diff --git a/tests/data/basic.owl.ttl b/tests/data/basic.owl.ttl new file mode 100644 index 00000000..cb03d880 --- /dev/null +++ b/tests/data/basic.owl.ttl @@ -0,0 +1,234 @@ +@prefix : . +@prefix a: . +@prefix x: . +@prefix y: . +@prefix z: . +@prefix owl: . +@prefix rdf: . +@prefix xml: . +@prefix xsd: . +@prefix rdfs: . +@prefix oio: . +@prefix xref: . +@prefix skos: . +@prefix UBERON: . +@prefix sh: . +@prefix category: . +@prefix anatomy: . +@base . +@prefix inca: . + + +:test.owl rdf:type owl:Ontology . + +[ inca:pattern "structure" ; + inca:replacement "" +]. + + +[ sh:declare + [ sh:prefix "biolink" ; sh:namespace "https://w3id.org/biolink/vocab/"], + [ sh:prefix "a" ; sh:namespace "http://example.org/a/"], + [ sh:prefix "x" ; sh:namespace "http://example.org/x/"], + [ sh:prefix "y" ; sh:namespace "http://example.org/y/"], + [ sh:prefix "z" ; sh:namespace "http://example.org/z/"] + ] . + + rdfs:label a owl:AnnotationProperty . + + +## X ontology (base) + +x:organ a owl:Class ; category: anatomy: ; + rdfs:label "organ"@en . +x:appendage a owl:Class ; category: anatomy: ; + rdfs:label "appendage" . +x:tissue a owl:Class ; category: anatomy: ; + rdfs:label "tissue" . +x:region a owl:Class ; category: anatomy: ; + rdfs:label "region" . + +x:lung a owl:Class ; category: anatomy: ; + rdfs:label "lung" ; + xref: "UBERON:0002048" ; # lung + xref: "BAD:ORGAN" ; ## deliberately broader + rdfs:subClassOf x:organ . + +x:heart a owl:Class ; category: anatomy: ; + rdfs:label "heart" ; + xref: "UBERON:0000948" ; ## heart + xref: "BAD:ORGAN" ; ## deliberately broader + rdfs:subClassOf x:organ . + +x:liver a owl:Class ; category: anatomy: ; + rdfs:label "liver" ; + xref: "UBERON:0002107" ; ## liver + xref: "BAD:ORGAN" ; ## deliberately broader + rdfs:subClassOf x:organ . + +x:bone_element a owl:Class ; category: anatomy: ; + rdfs:label "bone element" ; + xref: "UBERON:0001474" ; ## bone element + oio:hasBroadSynonym "bone" ; + rdfs:subClassOf x:organ . + +x:bone_tissue a owl:Class ; category: anatomy: ; + rdfs:label "bone tissue" ; + xref: "UBERON:0002481" ; ## bone tissue + oio:hasBroadSynonym "bone" ; + rdfs:subClassOf x:tissue . + +x:eyeball a owl:Class ; category: anatomy: ; + rdfs:label "eyeball" ; + xref: "UBERON:0010230" ; ## eyeball of camera-type eye + rdfs:subClassOf x:region . + +x:eye a owl:Class ; category: anatomy: ; + rdfs:label "eye" ; + xref: "UBERON:0000970" ; ## eye + rdfs:subClassOf x:organ . + +x:hand a owl:Class ; category: anatomy: ; + rdfs:label "manus" ; + oio:hasExactSynonym "hand" ; + xref: "UBERON:0002398" ; ## manus + rdfs:subClassOf x:appendage . + +x:foot a owl:Class ; category: anatomy: ; + rdfs:label "pes" ; + oio:hasExactSynonym "foot" ; + xref: "UBERON:0002387" ; ## pes + rdfs:subClassOf x:appendage . + +x:obsolete_leg a owl:Class ; category: anatomy: ; + rdfs:label "leg" ; + oio:hasRelatedSynonym "hindlimb" ; + owl:deprecated "true"^^xsd:boolean . + +x:hindlimb a owl:Class ; category: anatomy: ; + rdfs:label "hindlimb" ; + rdfs:subClassOf x:appendage . + +## Y ontology +## this ontology is less precise and has a single concept for bone and eye + +y:organ a owl:Class ; category: anatomy: ; + rdfs:label "organs" . +y:appendage a owl:Class ; category: anatomy: ; + rdfs:label "appendages" . +y:tissue a owl:Class ; category: anatomy: ; + rdfs:label "tissues" . +y:region a owl:Class ; category: anatomy: ; + rdfs:label "regions" . + +y:lung a owl:Class ; category: anatomy: ; + rdfs:label "lungs" ; + xref: "UBERON:0002048" ; # lung + rdfs:subClassOf y:organ . + +y:heart a owl:Class ; category: anatomy: ; + rdfs:label "hearts" ; + xref: "UBERON:0000948" ; ## heart + rdfs:subClassOf y:organ . + +y:liver a owl:Class ; category: anatomy: ; + rdfs:label "livers" ; + xref: "UBERON:0002107" ; ## liver + rdfs:subClassOf y:organ . + +y:bone a owl:Class ; category: anatomy: ; + rdfs:label "bones" ; + xref: "UBERON:0001474" ; ## bone element + oio:hasRelatedSynonym "bone element" ; + rdfs:subClassOf y:organ . + +y:eye a owl:Class ; category: anatomy: ; + rdfs:label "eyes" ; + xref: "UBERON:0000970" ; ## eye + rdfs:subClassOf y:organ . + +y:hand a owl:Class ; category: anatomy: ; + rdfs:label "hands" ; + xref: "UBERON:0002398" ; ## manus + rdfs:subClassOf y:appendage . + +y:foot a owl:Class ; category: anatomy: ; + rdfs:label "feet" ; + xref: "UBERON:0002387" ; ## pes + rdfs:subClassOf y:appendage . + +y:leg a owl:Class ; category: anatomy: ; + rdfs:label "legs" ; + oio:hasExactSynonym "leg" ; + rdfs:subClassOf y:appendage . + +## Z ontology + +z:organ a owl:Class ; category: anatomy: ; + xref: "BAD:ORGAN" ; ## deliberately broader + rdfs:label "ORGAN" . +z:appendage a owl:Class ; category: anatomy: ; + rdfs:label "APPENDAGE" . +z:tissue a owl:Class ; category: anatomy: ; + rdfs:label "TISSUE" . +z:region a owl:Class ; category: anatomy: ; + rdfs:label "REGION" . + +z:lung a owl:Class ; category: anatomy: ; + xref: "UBERON:0002048" ; # lung + rdfs:subClassOf z:organ . + +z:heart a owl:Class ; category: anatomy: ; + xref: "UBERON:0000948" ; ## heart + rdfs:subClassOf z:organ . + +z:liver a owl:Class ; category: anatomy: ; + xref: "UBERON:0002107" ; ## liver + rdfs:subClassOf z:organ . + +z:bone_element a owl:Class ; category: anatomy: ; + xref: "UBERON:0001474" ; ## bone element + oio:hasBroadSynonym "bone" ; + rdfs:subClassOf z:organ . + +z:bone_tissue a owl:Class ; category: anatomy: ; + xref: "UBERON:0002481" ; ## bone tissue + oio:hasBroadSynonym "bone" ; + rdfs:subClassOf z:tissue . + +z:eyeball a owl:Class ; category: anatomy: ; + xref: "UBERON:0010230" ; ## eyeball of camera-type eye + rdfs:subClassOf z:region . + +z:eye a owl:Class ; category: anatomy: ; + xref: "UBERON:0000970" ; ## eye + rdfs:subClassOf z:organ . + +z:hand a owl:Class ; category: anatomy: ; + oio:hasExactSynonym "hand" ; + xref: "UBERON:0002398" ; ## manus + rdfs:subClassOf z:appendage . + +z:foot a owl:Class ; category: anatomy: ; + oio:hasExactSynonym "foot" ; + xref: "UBERON:0002387" ; ## pes + rdfs:subClassOf z:appendage . + +z:hindlimb a owl:Class ; category: anatomy: ; + rdfs:label "hindlimb" ; + rdfs:subClassOf z:appendage . + +z:tail a owl:Class ; category: anatomy: ; + rdfs:label "tail" ; + rdfs:subClassOf z:appendage . + +x:tail_structure a owl:Class ; category: anatomy: ; + rdfs:label "tail structure" ; + rdfs:subClassOf z:appendage . + +a:bone_of_hand a owl:Class ; category: anatomy: ; + rdfs:label "bone of hand" ; + rdfs:subClassOf a:organ . +a:bone_of_foot a owl:Class ; category: anatomy: ; + rdfs:label "bone of foot" ; + rdfs:subClassOf a:organ . diff --git a/tests/data/basic.ptable.tsv b/tests/data/basic.ptable.tsv new file mode 100644 index 00000000..e44eb79e --- /dev/null +++ b/tests/data/basic.ptable.tsv @@ -0,0 +1,86 @@ +x:appendage y:appendage 0.03982139852307098 0.03982139852307098 0.8407144059077161 0.07964279704614197 +x:appendage z:appendage 0.02953594098668788 0.02953594098668788 0.8818562360532485 0.05907188197337576 +x:bone_element y:bone 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0.7387961250362586 0.1306019374818707 +z:liver y:liver 0.06530096874093538 0.06530096874093538 0.7387961250362586 0.1306019374818707 +z:lung x:lung 0.06530096874093538 0.06530096874093538 0.7387961250362586 0.1306019374818707 +z:lung y:lung 0.06530096874093538 0.06530096874093538 0.7387961250362586 0.1306019374818707 +z:organ x:heart 0.06530096874093538 0.06530096874093538 0.7387961250362586 0.1306019374818707 +z:organ x:liver 0.06530096874093538 0.06530096874093538 0.7387961250362586 0.1306019374818707 +z:organ x:lung 0.06530096874093538 0.06530096874093538 0.7387961250362586 0.1306019374818707 +z:organ x:organ 0.02953594098668788 0.02953594098668788 0.8818562360532485 0.05907188197337576 +z:organ y:organ 0.03982139852307098 0.03982139852307098 0.8407144059077161 0.07964279704614197 +z:region x:region 0.02953594098668788 0.02953594098668788 0.8818562360532485 0.05907188197337576 +z:region y:region 0.03982139852307098 0.03982139852307098 0.8407144059077161 0.07964279704614197 +z:tissue x:tissue 0.02953594098668788 0.02953594098668788 0.8818562360532485 0.05907188197337576 +z:tissue y:tissue 0.03982139852307098 0.03982139852307098 0.8407144059077161 0.07964279704614197 diff --git a/tests/data/empty.omn b/tests/data/empty.omn new file mode 100644 index 00000000..cba7be27 --- /dev/null +++ b/tests/data/empty.omn @@ -0,0 +1,3 @@ +Ontology: + +## empty ontology diff --git a/tests/data/prefixes.yaml b/tests/data/prefixes.yaml new file mode 100644 index 00000000..66f72028 --- /dev/null +++ b/tests/data/prefixes.yaml @@ -0,0 +1,4 @@ +a: http://example.org/a/ +x: http://example.org/x/ +y: http://example.org/y/ +z: http://example.org/z/