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Merge pull request #79 from ybradford/release20220214
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add exp cond to AGR slim
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@ybradford
ybradford authored Feb 14, 2022
2 parents 92e1cd6 + afa762a commit f1cf1d2
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Showing 18 changed files with 3,009 additions and 899 deletions.
804 changes: 653 additions & 151 deletions imports/ro_import.owl
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2 changes: 1 addition & 1 deletion reports/zeco-edit.owl-obo-report.tsv
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@@ -1,5 +1,4 @@
Level Rule Name Subject Property Value
WARN annotation_whitespace ZECO:0000100 IAO:0000115 The state in which an organism exists.
WARN missing_definition IAO:0000115 IAO:0000115
WARN missing_definition IAO:0100001 IAO:0000115
WARN missing_definition ZECO:0000131 IAO:0000115
Expand Down Expand Up @@ -49,4 +48,5 @@ WARN missing_definition oboInOwl:hasDbXref IAO:0000115
WARN missing_definition oboInOwl:hasExactSynonym IAO:0000115
WARN missing_definition oboInOwl:hasOBOFormatVersion IAO:0000115
WARN missing_definition oboInOwl:hasOBONamespace IAO:0000115
WARN annotation_whitespace ZECO:0000100 IAO:0000115 The state in which an organism exists.
INFO missing_superclass ZECO:0000100 rdfs:subClassOf
804 changes: 653 additions & 151 deletions src/ontology/imports/ro_import.owl
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4 changes: 2 additions & 2 deletions src/ontology/ontologyterms.txt
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Expand Up @@ -22,7 +22,6 @@ http://purl.obolibrary.org/obo/ZECO_0000115
http://purl.obolibrary.org/obo/ZECO_0000106
http://purl.obolibrary.org/obo/ZECO_0000110
http://purl.obolibrary.org/obo/ZECO_0000184
http://purl.obolibrary.org/obo/ZECO_0000214
http://purl.obolibrary.org/obo/ZECO_0000251
http://purl.obolibrary.org/obo/ZECO_0000121
http://purl.obolibrary.org/obo/ZECO_0000100
Expand Down Expand Up @@ -56,13 +55,14 @@ http://purl.obolibrary.org/obo/ZECO_0000164
http://purl.obolibrary.org/obo/ZECO_0000143
http://purl.obolibrary.org/obo/ZECO_0000101
http://purl.obolibrary.org/obo/ZECO_0000156
http://purl.obolibrary.org/obo/ZECO_0000213
http://purl.obolibrary.org/obo/ZECO_0000222
http://purl.obolibrary.org/obo/ZECO_0000151
http://purl.obolibrary.org/obo/ZECO_0000176
http://purl.obolibrary.org/obo/ZECO_0000259
http://purl.obolibrary.org/obo/ZECO_0000183
http://purl.obolibrary.org/obo/ZECO_0000213
http://purl.obolibrary.org/obo/ZECO_0000247
http://purl.obolibrary.org/obo/ZECO_0000214
http://purl.obolibrary.org/obo/ZECO_0000241
http://purl.obolibrary.org/obo/ZECO_0000232
http://purl.obolibrary.org/obo/ZECO_0000211
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2 changes: 1 addition & 1 deletion src/ontology/reports/zeco-edit.owl-obo-report.tsv
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Original file line number Diff line number Diff line change
@@ -1,5 +1,4 @@
Level Rule Name Subject Property Value
WARN annotation_whitespace ZECO:0000100 IAO:0000115 The state in which an organism exists.
WARN missing_definition IAO:0000115 IAO:0000115
WARN missing_definition IAO:0100001 IAO:0000115
WARN missing_definition ZECO:0000131 IAO:0000115
Expand Down Expand Up @@ -49,4 +48,5 @@ WARN missing_definition oboInOwl:hasDbXref IAO:0000115
WARN missing_definition oboInOwl:hasExactSynonym IAO:0000115
WARN missing_definition oboInOwl:hasOBOFormatVersion IAO:0000115
WARN missing_definition oboInOwl:hasOBONamespace IAO:0000115
WARN annotation_whitespace ZECO:0000100 IAO:0000115 The state in which an organism exists.
INFO missing_superclass ZECO:0000100 rdfs:subClassOf
3 changes: 2 additions & 1 deletion src/ontology/zeco-edit.owl
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Original file line number Diff line number Diff line change
Expand Up @@ -285,6 +285,7 @@ SubClassOf(obo:ZECO_0000103 obo:ZECO_0000100)
# Class: obo:ZECO_0000104 (experimental conditions)

AnnotationAssertion(obo:IAO_0000115 obo:ZECO_0000104 "Condition in which variables of the experiment are manipulated to determine the variables effect by comparing to a control condition.")
AnnotationAssertion(oboInOwl:inSubset obo:ZECO_0000104 obo:ZECO_0000267)
AnnotationAssertion(rdfs:label obo:ZECO_0000104 "experimental conditions"@en)
SubClassOf(obo:ZECO_0000104 obo:ZECO_0000100)

Expand Down Expand Up @@ -341,7 +342,7 @@ SubClassOf(obo:ZECO_0000112 obo:ZECO_0000104)

# Class: obo:ZECO_0000113 (food availability)

AnnotationAssertion(obo:IAO_0000115 obo:ZECO_0000113 "Experimental condition in which the availabity of food is manipulated.")
AnnotationAssertion(obo:IAO_0000115 obo:ZECO_0000113 "Experimental condition in which the availability of food is manipulated.")
AnnotationAssertion(oboInOwl:inSubset obo:ZECO_0000113 obo:ZECO_0000267)
AnnotationAssertion(rdfs:label obo:ZECO_0000113 "food availability"@en)
SubClassOf(obo:ZECO_0000113 obo:ZECO_0000104)
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93 changes: 47 additions & 46 deletions zeco-base.json
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Expand Up @@ -382,7 +382,7 @@
"id" : "http://purl.obolibrary.org/obo/ZECO_0000113",
"meta" : {
"definition" : {
"val" : "Experimental condition in which the availabity of food is manipulated.",
"val" : "Experimental condition in which the availability of food is manipulated.",
"xrefs" : [ ]
},
"subsets" : [ "http://purl.obolibrary.org/obo/ZECO_0000267" ]
Expand Down Expand Up @@ -1064,7 +1064,8 @@
"definition" : {
"val" : "Condition in which variables of the experiment are manipulated to determine the variables effect by comparing to a control condition.",
"xrefs" : [ ]
}
},
"subsets" : [ "http://purl.obolibrary.org/obo/ZECO_0000267" ]
},
"type" : "CLASS",
"lbl" : "experimental conditions"
Expand Down Expand Up @@ -1489,14 +1490,14 @@
"sub" : "http://purl.obolibrary.org/obo/ZECO_0000216",
"pred" : "is_a",
"obj" : "http://purl.obolibrary.org/obo/ZECO_0000209"
}, {
"sub" : "http://purl.obolibrary.org/obo/ZECO_0000122",
"pred" : "is_a",
"obj" : "http://purl.obolibrary.org/obo/ZECO_0000121"
}, {
"sub" : "http://purl.obolibrary.org/obo/ZECO_0000133",
"pred" : "is_a",
"obj" : "http://purl.obolibrary.org/obo/ZECO_0000132"
}, {
"sub" : "http://purl.obolibrary.org/obo/ZECO_0000122",
"pred" : "is_a",
"obj" : "http://purl.obolibrary.org/obo/ZECO_0000121"
}, {
"sub" : "http://purl.obolibrary.org/obo/ZECO_0000144",
"pred" : "is_a",
Expand All @@ -1518,17 +1519,17 @@
"pred" : "is_a",
"obj" : "http://purl.obolibrary.org/obo/ZECO_0000155"
}, {
"sub" : "http://purl.obolibrary.org/obo/ZECO_0000158",
"sub" : "http://purl.obolibrary.org/obo/ZECO_0000124",
"pred" : "is_a",
"obj" : "http://purl.obolibrary.org/obo/ZECO_0000157"
"obj" : "http://purl.obolibrary.org/obo/ZECO_0000122"
}, {
"sub" : "http://purl.obolibrary.org/obo/ZECO_0000147",
"pred" : "is_a",
"obj" : "http://purl.obolibrary.org/obo/ZECO_0000146"
}, {
"sub" : "http://purl.obolibrary.org/obo/ZECO_0000124",
"sub" : "http://purl.obolibrary.org/obo/ZECO_0000158",
"pred" : "is_a",
"obj" : "http://purl.obolibrary.org/obo/ZECO_0000122"
"obj" : "http://purl.obolibrary.org/obo/ZECO_0000157"
}, {
"sub" : "http://purl.obolibrary.org/obo/ZECO_0000122",
"pred" : "is_a",
Expand All @@ -1541,14 +1542,14 @@
"sub" : "http://purl.obolibrary.org/obo/ZECO_0000255",
"pred" : "is_a",
"obj" : "http://purl.obolibrary.org/obo/ZECO_0000253"
}, {
"sub" : "http://purl.obolibrary.org/obo/ZECO_0000243",
"pred" : "is_a",
"obj" : "http://purl.obolibrary.org/obo/ZECO_0000131"
}, {
"sub" : "http://purl.obolibrary.org/obo/ZECO_0000201",
"pred" : "is_a",
"obj" : "http://purl.obolibrary.org/obo/ZECO_0000200"
}, {
"sub" : "http://purl.obolibrary.org/obo/ZECO_0000243",
"pred" : "is_a",
"obj" : "http://purl.obolibrary.org/obo/ZECO_0000131"
}, {
"sub" : "http://purl.obolibrary.org/obo/ZECO_0000223",
"pred" : "is_a",
Expand Down Expand Up @@ -1625,14 +1626,14 @@
"sub" : "http://purl.obolibrary.org/obo/ZECO_0000126",
"pred" : "is_a",
"obj" : "http://purl.obolibrary.org/obo/ZECO_0000125"
}, {
"sub" : "http://purl.obolibrary.org/obo/ZECO_0000148",
"pred" : "is_a",
"obj" : "http://purl.obolibrary.org/obo/ZECO_0000147"
}, {
"sub" : "http://purl.obolibrary.org/obo/ZECO_0000137",
"pred" : "is_a",
"obj" : "http://purl.obolibrary.org/obo/ZECO_0000136"
}, {
"sub" : "http://purl.obolibrary.org/obo/ZECO_0000148",
"pred" : "is_a",
"obj" : "http://purl.obolibrary.org/obo/ZECO_0000147"
}, {
"sub" : "http://purl.obolibrary.org/obo/ZECO_0000128",
"pred" : "is_a",
Expand Down Expand Up @@ -1669,14 +1670,14 @@
"sub" : "http://purl.obolibrary.org/obo/ZECO_0000235",
"pred" : "is_a",
"obj" : "http://purl.obolibrary.org/obo/ZECO_0000110"
}, {
"sub" : "http://purl.obolibrary.org/obo/ZECO_0000138",
"pred" : "is_a",
"obj" : "http://purl.obolibrary.org/obo/ZECO_0000136"
}, {
"sub" : "http://purl.obolibrary.org/obo/ZECO_0000149",
"pred" : "is_a",
"obj" : "http://purl.obolibrary.org/obo/ZECO_0000147"
}, {
"sub" : "http://purl.obolibrary.org/obo/ZECO_0000138",
"pred" : "is_a",
"obj" : "http://purl.obolibrary.org/obo/ZECO_0000136"
}, {
"sub" : "http://purl.obolibrary.org/obo/ZECO_0000116",
"pred" : "is_a",
Expand All @@ -1693,14 +1694,14 @@
"sub" : "http://purl.obolibrary.org/obo/ZECO_0000125",
"pred" : "is_a",
"obj" : "http://purl.obolibrary.org/obo/ZECO_0000121"
}, {
"sub" : "http://purl.obolibrary.org/obo/ZECO_0000245",
"pred" : "is_a",
"obj" : "http://purl.obolibrary.org/obo/ZECO_0000229"
}, {
"sub" : "http://purl.obolibrary.org/obo/ZECO_0000233",
"pred" : "is_a",
"obj" : "http://purl.obolibrary.org/obo/ZECO_0000107"
}, {
"sub" : "http://purl.obolibrary.org/obo/ZECO_0000245",
"pred" : "is_a",
"obj" : "http://purl.obolibrary.org/obo/ZECO_0000229"
}, {
"sub" : "http://purl.obolibrary.org/obo/ZECO_0000192",
"pred" : "is_a",
Expand All @@ -1717,10 +1718,6 @@
"sub" : "http://purl.obolibrary.org/obo/ZECO_0000146",
"pred" : "is_a",
"obj" : "http://purl.obolibrary.org/obo/ZECO_0000104"
}, {
"sub" : "http://purl.obolibrary.org/obo/ZECO_0000193",
"pred" : "is_a",
"obj" : "http://purl.obolibrary.org/obo/ZECO_0000191"
}, {
"sub" : "http://purl.obolibrary.org/obo/ZECO_0000161",
"pred" : "is_a",
Expand All @@ -1729,6 +1726,10 @@
"sub" : "http://purl.obolibrary.org/obo/ZECO_0000172",
"pred" : "is_a",
"obj" : "http://purl.obolibrary.org/obo/ZECO_0000171"
}, {
"sub" : "http://purl.obolibrary.org/obo/ZECO_0000193",
"pred" : "is_a",
"obj" : "http://purl.obolibrary.org/obo/ZECO_0000191"
}, {
"sub" : "http://purl.obolibrary.org/obo/ZECO_0000183",
"pred" : "is_a",
Expand All @@ -1754,17 +1755,17 @@
"pred" : "is_a",
"obj" : "http://purl.obolibrary.org/obo/ZECO_0000104"
}, {
"sub" : "http://purl.obolibrary.org/obo/ZECO_0000152",
"sub" : "http://purl.obolibrary.org/obo/ZECO_0000141",
"pred" : "is_a",
"obj" : "http://purl.obolibrary.org/obo/ZECO_0000151"
"obj" : "http://purl.obolibrary.org/obo/ZECO_0000140"
}, {
"sub" : "http://purl.obolibrary.org/obo/ZECO_0000130",
"pred" : "is_a",
"obj" : "http://purl.obolibrary.org/obo/ZECO_0000250"
}, {
"sub" : "http://purl.obolibrary.org/obo/ZECO_0000141",
"sub" : "http://purl.obolibrary.org/obo/ZECO_0000152",
"pred" : "is_a",
"obj" : "http://purl.obolibrary.org/obo/ZECO_0000140"
"obj" : "http://purl.obolibrary.org/obo/ZECO_0000151"
}, {
"sub" : "http://purl.obolibrary.org/obo/ZECO_0000185",
"pred" : "is_a",
Expand Down Expand Up @@ -1825,14 +1826,14 @@
"sub" : "http://purl.obolibrary.org/obo/ZECO_0000142",
"pred" : "is_a",
"obj" : "http://purl.obolibrary.org/obo/ZECO_0000140"
}, {
"sub" : "http://purl.obolibrary.org/obo/ZECO_0000165",
"pred" : "is_a",
"obj" : "http://purl.obolibrary.org/obo/ZECO_0000164"
}, {
"sub" : "http://purl.obolibrary.org/obo/ZECO_0000186",
"pred" : "is_a",
"obj" : "http://purl.obolibrary.org/obo/ZECO_0000184"
}, {
"sub" : "http://purl.obolibrary.org/obo/ZECO_0000165",
"pred" : "is_a",
"obj" : "http://purl.obolibrary.org/obo/ZECO_0000164"
}, {
"sub" : "http://purl.obolibrary.org/obo/ZECO_0000198",
"pred" : "is_a",
Expand Down Expand Up @@ -1986,11 +1987,11 @@
"pred" : "is_a",
"obj" : "http://purl.obolibrary.org/obo/ZECO_0000209"
}, {
"sub" : "http://purl.obolibrary.org/obo/ZECO_0000254",
"sub" : "http://purl.obolibrary.org/obo/ZECO_0000231",
"pred" : "is_a",
"obj" : "http://purl.obolibrary.org/obo/ZECO_0000106"
}, {
"sub" : "http://purl.obolibrary.org/obo/ZECO_0000231",
"sub" : "http://purl.obolibrary.org/obo/ZECO_0000254",
"pred" : "is_a",
"obj" : "http://purl.obolibrary.org/obo/ZECO_0000106"
}, {
Expand Down Expand Up @@ -2041,14 +2042,14 @@
"sub" : "http://purl.obolibrary.org/obo/ZECO_0000229",
"pred" : "is_a",
"obj" : "http://purl.obolibrary.org/obo/ZECO_0000104"
}, {
"sub" : "http://purl.obolibrary.org/obo/ZECO_0000226",
"pred" : "is_a",
"obj" : "http://purl.obolibrary.org/obo/ZECO_0000122"
}, {
"sub" : "http://purl.obolibrary.org/obo/ZECO_0000238",
"pred" : "is_a",
"obj" : "http://purl.obolibrary.org/obo/ZECO_0000111"
}, {
"sub" : "http://purl.obolibrary.org/obo/ZECO_0000226",
"pred" : "is_a",
"obj" : "http://purl.obolibrary.org/obo/ZECO_0000122"
}, {
"sub" : "http://purl.obolibrary.org/obo/ZECO_0000261",
"pred" : "is_a",
Expand Down Expand Up @@ -2155,9 +2156,9 @@
"val" : "zebrafish_experimental_conditions_ontology"
}, {
"pred" : "http://www.w3.org/2002/07/owl#versionInfo",
"val" : "2021-06-04"
"val" : "2022-02-14"
} ],
"version" : "http://purl.obolibrary.org/obo/zeco/releases/2021-06-04/zeco-base.json"
"version" : "http://purl.obolibrary.org/obo/zeco/releases/2022-02-14/zeco-base.json"
},
"equivalentNodesSets" : [ ],
"logicalDefinitionAxioms" : [ ],
Expand Down
7 changes: 4 additions & 3 deletions zeco-base.obo
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
format-version: 1.2
data-version: zeco/releases/2021-06-04/zeco-base.owl
data-version: zeco/releases/2022-02-14/zeco-base.owl
subsetdef: ubprop:upper_level "abstract upper-level terms not directly useful for analysis"
subsetdef: ZECO:0000267 ""
default-namespace: zebrafish_experimental_conditions_ontology
Expand All @@ -8,7 +8,7 @@ property_value: http://purl.org/dc/elements/1.1/description "Ontology of Zebrafi
property_value: http://purl.org/dc/elements/1.1/title "Zebrafish Experimental Conditions Ontology" 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 "2021-06-04" xsd:string
property_value: owl:versionInfo "2022-02-14" xsd:string

[Term]
id: ZECO:0000100
Expand Down Expand Up @@ -40,6 +40,7 @@ is_a: ZECO:0000100 ! conditions
id: ZECO:0000104
name: experimental conditions
def: "Condition in which variables of the experiment are manipulated to determine the variables effect by comparing to a control condition." []
subset: ZECO:0000267
is_a: ZECO:0000100 ! conditions

[Term]
Expand Down Expand Up @@ -96,7 +97,7 @@ is_a: ZECO:0000104 ! experimental conditions
[Term]
id: ZECO:0000113
name: food availability
def: "Experimental condition in which the availabity of food is manipulated." []
def: "Experimental condition in which the availability of food is manipulated." []
subset: ZECO:0000267
is_a: ZECO:0000104 ! experimental conditions

Expand Down
7 changes: 4 additions & 3 deletions zeco-base.owl
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Original file line number Diff line number Diff line change
Expand Up @@ -12,13 +12,13 @@
xmlns:ubprop="http://purl.obolibrary.org/obo/ubprop#"
xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
<owl:Ontology rdf:about="http://purl.obolibrary.org/obo/zeco/zeco-base.owl">
<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/zeco/releases/2021-06-04/zeco-base.owl"/>
<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/zeco/releases/2022-02-14/zeco-base.owl"/>
<dc:description>Ontology of Zebrafish Experimental Conditions</dc:description>
<dc:title>Zebrafish Experimental Conditions Ontology</dc:title>
<dc:type rdf:resource="http://purl.obolibrary.org/obo/IAO_8000001"/>
<terms:license rdf:resource="https://creativecommons.org/licenses/by/3.0/"/>
<oboInOwl:default-namespace rdf:datatype="http://www.w3.org/2001/XMLSchema#string">zebrafish_experimental_conditions_ontology</oboInOwl:default-namespace>
<owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2021-06-04</owl:versionInfo>
<owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2022-02-14</owl:versionInfo>
</owl:Ontology>


Expand Down Expand Up @@ -291,6 +291,7 @@
<owl:Class rdf:about="http://purl.obolibrary.org/obo/ZECO_0000104">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/ZECO_0000100"/>
<obo:IAO_0000115>Condition in which variables of the experiment are manipulated to determine the variables effect by comparing to a control condition.</obo:IAO_0000115>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/ZECO_0000267"/>
<rdfs:label xml:lang="en">experimental conditions</rdfs:label>
</owl:Class>

Expand Down Expand Up @@ -383,7 +384,7 @@

<owl:Class rdf:about="http://purl.obolibrary.org/obo/ZECO_0000113">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/ZECO_0000104"/>
<obo:IAO_0000115>Experimental condition in which the availabity of food is manipulated.</obo:IAO_0000115>
<obo:IAO_0000115>Experimental condition in which the availability of food is manipulated.</obo:IAO_0000115>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/ZECO_0000267"/>
<rdfs:label xml:lang="en">food availability</rdfs:label>
</owl:Class>
Expand Down
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