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test files #10

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234 changes: 234 additions & 0 deletions tests/data/basic.owl.ttl
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@prefix : <http://example.org/> .
@prefix a: <http://example.org/a/> .
@prefix x: <http://example.org/x/> .
@prefix y: <http://example.org/y/> .
@prefix z: <http://example.org/z/> .
@prefix owl: <http://www.w3.org/2002/07/owl#> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix xml: <http://www.w3.org/XML/1998/namespace> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix oio: <http://www.geneontology.org/formats/oboInOwl#> .
@prefix xref: <http://www.geneontology.org/formats/oboInOwl#hasDbXref> .
@prefix skos: <http://www.w3.org/2004/02/skos/core#> .
@prefix UBERON: <http://purl.obolibrary.org/obo/UBERON_> .
@prefix sh: <http://www.w3.org/ns/shacl#> .
@prefix category: <http://dbpedia.org/ontology/category> .
@prefix anatomy: <https://w3id.org/biolink/vocab/AnatomicalEntity> .
@base <http://example.org> .
@prefix inca: <https://w3id.org/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 .
86 changes: 86 additions & 0 deletions tests/data/basic.ptable.tsv
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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 0.05883724076724989 0.05883724076724989 0.7646510369310004 0.11767448153449978
x:bone_element z:bone_element 0.06530096874093538 0.06530096874093538 0.7387961250362586 0.1306019374818707
x:bone_element z:bone_tissue 0.18469903125906462 0.18469903125906462 0.2612038749637414 0.3693980625181293
x:bone_tissue y:bone 0.11634950965480911 0.11634950965480911 0.5346019613807635 0.23269901930961823
x:bone_tissue z:bone_element 0.18469903125906462 0.18469903125906462 0.2612038749637414 0.3693980625181293
x:bone_tissue z:bone_tissue 0.06530096874093538 0.06530096874093538 0.7387961250362586 0.1306019374818707
x:eye y:eye 0.06530096874093538 0.06530096874093538 0.7387961250362586 0.1306019374818707
x:eye z:eye 0.06530096874093538 0.06530096874093538 0.7387961250362586 0.1306019374818707
x:eyeball z:eyeball 0.06530096874093538 0.06530096874093538 0.7387961250362586 0.1306019374818707
x:foot y:foot 0.06530096874093538 0.06530096874093538 0.7387961250362586 0.1306019374818707
x:foot z:foot 0.03755527620558374 0.03755527620558374 0.8497788951776651 0.07511055241116743
x:hand y:hand 0.04468440230640902 0.04468440230640902 0.8212623907743639 0.08936880461281804
x:hand z:hand 0.03755527620558374 0.03755527620558374 0.8497788951776651 0.07511055241116743
x:heart y:heart 0.03982139852307098 0.03982139852307098 0.8407144059077161 0.07964279704614197
x:heart z:heart 0.06530096874093538 0.06530096874093538 0.7387961250362586 0.1306019374818707
x:heart z:organ 0.06530096874093538 0.06530096874093538 0.7387961250362586 0.1306019374818707
x:hindlimb z:hindlimb 0.02953594098668788 0.02953594098668788 0.8818562360532485 0.05907188197337576
x:liver y:liver 0.03982139852307098 0.03982139852307098 0.8407144059077161 0.07964279704614197
x:liver z:liver 0.06530096874093538 0.06530096874093538 0.7387961250362586 0.1306019374818707
x:liver z:organ 0.06530096874093538 0.06530096874093538 0.7387961250362586 0.1306019374818707
x:lung y:lung 0.03982139852307098 0.03982139852307098 0.8407144059077161 0.07964279704614197
x:lung z:lung 0.06530096874093538 0.06530096874093538 0.7387961250362586 0.1306019374818707
x:lung z:organ 0.06530096874093538 0.06530096874093538 0.7387961250362586 0.1306019374818707
x:organ y:organ 0.03982139852307098 0.03982139852307098 0.8407144059077161 0.07964279704614197
x:organ z:organ 0.02953594098668788 0.02953594098668788 0.8818562360532485 0.05907188197337576
x:region y:region 0.03982139852307098 0.03982139852307098 0.8407144059077161 0.07964279704614197
x:region z:region 0.02953594098668788 0.02953594098668788 0.8818562360532485 0.05907188197337576
x:tissue y:tissue 0.03982139852307098 0.03982139852307098 0.8407144059077161 0.07964279704614197
x:tissue z:tissue 0.02953594098668788 0.02953594098668788 0.8818562360532485 0.05907188197337576
y:appendage x:appendage 0.03982139852307098 0.03982139852307098 0.8407144059077161 0.07964279704614197
y:appendage z:appendage 0.03982139852307098 0.03982139852307098 0.8407144059077161 0.07964279704614197
y:bone x:bone_element 0.05883724076724989 0.05883724076724989 0.7646510369310004 0.11767448153449978
y:bone x:bone_tissue 0.11634950965480911 0.11634950965480911 0.5346019613807635 0.23269901930961823
y:bone z:bone_element 0.06530096874093538 0.06530096874093538 0.7387961250362586 0.1306019374818707
y:bone z:bone_tissue 0.11634950965480911 0.11634950965480911 0.5346019613807635 0.23269901930961823
y:eye x:eye 0.06530096874093538 0.06530096874093538 0.7387961250362586 0.1306019374818707
y:eye z:eye 0.06530096874093538 0.06530096874093538 0.7387961250362586 0.1306019374818707
y:foot x:foot 0.06530096874093538 0.06530096874093538 0.7387961250362586 0.1306019374818707
y:foot z:foot 0.06530096874093538 0.06530096874093538 0.7387961250362586 0.1306019374818707
y:hand x:hand 0.04468440230640902 0.04468440230640902 0.8212623907743639 0.08936880461281804
y:hand z:hand 0.04468440230640902 0.04468440230640902 0.8212623907743639 0.08936880461281804
y:heart x:heart 0.03982139852307098 0.03982139852307098 0.8407144059077161 0.07964279704614197
y:heart z:heart 0.06530096874093538 0.06530096874093538 0.7387961250362586 0.1306019374818707
y:liver x:liver 0.03982139852307098 0.03982139852307098 0.8407144059077161 0.07964279704614197
y:liver z:liver 0.06530096874093538 0.06530096874093538 0.7387961250362586 0.1306019374818707
y:lung x:lung 0.03982139852307098 0.03982139852307098 0.8407144059077161 0.07964279704614197
y:lung z:lung 0.06530096874093538 0.06530096874093538 0.7387961250362586 0.1306019374818707
y:organ x:organ 0.03982139852307098 0.03982139852307098 0.8407144059077161 0.07964279704614197
y:organ z:organ 0.03982139852307098 0.03982139852307098 0.8407144059077161 0.07964279704614197
y:region x:region 0.03982139852307098 0.03982139852307098 0.8407144059077161 0.07964279704614197
y:region z:region 0.03982139852307098 0.03982139852307098 0.8407144059077161 0.07964279704614197
y:tissue x:tissue 0.03982139852307098 0.03982139852307098 0.8407144059077161 0.07964279704614197
y:tissue z:tissue 0.03982139852307098 0.03982139852307098 0.8407144059077161 0.07964279704614197
z:appendage x:appendage 0.02953594098668788 0.02953594098668788 0.8818562360532485 0.05907188197337576
z:appendage y:appendage 0.03982139852307098 0.03982139852307098 0.8407144059077161 0.07964279704614197
z:bone_element x:bone_element 0.06530096874093538 0.06530096874093538 0.7387961250362586 0.1306019374818707
z:bone_element x:bone_tissue 0.18469903125906462 0.18469903125906462 0.2612038749637414 0.3693980625181293
z:bone_element y:bone 0.06530096874093538 0.06530096874093538 0.7387961250362586 0.1306019374818707
z:bone_tissue x:bone_element 0.18469903125906462 0.18469903125906462 0.2612038749637414 0.3693980625181293
z:bone_tissue x:bone_tissue 0.06530096874093538 0.06530096874093538 0.7387961250362586 0.1306019374818707
z:bone_tissue y:bone 0.11634950965480911 0.11634950965480911 0.5346019613807635 0.23269901930961823
z:eye x:eye 0.06530096874093538 0.06530096874093538 0.7387961250362586 0.1306019374818707
z:eye y:eye 0.06530096874093538 0.06530096874093538 0.7387961250362586 0.1306019374818707
z:eyeball x:eyeball 0.06530096874093538 0.06530096874093538 0.7387961250362586 0.1306019374818707
z:foot x:foot 0.03755527620558374 0.03755527620558374 0.8497788951776651 0.07511055241116743
z:foot y:foot 0.06530096874093538 0.06530096874093538 0.7387961250362586 0.1306019374818707
z:hand x:hand 0.03755527620558374 0.03755527620558374 0.8497788951776651 0.07511055241116743
z:hand y:hand 0.04468440230640902 0.04468440230640902 0.8212623907743639 0.08936880461281804
z:heart x:heart 0.06530096874093538 0.06530096874093538 0.7387961250362586 0.1306019374818707
z:heart y:heart 0.06530096874093538 0.06530096874093538 0.7387961250362586 0.1306019374818707
z:hindlimb x:hindlimb 0.02953594098668788 0.02953594098668788 0.8818562360532485 0.05907188197337576
z:liver x:liver 0.06530096874093538 0.06530096874093538 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
3 changes: 3 additions & 0 deletions tests/data/empty.omn
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Ontology: <http://example.org/empty.owl>

## empty ontology
4 changes: 4 additions & 0 deletions tests/data/prefixes.yaml
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a: http://example.org/a/
x: http://example.org/x/
y: http://example.org/y/
z: http://example.org/z/