:ErrorDistribution ; - prov:definition "Probability distribution estimated empirically on the data assuming a symmetric probability distribution. Non-parametric distribution are usually estimated using permutation of the class labels or sign-flipping." ; + prov:definition "Probability distribution estimated empirically on the data assuming only symmetry of the probability distribution." ; - obo:IAO_0000114 obo:IAO_0000125 . + obo:IAO_0000114 obo:IAO_0000122 . @@ -1947,7 +1947,7 @@ nidm:ErrorDistribution rdf:type owl:Class ; obo:IAO_0000115 "Probability distribution used to model the error." ; - obo:IAO_0000114 obo:IAO_0000125 . + obo:IAO_0000114 obo:IAO_0000122 . @@ -2282,9 +2282,9 @@ nidm:NonParametricDistribution rdf:type owl:Class ; rdfs:subClassOf nidm:ErrorDistribution ; - prov:definition "Probability distribution estimated empirically on the data without assumption on the shape of the probability distribution. Non-parametric distribution are usually estimated using permutation of the class labels or sign-flipping." ; + prov:definition "Probability distribution estimated empirically on the data without assumptions on the shape of the probability distribution." ; - obo:IAO_0000114 obo:IAO_0000125 . + obo:IAO_0000114 obo:IAO_0000122 . From a8fb7dd9fa421883a75e68205f9ad1747918388c Mon Sep 17 00:00:00 2001 From: cmaumet Date: Fri, 7 Nov 2014 16:19:58 +0000 Subject: [PATCH 14/14] Update terms README --- nidm/nidm-results/terms/README.md | 14 -------------- 1 file changed, 14 deletions(-) diff --git a/nidm/nidm-results/terms/README.md b/nidm/nidm-results/terms/README.md index a58559076..234233fe7 100644 --- a/nidm/nidm-results/terms/README.md +++ b/nidm/nidm-results/terms/README.md @@ -6,10 +6,6 @@

Classes

Curation StatusTerm
fsl:NonParametricSymmetricDistribution: Probability distribution defined empirically on the data assuming a symmetric probability distribution. Non-parametric distribution are usually defined using permutation of the class labels or sign-flipping.
nidm:ContrastMap: A map whose value at each location is statistical contrast estimate.nidm:HeightThreshold: A numerical value that establishes a bound on a range of voxelwise or vertex-wise defined statistic.
nidm:NonParametricDistribution: Probability distribution defined empirically on the data without assumption on the shape of the probability distribution. Non-parametric distribution are usually defined using permutation of the class labels or sign-flipping.
nidm:ResidualMeanSquaresMap: A map whose value at each location is the residual of the mean squares fit to the data. (editor: KH)nidm:Data xsd:boolean
nidm:hasErrorDistribution: Property that associates a NoiseDistribution with a NoiseModel.nidm:ErrorModel nidm:ErrorDistribution
nidm:maskedMedian: Median value considering only in-mask voxels. Useful diagnostic when computed on grand mean image when grandMeanScaling is TRUE, as the median should be close to targetIntensity. (editor: TN, Naming discussed at: https://github.com/incf-nidash/nidm/issues/70)
Curation StatusTerm
fsl:NonParametricSymmetricDistribution: Probability distribution defined empirically on the data assuming a symmetric probability distribution. Non-parametric distribution are usually defined using permutation of the class labels or sign-flipping.fsl:NonParametricSymmetricDistribution: Probability distribution estimated empirically on the data assuming a symmetric probability distribution. Non-parametric distribution are usually estimated using permutation of the class labels or sign-flipping.
nidm:NonParametricDistribution: Probability distribution defined empirically on the data without assumption on the shape of the probability distribution. Non-parametric distribution are usually defined using permutation of the class labels or sign-flipping.nidm:NonParametricDistribution: Probability distribution estimated empirically on the data without assumption on the shape of the probability distribution. Non-parametric distribution are usually estimated using permutation of the class labels or sign-flipping.
nidm:hasErrorDistribution: Property that associates a NoiseDistribution with a NoiseModel.nidm:hasErrorDistribution: Property that associates an ErrorDistribution with an ErrorModel. nidm:ErrorModel nidm:ErrorDistribution
- - - - @@ -39,10 +35,6 @@ - - - - @@ -149,12 +141,6 @@ - - - - - -
Curation StatusTerm
fsl:NonParametricSymmetricDistribution: Probability distribution estimated empirically on the data assuming a symmetric probability distribution. Non-parametric distribution are usually estimated using permutation of the class labels or sign-flipping.
nidm:ContrastMap: A map whose value at each location is statistical contrast estimate.nidm:HeightThreshold: A numerical value that establishes a bound on a range of voxelwise or vertex-wise defined statistic.
nidm:NonParametricDistribution: Probability distribution estimated empirically on the data without assumption on the shape of the probability distribution. Non-parametric distribution are usually estimated using permutation of the class labels or sign-flipping.
nidm:ResidualMeanSquaresMap: A map whose value at each location is the residual of the mean squares fit to the data. (editor: KH)nidm:Data xsd:boolean
nidm:hasErrorDistribution: Property that associates an ErrorDistribution with an ErrorModel.nidm:ErrorModel nidm:ErrorDistribution
nidm:maskedMedian: Median value considering only in-mask voxels. Useful diagnostic when computed on grand mean image when grandMeanScaling is TRUE, as the median should be close to targetIntensity. (editor: TN, Naming discussed at: https://github.com/incf-nidash/nidm/issues/70)