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Zp zapp improvements #75
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156234a
Add upheno plugin to ODK config
ptgolden d445b8d
Add ZFA and GO terms to ZAPP subset
ptgolden 8f71625
Improvements to zp-zapp subset
ptgolden e27e8f0
Add two manual labels to zp-zapp (and include provenance)
ptgolden 719f2cc
Several changes to zp-zapp label handling
ptgolden 6d36539
Don't special case inclusion of ZP:0000000
ptgolden 378a01f
Add QC for zapp-zp subset
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,2 +1,6 @@ | ||
| ID LABEL | ||
| ID LABEL | ||
| ID Preferred label Label submitter Exact synonym Synonym submitter | ||
| ID A skos:preferredLabel >AI dc:contributor A oboInOwl:exactSynonym >AI dc:contributor | ||
| ZP:0000711 microencephaly orcid:0000-0002-4142-7153 | ||
| ZP:0000711 undersized brain orcid:0000-0002-4142-7153 | ||
| ZP:0003410 macroencephaly orcid:0000-0002-4142-7153 | ||
| ZP:0003410 oversized brain orcid:0000-0002-4142-7153 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,13 @@ | ||
| ZAPP_GRAPH_TERMS=$(grep 'owl:Class rdf:about="http://purl.obolibrary.org/obo/ZP_' zp-zapp.owl | sort | uniq) | ||
| ZAPP_GRAPH_COUNT=$(echo "$ZAPP_GRAPH_TERMS" | wc -l) | ||
|
|
||
| ZAPP_CSV_TERMS=$(grep 'ZP_' ../ontology/tmp/zp-zapp.csv | sort | uniq) | ||
| ZAPP_CSV_COUNT=$(echo "$ZAPP_CSV_TERMS" | wc -l) | ||
|
|
||
| echo "Expected number of ZAPP terms from CSV: $ZAPP_CSV_COUNT" | ||
| echo "Actual number of ZAPP terms in graph: $ZAPP_GRAPH_COUNT" | ||
|
|
||
| if [ $ZAPP_GRAPH_COUNT -ne $ZAPP_CSV_COUNT ] | ||
| then | ||
| exit 1 | ||
| fi |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,30 @@ | ||
| PREFIX iao: <http://purl.obolibrary.org/obo/IAO_> | ||
| PREFIX infores: <https://w3id.org/biolink/infores/> | ||
| PREFIX obo: <http://purl.obolibrary.org/obo/> | ||
| PREFIX oboInOwl: <http://www.geneontology.org/formats/oboInOwl#> | ||
| PREFIX owl: <http://www.w3.org/2002/07/owl#> | ||
| PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> | ||
|
|
||
| DELETE { | ||
| ?entity rdfs:label ?zfinLabel . | ||
| ?entity obo:IAO_0000115 ?zfinDefinition . | ||
| } | ||
|
|
||
| INSERT { | ||
| [ | ||
| a owl:Axiom ; | ||
| owl:annotatedSource ?entity ; | ||
| owl:annotatedProperty oboInOwl:hasExactSynonym ; | ||
| owl:annotatedTarget ?zfinLabel ; | ||
| oboInOwl:source infores:zfin | ||
| ] | ||
| } | ||
|
|
||
| WHERE { | ||
| ?entity a owl:Class . | ||
| ?entity rdfs:label ?zfinLabel . | ||
| ?entity obo:IAO_0000115 ?zfinDefinition . | ||
| FILTER(isIRI(?entity) && regex(str(?entity), "ZP_")) | ||
| FILTER(STRENDS(?zfinLabel, ", abnormal")) | ||
| FILTER(STRSTARTS(?zfinDefinition, "Abnormal(ly)")) | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,25 @@ | ||
| PREFIX oboInOwl: <http://www.geneontology.org/formats/oboInOwl#> | ||
| PREFIX owl: <http://www.w3.org/2002/07/owl#> | ||
| PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> | ||
|
|
||
| SELECT ?entity ?label ?source WHERE { | ||
| { | ||
| SELECT ?entity WHERE { | ||
| ?entity a owl:Class . | ||
| ?entity rdfs:label ?_label . | ||
| } | ||
| GROUP BY ?entity | ||
| HAVING(COUNT(?_label) > 1) | ||
| } | ||
| ?entity rdfs:label ?label . | ||
| OPTIONAL { | ||
| [ | ||
| a owl:Axiom ; | ||
| owl:annotatedSource ?entity ; | ||
| owl:annotatedProperty rdfs:label ; | ||
| owl:annotatedTarget ?label ; | ||
| oboInOwl:source ?source | ||
| ] | ||
| } | ||
| } | ||
| ORDER BY ?cls |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,40 @@ | ||
| PREFIX oboInOwl: <http://www.geneontology.org/formats/oboInOwl#> | ||
| PREFIX owl: <http://www.w3.org/2002/07/owl#> | ||
| PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> | ||
| PREFIX skos: <http://www.w3.org/2004/02/skos/core#> | ||
|
|
||
| DELETE { | ||
| ?entity rdfs:label ?originalLabel . | ||
| ?originalLabelAxiom owl:annotatedProperty rdfs:label . | ||
|
|
||
| ?entity skos:preferredLabel ?zappLabel . | ||
| ?zappLabelAxiom owl:annotatedProperty skos:preferredLabel . | ||
| } | ||
|
|
||
| INSERT { | ||
| ?entity oboInOwl:exactSynonym ?originalLabel . | ||
| ?originalLabelAxiom owl:annotatedProperty oboInOwl:exactSynonym . | ||
|
|
||
| ?entity rdfs:label ?zappLabel . | ||
| ?zappLabelAxiom owl:annotatedProperty rdfs:label . | ||
| } | ||
|
|
||
| WHERE { | ||
| ?entity a owl:Class . | ||
| ?entity skos:preferredLabel ?zappLabel . | ||
| ?entity rdfs:label ?originalLabel . | ||
|
|
||
| ?zappLabelAxiom | ||
| a owl:Axiom ; | ||
| owl:annotatedSource ?entity ; | ||
| owl:annotatedProperty skos:preferredLabel ; | ||
| owl:annotatedTarget ?zappLabel . | ||
|
|
||
| ?originalLabelAxiom | ||
| a owl:Axiom ; | ||
| owl:annotatedSource ?entity ; | ||
| owl:annotatedProperty rdfs:label ; | ||
| owl:annotatedTarget ?originalLabel . | ||
|
|
||
| FILTER(isIRI(?entity) && regex(str(?entity), "ZP_")) | ||
| } |
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