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Merge pull request #164 from cerivs/3-15-2022
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migration to ODK 1.3.0
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@ybradford
ybradford authored Mar 15, 2022
2 parents dc76ef8 + 8f74dda commit 199faf5
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4 changes: 2 additions & 2 deletions src/ontology/imports/ro_import.owl
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Expand Up @@ -16,9 +16,9 @@
xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#"
xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
<owl:Ontology rdf:about="http://purl.obolibrary.org/obo/zfa/imports/ro_import.owl">
<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/zfa/releases/2022-02-28/imports/ro_import.owl"/>
<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/zfa/releases/2022-03-15/imports/ro_import.owl"/>
<dc:source rdf:resource="http://purl.obolibrary.org/obo/ro/releases/2022-02-07/ro.owl"/>
<owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2022-02-28</owl:versionInfo>
<owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2022-03-15</owl:versionInfo>
</owl:Ontology>


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1 change: 1 addition & 0 deletions src/ontology/reports/validate_profile_owl2dl_zfa.owl.txt
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@@ -0,0 +1 @@
OWL 2 DL Profile Report: [Ontology and imports closure in profile]
138 changes: 69 additions & 69 deletions src/ontology/reports/zfa-edit.obo-obo-report.tsv
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Expand Up @@ -3,59 +3,6 @@ ERROR duplicate_definition myotome somite 26 definition Portion of somite 16 tha
ERROR duplicate_definition myotome somite 16 definition Portion of somite 16 that gives rise to body wall muscle masses.
ERROR duplicate_definition posterior lateral line definition One of eight distinct lateral lines in the 4-day larva. A sensory system on the surface of the fish, consisting of small sensory patches (neuromasts) distributed in discrete lines over the body surface. The lateral line system is stimulated by local water displacements and vibrations, and detects propulsion of the fish through the water, as well as facilitating shoaling, prey capture, and predator and obstacle avoidance. (See Anatomical Atlas entry for <a href='http://zfin.org/zf_info/anatomy/dict/lat_line/lat_line.html'>lateral line</a> by T. Whitfield.)
ERROR duplicate_definition dorsal lateral line definition One of eight distinct lateral lines in the 4-day larva. A sensory system on the surface of the fish, consisting of small sensory patches (neuromasts) distributed in discrete lines over the body surface. The lateral line system is stimulated by local water displacements and vibrations, and detects propulsion of the fish through the water, as well as facilitating shoaling, prey capture, and predator and obstacle avoidance. (See Anatomical Atlas entry for <a href='http://zfin.org/zf_info/anatomy/dict/lat_line/lat_line.html'>lateral line</a> by T. Whitfield.)
WARN missing_obsolete_label anatomical set rdfs:label anatomical set
WARN missing_obsolete_label sensory axons peripheral rdfs:label sensory axons peripheral
WARN missing_obsolete_label embryo rdfs:label embryo
WARN missing_obsolete_label lateral cells rdfs:label lateral cells
WARN missing_obsolete_label mesenchyme condensations rdfs:label mesenchyme condensations
WARN missing_obsolete_label antorbital rdfs:label antorbital
WARN missing_obsolete_label basisphenoid rdfs:label basisphenoid
WARN missing_obsolete_label epicentrals rdfs:label epicentrals
WARN missing_obsolete_label hypobranchial vessel rdfs:label hypobranchial vessel
WARN missing_obsolete_label larva rdfs:label larva
WARN missing_obsolete_label opercular-branchiostegal series rdfs:label opercular-branchiostegal series
WARN missing_obsolete_label supramaxillae rdfs:label supramaxillae
WARN missing_obsolete_label hypural arches rdfs:label hypural arches
WARN missing_obsolete_label dermopalatine rdfs:label dermopalatine
WARN missing_obsolete_label duodenum rdfs:label duodenum
WARN missing_obsolete_label infraorbital bridge rdfs:label infraorbital bridge
WARN missing_obsolete_label juvenile rdfs:label juvenile
WARN missing_obsolete_label last preural centrum rdfs:label last preural centrum
WARN missing_obsolete_label stomach rdfs:label stomach
WARN missing_obsolete_label Mauthner axon rdfs:label Mauthner axon
WARN missing_obsolete_label medial pterygiophores anal fin rdfs:label medial pterygiophores anal fin
WARN missing_obsolete_label supraorbital series rdfs:label supraorbital series
WARN missing_obsolete_label brachium conjunctivum rdfs:label brachium conjunctivum
WARN missing_obsolete_label dental plate rdfs:label dental plate
WARN missing_obsolete_label ural ossification rdfs:label ural ossification
WARN missing_obsolete_label presumptive neuron neural tube rdfs:label presumptive neuron neural tube
WARN missing_obsolete_label facial neural crest rdfs:label facial neural crest
WARN missing_obsolete_label medial pterygiophores dorsal fin rdfs:label medial pterygiophores dorsal fin
WARN missing_obsolete_label peripheral motor axons rdfs:label peripheral motor axons
WARN missing_obsolete_label adult rdfs:label adult
WARN missing_obsolete_label pars tuberalis rdfs:label pars tuberalis
WARN missing_obsolete_label pharyngobranchial 1 rdfs:label pharyngobranchial 1
WARN missing_obsolete_label pharyngobranchial 2+3 rdfs:label pharyngobranchial 2+3
WARN missing_obsolete_label cranial motoneurons rdfs:label cranial motoneurons
WARN missing_obsolete_label mentomeckelian rdfs:label mentomeckelian
WARN missing_obsolete_label visceral organ rdfs:label visceral organ
WARN missing_obsolete_label presumptive cardinal organ rdfs:label presumptive cardinal organ
WARN missing_obsolete_label presumptive organ rdfs:label presumptive organ
WARN missing_obsolete_label presumptive organ system rdfs:label presumptive organ system
WARN missing_obsolete_label axial bone rdfs:label axial bone
WARN missing_obsolete_label chondrocranium bone rdfs:label chondrocranium bone
WARN missing_obsolete_label cranial bone rdfs:label cranial bone
WARN missing_obsolete_label pharyngeal arch bone rdfs:label pharyngeal arch bone
WARN missing_obsolete_label dermatocranium bone rdfs:label dermatocranium bone
WARN missing_obsolete_label axial fin bone rdfs:label axial fin bone
WARN missing_obsolete_label paired fin bone rdfs:label paired fin bone
WARN missing_obsolete_label fin bone rdfs:label fin bone
WARN missing_obsolete_label pons rdfs:label pons
WARN missing_obsolete_label distal conduction system rdfs:label distal conduction system
WARN missing_obsolete_label lymph node rdfs:label lymph node
WARN missing_obsolete_label metanephric mesenchyme stem cell rdfs:label metanephric mesenchyme stem cell
WARN missing_obsolete_label non-visual cell (sensu Vertebrata) rdfs:label non-visual cell (sensu Vertebrata)
WARN duplicate_label_synonym maxillo-mandibular ligament has_exact_synonym maxillo-mandibular ligament
WARN missing_definition part of definition
WARN missing_definition has_part definition
WARN missing_definition definition definition
Expand Down Expand Up @@ -446,6 +393,73 @@ WARN missing_definition has_synonym_type definition
WARN missing_definition in_subset definition
WARN missing_definition shorthand definition
WARN missing_definition treat-xrefs-as-genus-differentia definition
WARN duplicate_exact_synonym renal capsular space has_exact_synonym urinary space
WARN duplicate_exact_synonym pronephric capsular space has_exact_synonym urinary space
WARN duplicate_exact_synonym rostral octaval nerve motor nucleus has_exact_synonym rostral cranial nerve VIII motor nucleus
WARN duplicate_exact_synonym caudal octaval nerve motor nucleus has_exact_synonym rostral cranial nerve VIII motor nucleus
WARN duplicate_exact_synonym renal capsular space has_exact_synonym inter-glomerular space
WARN duplicate_exact_synonym pronephric capsular space has_exact_synonym inter-glomerular space
WARN duplicate_exact_synonym follicle stimulating hormone secreting cell has_exact_synonym gonadotrope
WARN duplicate_exact_synonym luteinizing hormone secreting cell has_exact_synonym gonadotrope
WARN duplicate_exact_synonym renal capsular space has_exact_synonym Bowman's space
WARN duplicate_exact_synonym pronephric capsular space has_exact_synonym Bowman's space
WARN duplicate_exact_synonym renal glomerular capsule has_exact_synonym Bowman's capsule
WARN duplicate_exact_synonym pronephric glomerular capsule has_exact_synonym Bowman's capsule
WARN duplicate_exact_synonym supracleithrum-vertebral ligament has_exact_synonym Baudelot's ligament
WARN duplicate_exact_synonym cleithrum-vertebral ligament has_exact_synonym Baudelot's ligament
WARN missing_obsolete_label anatomical set rdfs:label anatomical set
WARN missing_obsolete_label sensory axons peripheral rdfs:label sensory axons peripheral
WARN missing_obsolete_label embryo rdfs:label embryo
WARN missing_obsolete_label lateral cells rdfs:label lateral cells
WARN missing_obsolete_label mesenchyme condensations rdfs:label mesenchyme condensations
WARN missing_obsolete_label antorbital rdfs:label antorbital
WARN missing_obsolete_label basisphenoid rdfs:label basisphenoid
WARN missing_obsolete_label epicentrals rdfs:label epicentrals
WARN missing_obsolete_label hypobranchial vessel rdfs:label hypobranchial vessel
WARN missing_obsolete_label larva rdfs:label larva
WARN missing_obsolete_label opercular-branchiostegal series rdfs:label opercular-branchiostegal series
WARN missing_obsolete_label supramaxillae rdfs:label supramaxillae
WARN missing_obsolete_label hypural arches rdfs:label hypural arches
WARN missing_obsolete_label dermopalatine rdfs:label dermopalatine
WARN missing_obsolete_label duodenum rdfs:label duodenum
WARN missing_obsolete_label infraorbital bridge rdfs:label infraorbital bridge
WARN missing_obsolete_label juvenile rdfs:label juvenile
WARN missing_obsolete_label last preural centrum rdfs:label last preural centrum
WARN missing_obsolete_label stomach rdfs:label stomach
WARN missing_obsolete_label Mauthner axon rdfs:label Mauthner axon
WARN missing_obsolete_label medial pterygiophores anal fin rdfs:label medial pterygiophores anal fin
WARN missing_obsolete_label supraorbital series rdfs:label supraorbital series
WARN missing_obsolete_label brachium conjunctivum rdfs:label brachium conjunctivum
WARN missing_obsolete_label dental plate rdfs:label dental plate
WARN missing_obsolete_label ural ossification rdfs:label ural ossification
WARN missing_obsolete_label presumptive neuron neural tube rdfs:label presumptive neuron neural tube
WARN missing_obsolete_label facial neural crest rdfs:label facial neural crest
WARN missing_obsolete_label medial pterygiophores dorsal fin rdfs:label medial pterygiophores dorsal fin
WARN missing_obsolete_label peripheral motor axons rdfs:label peripheral motor axons
WARN missing_obsolete_label adult rdfs:label adult
WARN missing_obsolete_label pars tuberalis rdfs:label pars tuberalis
WARN missing_obsolete_label pharyngobranchial 1 rdfs:label pharyngobranchial 1
WARN missing_obsolete_label pharyngobranchial 2+3 rdfs:label pharyngobranchial 2+3
WARN missing_obsolete_label cranial motoneurons rdfs:label cranial motoneurons
WARN missing_obsolete_label mentomeckelian rdfs:label mentomeckelian
WARN missing_obsolete_label visceral organ rdfs:label visceral organ
WARN missing_obsolete_label presumptive cardinal organ rdfs:label presumptive cardinal organ
WARN missing_obsolete_label presumptive organ rdfs:label presumptive organ
WARN missing_obsolete_label presumptive organ system rdfs:label presumptive organ system
WARN missing_obsolete_label axial bone rdfs:label axial bone
WARN missing_obsolete_label chondrocranium bone rdfs:label chondrocranium bone
WARN missing_obsolete_label cranial bone rdfs:label cranial bone
WARN missing_obsolete_label pharyngeal arch bone rdfs:label pharyngeal arch bone
WARN missing_obsolete_label dermatocranium bone rdfs:label dermatocranium bone
WARN missing_obsolete_label axial fin bone rdfs:label axial fin bone
WARN missing_obsolete_label paired fin bone rdfs:label paired fin bone
WARN missing_obsolete_label fin bone rdfs:label fin bone
WARN missing_obsolete_label pons rdfs:label pons
WARN missing_obsolete_label distal conduction system rdfs:label distal conduction system
WARN missing_obsolete_label lymph node rdfs:label lymph node
WARN missing_obsolete_label metanephric mesenchyme stem cell rdfs:label metanephric mesenchyme stem cell
WARN missing_obsolete_label non-visual cell (sensu Vertebrata) rdfs:label non-visual cell (sensu Vertebrata)
WARN duplicate_label_synonym maxillo-mandibular ligament has_exact_synonym maxillo-mandibular ligament
WARN annotation_whitespace corpus cerebelli has_exact_synonym corpus cerebelli granular layer
WARN annotation_whitespace superior caudal dorsal flexor has_exact_synonym flexor caudalis dorsalis superioris
WARN annotation_whitespace upper oral valve has_exact_synonym upper semilunar valve
Expand Down Expand Up @@ -537,22 +551,8 @@ WARN annotation_whitespace posterior hypaxial muscle has_exact_synonym anterior
WARN annotation_whitespace posterior hypaxial muscle has_exact_synonym ventral-most hypaxial muscle
WARN annotation_whitespace norepinephrine secreting cell has_exact_synonym noradrenergic cell
WARN annotation_whitespace immature natural killer cell has_exact_synonym immature NK cell
WARN duplicate_exact_synonym renal capsular space has_exact_synonym urinary space
WARN duplicate_exact_synonym pronephric capsular space has_exact_synonym urinary space
WARN duplicate_exact_synonym rostral octaval nerve motor nucleus has_exact_synonym rostral cranial nerve VIII motor nucleus
WARN duplicate_exact_synonym caudal octaval nerve motor nucleus has_exact_synonym rostral cranial nerve VIII motor nucleus
WARN duplicate_exact_synonym renal capsular space has_exact_synonym inter-glomerular space
WARN duplicate_exact_synonym pronephric capsular space has_exact_synonym inter-glomerular space
WARN duplicate_exact_synonym follicle stimulating hormone secreting cell has_exact_synonym gonadotrope
WARN duplicate_exact_synonym luteinizing hormone secreting cell has_exact_synonym gonadotrope
WARN duplicate_exact_synonym renal capsular space has_exact_synonym Bowman's space
WARN duplicate_exact_synonym pronephric capsular space has_exact_synonym Bowman's space
WARN duplicate_exact_synonym renal glomerular capsule has_exact_synonym Bowman's capsule
WARN duplicate_exact_synonym pronephric glomerular capsule has_exact_synonym Bowman's capsule
WARN duplicate_exact_synonym supracleithrum-vertebral ligament has_exact_synonym Baudelot's ligament
WARN duplicate_exact_synonym cleithrum-vertebral ligament has_exact_synonym Baudelot's ligament
INFO missing_superclass zebrafish anatomical entity rdfs:subClassOf
INFO missing_superclass Stages rdfs:subClassOf
INFO lowercase_definition has developmental contribution from definition x has developmental contribution from y iff x has some part z such that z develops from y.
INFO lowercase_definition start stage definition c existence starts during s iff start_of(c) part_of s.
INFO lowercase_definition end stage definition c existence ends during s iff end_of(c) part_of s.
INFO missing_superclass zebrafish anatomical entity rdfs:subClassOf
INFO missing_superclass Stages rdfs:subClassOf
4 changes: 2 additions & 2 deletions zfa-base.json
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Expand Up @@ -60782,11 +60782,11 @@
},
{
"pred": "http://www.w3.org/2002/07/owl#versionInfo",
"val": "2022-02-28"
"val": "2022-03-15"
}
],
"subsets": [],
"version": "http://purl.obolibrary.org/obo/zfa/releases/2022-02-28/zfa-base.json",
"version": "http://purl.obolibrary.org/obo/zfa/releases/2022-03-15/zfa-base.json",
"xrefs": []
},
"nodes": [
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4 changes: 2 additions & 2 deletions zfa-base.obo
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@@ -1,5 +1,5 @@
format-version: 1.2
data-version: zfa/releases/2022-02-28/zfa-base.owl
data-version: zfa/releases/2022-03-15/zfa-base.owl
date: 08:03:2021 11:16
saved-by: ceriv
auto-generated-by: OBO-Edit 2.3.1
Expand All @@ -16,7 +16,7 @@ property_value: http://purl.org/dc/elements/1.1/description "ZFA description." x
property_value: http://purl.org/dc/elements/1.1/title "Zebrafish Anatomy Ontology (ZFA)" xsd:string
property_value: http://purl.org/dc/elements/1.1/type IAO:8000001
property_value: http://purl.org/dc/terms/license https://creativecommons.org/licenses/by/3.0/
property_value: owl:versionInfo "2022-02-28" xsd:string
property_value: owl:versionInfo "2022-03-15" xsd:string

[Term]
id: ZFA:0000000
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4 changes: 2 additions & 2 deletions zfa-base.owl
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Expand Up @@ -12,7 +12,7 @@
xmlns:terms="http://purl.org/dc/terms/"
xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
<owl:Ontology rdf:about="http://purl.obolibrary.org/obo/zfa/zfa-base.owl">
<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/zfa/releases/2022-02-28/zfa-base.owl"/>
<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/zfa/releases/2022-03-15/zfa-base.owl"/>
<dc:description rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ZFA description.</dc:description>
<dc:title rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Zebrafish Anatomy Ontology (ZFA)</dc:title>
<dc:type rdf:resource="http://purl.obolibrary.org/obo/IAO_8000001"/>
Expand All @@ -27,7 +27,7 @@
<oboInOwl:treat-xrefs-as-genus-differentia rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TAO part_of NCBITaxon:7955</oboInOwl:treat-xrefs-as-genus-differentia>
<oboInOwl:treat-xrefs-as-genus-differentia rdf:datatype="http://www.w3.org/2001/XMLSchema#string">VSAO part_of NCBITaxon:7955</oboInOwl:treat-xrefs-as-genus-differentia>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SVN version: $Revision: 1.100$</rdfs:comment>
<owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2022-02-28</owl:versionInfo>
<owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2022-03-15</owl:versionInfo>
</owl:Ontology>


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4 changes: 2 additions & 2 deletions zfa-full.json
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Expand Up @@ -39973,11 +39973,11 @@
},
{
"pred": "http://www.w3.org/2002/07/owl#versionInfo",
"val": "2022-02-28"
"val": "2022-03-15"
}
],
"subsets": [],
"version": "http://purl.obolibrary.org/obo/zfa/releases/2022-02-28/zfa-full.json",
"version": "http://purl.obolibrary.org/obo/zfa/releases/2022-03-15/zfa-full.json",
"xrefs": []
},
"nodes": [
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4 changes: 2 additions & 2 deletions zfa-full.obo
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@@ -1,5 +1,5 @@
format-version: 1.2
data-version: zfa/releases/2022-02-28/zfa-full.owl
data-version: zfa/releases/2022-03-15/zfa-full.owl
date: 08:03:2021 11:16
saved-by: ceriv
auto-generated-by: OBO-Edit 2.3.1
Expand All @@ -15,7 +15,7 @@ ontology: zfa/zfa-full
property_value: http://purl.org/dc/elements/1.1/description "ZFA description." xsd:string
property_value: http://purl.org/dc/elements/1.1/title "Zebrafish Anatomy Ontology (ZFA)" xsd:string
property_value: http://purl.org/dc/terms/license https://creativecommons.org/licenses/by/3.0/
property_value: owl:versionInfo "2022-02-28" xsd:string
property_value: owl:versionInfo "2022-03-15" xsd:string

[Term]
id: ZFA:0000000
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4 changes: 2 additions & 2 deletions zfa-full.owl
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Expand Up @@ -12,7 +12,7 @@
xmlns:terms="http://purl.org/dc/terms/"
xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
<owl:Ontology rdf:about="http://purl.obolibrary.org/obo/zfa/zfa-full.owl">
<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/zfa/releases/2022-02-28/zfa-full.owl"/>
<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/zfa/releases/2022-03-15/zfa-full.owl"/>
<dc:description rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ZFA description.</dc:description>
<dc:title rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Zebrafish Anatomy Ontology (ZFA)</dc:title>
<terms:license rdf:resource="https://creativecommons.org/licenses/by/3.0/"/>
Expand All @@ -26,7 +26,7 @@
<oboInOwl:treat-xrefs-as-genus-differentia rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TAO part_of NCBITaxon:7955</oboInOwl:treat-xrefs-as-genus-differentia>
<oboInOwl:treat-xrefs-as-genus-differentia rdf:datatype="http://www.w3.org/2001/XMLSchema#string">VSAO part_of NCBITaxon:7955</oboInOwl:treat-xrefs-as-genus-differentia>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">SVN version: $Revision: 1.100$</rdfs:comment>
<owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2022-02-28</owl:versionInfo>
<owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2022-03-15</owl:versionInfo>
</owl:Ontology>


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