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#97 basic dosdp templates implemented
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src/patterns/data/default/CCN202002013_equivalent_reification.tsv
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src/patterns/data/default/CCN202002013_minimal_markers.tsv
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src/patterns/data/default/CCN202002013_non_taxonomy_classification.tsv
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| defined_class Classification | ||
| http://www.semanticweb.org/brain_data_standards/AllenDendClass_CS202002013_28 CL:4023017 | ||
| http://www.semanticweb.org/brain_data_standards/AllenDendClass_CS202002013_29 CL:4023017 | ||
| http://www.semanticweb.org/brain_data_standards/AllenDendClass_CS202002013_30 CL:4023017 | ||
| http://www.semanticweb.org/brain_data_standards/AllenDendClass_CS202002013_31 CL:4023017 | ||
| http://www.semanticweb.org/brain_data_standards/AllenDendClass_CS202002013_32 CL:4023017 | ||
| http://www.semanticweb.org/brain_data_standards/AllenDendClass_CS202002013_33 CL:4023017 | ||
| http://www.semanticweb.org/brain_data_standards/AllenDendClass_CS202002013_34 CL:4023017 | ||
| http://www.semanticweb.org/brain_data_standards/AllenDendClass_CS202002013_35 CL:4023017 | ||
| http://www.semanticweb.org/brain_data_standards/AllenDendClass_CS202002013_36 CL:4023017 | ||
| http://www.semanticweb.org/brain_data_standards/AllenDendClass_CS202002013_37 CL:4023017 | ||
| http://www.semanticweb.org/brain_data_standards/AllenDendClass_CS202002013_38 CL:4023017 | ||
| http://www.semanticweb.org/brain_data_standards/AllenDendClass_CS202002013_39 CL:4023017 | ||
| http://www.semanticweb.org/brain_data_standards/AllenDendClass_CS202002013_40 CL:4023017 | ||
| http://www.semanticweb.org/brain_data_standards/AllenDendClass_CS202002013_41 CL:4023017 | ||
| http://www.semanticweb.org/brain_data_standards/AllenDendClass_CS202002013_42 CL:4023017 | ||
| http://www.semanticweb.org/brain_data_standards/AllenDendClass_CS202002013_43 CL:4023017 | ||
| http://www.semanticweb.org/brain_data_standards/AllenDendClass_CS202002013_44 CL:4023017 | ||
| http://www.semanticweb.org/brain_data_standards/AllenDendClass_CS202002013_45 CL:4023017 | ||
| http://www.semanticweb.org/brain_data_standards/AllenDendClass_CS202002013_46 CL:4023017 | ||
| http://www.semanticweb.org/brain_data_standards/AllenDendClass_CS202002013_47 CL:4023017 | ||
| http://www.semanticweb.org/brain_data_standards/AllenDendClass_CS202002013_48 CL:4023018 | ||
| http://www.semanticweb.org/brain_data_standards/AllenDendClass_CS202002013_49 CL:4023018 | ||
| http://www.semanticweb.org/brain_data_standards/AllenDendClass_CS202002013_50 CL:4023018 | ||
| http://www.semanticweb.org/brain_data_standards/AllenDendClass_CS202002013_51 CL:4023018 | ||
| http://www.semanticweb.org/brain_data_standards/AllenDendClass_CS202002013_52 CL:4023018 | ||
| http://www.semanticweb.org/brain_data_standards/AllenDendClass_CS202002013_53 CL:4023018 | ||
| http://www.semanticweb.org/brain_data_standards/AllenDendClass_CS202002013_54 CL:4023018 | ||
| http://www.semanticweb.org/brain_data_standards/AllenDendClass_CS202002013_55 CL:4023018 | ||
| http://www.semanticweb.org/brain_data_standards/AllenDendClass_CS202002013_56 CL:4023018 | ||
| http://www.semanticweb.org/brain_data_standards/AllenDendClass_CS202002013_57 CL:4023018 | ||
| http://www.semanticweb.org/brain_data_standards/AllenDendClass_CS202002013_91 CL:0000125 | ||
| http://www.semanticweb.org/brain_data_standards/AllenDendClass_CS202002013_92 CL:0000125 | ||
| http://www.semanticweb.org/brain_data_standards/AllenDendClass_CS202002013_93 CL:0000125 | ||
| http://www.semanticweb.org/brain_data_standards/AllenDendClass_CS202002013_94 CL:0000125 | ||
| http://www.semanticweb.org/brain_data_standards/AllenDendClass_CS202002013_95 CL:0000125 | ||
| http://www.semanticweb.org/brain_data_standards/AllenDendClass_CS202002013_96 CL:0000125 | ||
| http://www.semanticweb.org/brain_data_standards/AllenDendClass_CS202002013_97 CL:0000125 | ||
| http://www.semanticweb.org/brain_data_standards/AllenDendClass_CS202002013_98 CL:0000125 | ||
| http://www.semanticweb.org/brain_data_standards/AllenDendClass_CS202002013_99 CL:0000125 | ||
| http://www.semanticweb.org/brain_data_standards/AllenDendClass_CS202002013_100 CL:0000125 | ||
| http://www.semanticweb.org/brain_data_standards/AllenDendClass_CS202002013_101 CL:0000125 | ||
| http://www.semanticweb.org/brain_data_standards/AllenDendClass_CS202002013_102 CL:0000125 | ||
| http://www.semanticweb.org/brain_data_standards/AllenDendClass_CS202002013_103 CL:0000125 | ||
| http://www.semanticweb.org/brain_data_standards/AllenDendClass_CS202002013_104 CL:0000125 | ||
| http://www.semanticweb.org/brain_data_standards/AllenDendClass_CS202002013_105 CL:0000125 | ||
| http://www.semanticweb.org/brain_data_standards/AllenDendClass_CS202002013_106 CL:0000125 | ||
| http://www.semanticweb.org/brain_data_standards/AllenDendClass_CS202002013_107 CL:0000125 | ||
| http://www.semanticweb.org/brain_data_standards/AllenDendClass_CS202002013_108 CL:0000125 | ||
| http://www.semanticweb.org/brain_data_standards/AllenDendClass_CS202002013_109 CL:0000125 | ||
| http://www.semanticweb.org/brain_data_standards/AllenDendClass_CS202002013_110 CL:0000125 | ||
| http://www.semanticweb.org/brain_data_standards/AllenDendClass_CS202002013_111 CL:0000125 | ||
| http://www.semanticweb.org/brain_data_standards/AllenDendClass_CS202002013_112 CL:0000125 | ||
| http://www.semanticweb.org/brain_data_standards/AllenDendClass_CS202002013_113 CL:0000125 | ||
| http://www.semanticweb.org/brain_data_standards/AllenDendClass_CS202002013_114 CL:0000125 | ||
| http://www.semanticweb.org/brain_data_standards/AllenDendClass_CS202002013_115 CL:0000125 | ||
| http://www.semanticweb.org/brain_data_standards/AllenDendClass_CS202002013_116 CL:0000125 | ||
| http://www.semanticweb.org/brain_data_standards/AllenDendClass_CS202002013_114 CL:0000881 | ||
| http://www.semanticweb.org/brain_data_standards/AllenDendClass_CS202002013_115 CL:0000881 | ||
| http://www.semanticweb.org/brain_data_standards/AllenDendClass_CS202002013_116 CL:0000881 | ||
| http://www.semanticweb.org/brain_data_standards/AllenDendClass_CS202002013_21 CL:4023007 | ||
| http://www.semanticweb.org/brain_data_standards/AllenDendClass_CS202002013_22 CL:4023007 | ||
| http://www.semanticweb.org/brain_data_standards/AllenDendClass_CS202002013_23 CL:4023007 | ||
| http://www.semanticweb.org/brain_data_standards/AllenDendClass_CS202002013_24 CL:4023007 | ||
| http://www.semanticweb.org/brain_data_standards/AllenDendClass_CS202002013_25 CL:4023007 | ||
| http://www.semanticweb.org/brain_data_standards/AllenDendClass_CS202002013_30 CL:4023027 | ||
| http://www.semanticweb.org/brain_data_standards/AllenDendClass_CS202002013_31 CL:4023027 | ||
| http://www.semanticweb.org/brain_data_standards/AllenDendClass_CS202002013_32 CL:4023027 | ||
| http://www.semanticweb.org/brain_data_standards/AllenDendClass_CS202002013_70 CL:4023045 | ||
| http://www.semanticweb.org/brain_data_standards/AllenDendClass_CS202002013_71 CL:4023045 | ||
| http://www.semanticweb.org/brain_data_standards/AllenDendClass_CS202002013_72 CL:4023044 | ||
| http://www.semanticweb.org/brain_data_standards/AllenDendClass_CS202002013_73 CL:4023044 |
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| pattern_name: brainCellClasses | ||
| pattern_iri: http://purl.obolibrary.org/obo/odk/brainCellClasses.yaml | ||
| description: "Class template for BDS." | ||
|
|
||
| classes: | ||
| "cell": "CL:0000000" | ||
| "thing": "owl:Thing" | ||
|
|
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| relations: | ||
| expresses: "RO:0002292" | ||
|
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| annotationProperties: | ||
| skosPrefLabel: "skos:prefLabel" | ||
| hasExactSynonym: "oboInOwl:hasExactSynonym" | ||
| rdfsComment: "rdfs:comment" | ||
| hasDbXref: "oboInOwl:hasDbXref" | ||
|
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| list_vars: | ||
| Expresses: "'thing'" | ||
|
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| vars: | ||
| Classification: "'cell'" | ||
|
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| data_list_vars: | ||
| Synonyms_from_taxonomy: "xsd:string" | ||
| Curated_synonyms: "xsd:string" | ||
| Classification_pub: "xsd:string" | ||
| Expresses_comment: "xsd:string" | ||
| Expresses_pub: "xsd:string" | ||
|
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| data_vars: | ||
| prefLabel: "xsd:string" | ||
| Comment: "xsd:string" | ||
| Classification_comment: "xsd:string" | ||
|
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| comment: | ||
| text: "%s" | ||
| vars: | ||
| - Comment | ||
|
|
||
| logical_axioms: | ||
| - axiom_type: subClassOf | ||
| text: "%s" | ||
| vars: | ||
| - Classification | ||
| annotations: | ||
| - annotationProperty: rdfsComment | ||
| text: "%s" | ||
| vars: | ||
| - Classification_comment | ||
| - annotationProperty: hasDbXref | ||
| multi_clause: | ||
| sep: " " | ||
| clauses: | ||
| - text: '%s' | ||
| vars: | ||
| - Classification_pub | ||
| - axiom_type: subClassOf | ||
| multi_clause: | ||
| sep: " and " | ||
| clauses: | ||
| - text: "'expresses' some %s" | ||
| vars: | ||
| - Expresses | ||
| annotations: | ||
| - annotationProperty: rdfsComment | ||
| text: "%s" | ||
| vars: | ||
| - Expresses_comment | ||
| - annotationProperty: hasDbXref | ||
| multi_clause: | ||
| sep: " " | ||
| clauses: | ||
| - text: '%s' | ||
| vars: | ||
| - Expresses_pub | ||
|
|
||
| annotations: | ||
| - annotationProperty: skosPrefLabel | ||
| text: "%s" | ||
| vars: | ||
| - prefLabel | ||
| - annotationProperty: hasExactSynonym | ||
| multi_clause: | ||
| sep: " " | ||
| clauses: | ||
| - text: '%s' | ||
| vars: | ||
| - Synonyms_from_taxonomy | ||
| - annotationProperty: hasExactSynonym | ||
| multi_clause: | ||
| sep: " " | ||
| clauses: | ||
| - text: '%s' | ||
| vars: | ||
| - Curated_synonyms |
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24
src/patterns/dosdp-patterns/taxonomy_equivalent_class.yaml
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| pattern_name: brainCellEquivalentClasses | ||
| pattern_iri: http://purl.obolibrary.org/obo/odk/brainCellEquivalentClasses.yaml | ||
| description: "Equivalent class template for BDS." | ||
|
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| classes: | ||
| "thing": "owl:Thing" | ||
| "native_cell": "CL:0000003" | ||
|
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| relations: | ||
| has_exemplar: "http://www.semanticweb.org/brain_data_standards/helper.owl#has_exemplar" | ||
|
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| vars: | ||
| Exemplar_SC: "'thing'" | ||
| Exemplar: "'thing'" | ||
|
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| logical_axioms: | ||
| - axiom_type: subClassOf | ||
| text: "'has_exemplar' value %s" | ||
| vars: | ||
| - Exemplar_SC | ||
| - axiom_type: subClassOf | ||
| text: "'native_cell' and 'has_exemplar' value %s" | ||
| vars: | ||
| - Exemplar |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,35 @@ | ||
| pattern_name: brainCellMinimalMarkers | ||
| pattern_iri: http://purl.obolibrary.org/obo/odk/brainCellMinimalMarkers.yaml | ||
| description: "Minimal marker expression template for BDS." | ||
|
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| classes: | ||
| "thing": "owl:Thing" | ||
|
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| relations: | ||
| expresses: "RO:0002292" | ||
| partOf: "BFO:0000050" | ||
| hasSomaLocation: "RO:0002100" | ||
|
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| list_vars: | ||
| Markers: "'thing'" | ||
|
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| vars: | ||
| part_of: "'thing'" | ||
| has_soma_location: "'thing'" | ||
|
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| logical_axioms: | ||
| - axiom_type: subClassOf | ||
| multi_clause: | ||
| sep: " and " | ||
| clauses: | ||
| - text: "'expresses' some %s" | ||
| vars: | ||
| - Markers | ||
| - axiom_type: subClassOf | ||
| text: "'partOf' some %s" | ||
| vars: | ||
| - part_of | ||
| - axiom_type: subClassOf | ||
| text: "'hasSomaLocation' some %s" | ||
| vars: | ||
| - has_soma_location |
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15
src/patterns/dosdp-patterns/taxonomy_non_taxonomy_classification.yaml
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| pattern_name: brainCellNonTaxonClassification | ||
| pattern_iri: http://purl.obolibrary.org/obo/odk/brainCellNonTaxonClassification.yaml | ||
| description: "Non-taxonomy classification template for BDS." | ||
|
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| classes: | ||
| "cell": "CL:0000000" | ||
|
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| vars: | ||
| Classification: "'cell'" | ||
|
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| logical_axioms: | ||
| - axiom_type: subClassOf | ||
| text: "%s" | ||
| vars: | ||
| - Classification |