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Update DOSDP template and SPARQL qc documentation (#6496)
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Co-authored-by: nicolevasilevsky <[email protected]>
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github-actions[bot] and nicolevasilevsky authored Jul 26, 2023
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131 changes: 118 additions & 13 deletions docs/editors-guide/quality-control-tests.md
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Original file line number Diff line number Diff line change
Expand Up @@ -197,19 +197,19 @@ prefix oboInOwl: <http://www.geneontology.org/formats/oboInOwl#>
SELECT DISTINCT ?cls ?property ?prefix ?source
WHERE
WHERE
{
VALUES ?property { oboInOwl:source oboInOwl:hasDbXref }
?cls a owl:Class;
?cls a owl:Class;
rdfs:subClassOf+ <http://purl.obolibrary.org/obo/MONDO_0000001> ;
?mapping ?value .
?axiom owl:annotatedSource ?cls ;
owl:annotatedProperty ?mapping ;
owl:annotatedTarget ?value ;
?property ?source .
FILTER NOT EXISTS {
?cls owl:deprecated ?deprecated .
}
Expand Down Expand Up @@ -258,6 +258,7 @@ WHERE
"OGMS",
"OMIM",
"OMIMPS",
"OMIA",
"OMIT",
"OMOP",
"ONCOTREE",
Expand Down Expand Up @@ -295,12 +296,12 @@ prefix oboInOwl: <http://www.geneontology.org/formats/oboInOwl#>
SELECT DISTINCT ?cls ?prefix
WHERE
WHERE
{
VALUES ?mapping { oboInOwl:hasDbXref }
?cls a owl:Class;
?cls a owl:Class;
?mapping ?value .
FILTER NOT EXISTS {
?cls owl:deprecated ?deprecated .
}
Expand Down Expand Up @@ -339,6 +340,7 @@ WHERE
"OGMS",
"OMIM",
"OMIMPS",
"OMIA",
"OMOP",
"ONCOTREE",
"Orphanet",
Expand All @@ -353,7 +355,7 @@ WHERE
))
FILTER( !isBlank(?cls) && STRSTARTS(str(?cls), "http://purl.obolibrary.org/obo/MONDO_"))
BIND( STRBEFORE(str(?value),":") AS ?prefix)
} ORDER BY ?cls
Expand Down Expand Up @@ -708,6 +710,19 @@ ORDER BY ?entity

## General quality checks

### orcid-contributor-violation.sparql

```
PREFIX dc_terms: <http://purl.org/dc/terms/>
SELECT ?subject ?orcid
WHERE {
VALUES ?property { dc_terms:contributor dc_terms:creator }
?subject ?property ?orcid .
FILTER(!regex(str(?orcid), "^(https://orcid.org/)[0-9]{4}-[0-9]{4}-[0-9]{4}-[0-9]{3}(?:[0-9]|X)"))
}
```

### qc-def-lacks-xref.sparql

```
Expand Down Expand Up @@ -1144,13 +1159,103 @@ prefix skos: <http://www.w3.org/2004/02/skos/core#>
prefix dce: <http://purl.org/dc/elements/1.1/>
prefix dc: <http://purl.org/dc/terms/>
SELECT DISTINCT ?term ?property ?value WHERE
SELECT DISTINCT ?term ?property WHERE
{
?term ?property ?value .
?property a owl:AnnotationProperty .
FILTER (isIRI(?term) && regex(str(?term), "^http://purl.obolibrary.org/obo/MONDO_"))
FILTER(!isBlank(?value))
FILTER (?property NOT IN (dce:creator, dce:date, IAO:0000115, IAO:0000231, IAO:0100001, mondo:excluded_subClassOf, mondo:excluded_from_qc_check, mondo:excluded_synonym, mondo:pathogenesis, mondo:related, mondo:confidence, dc:conformsTo, mondo:should_conform_to, oboInOwl:consider, oboInOwl:created_by, oboInOwl:creation_date, oboInOwl:hasAlternativeId, oboInOwl:hasBroadSynonym, oboInOwl:hasDbXref, oboInOwl:hasExactSynonym, oboInOwl:hasNarrowSynonym, oboInOwl:hasRelatedSynonym, oboInOwl:id, oboInOwl:inSubset, owl:deprecated, rdfs:comment, rdfs:isDefinedBy, rdfs:label, rdfs:seeAlso, RO:0002161, skos:broadMatch, skos:closeMatch, skos:exactMatch, skos:narrowMatch))
FILTER (?property NOT IN (
IAO:0000115,
IAO:0000231,
IAO:0000233,
IAO:0000589,
IAO:0006012,
IAO:0100001,
RO:0002161,
RO:0002175,
dc:conformsTo,
dc:creator,
dce:date,
mondo:confidence,
mondo:excluded_from_qc_check,
mondo:excluded_subClassOf,
mondo:excluded_synonym,
mondo:pathogenesis,
mondo:related,
mondo:should_conform_to,
oboInOwl:consider,
oboInOwl:creation_date,
oboInOwl:hasAlternativeId,
oboInOwl:hasBroadSynonym,
oboInOwl:hasDbXref,
oboInOwl:hasExactSynonym,
oboInOwl:hasNarrowSynonym,
oboInOwl:hasRelatedSynonym,
oboInOwl:id,
oboInOwl:inSubset,
owl:deprecated,
owl:disjointWith,
owl:equivalentClass,
rdf:type,
rdfs:comment,
rdfs:isDefinedBy,
rdfs:label,
rdfs:seeAlso,
rdfs:subClassOf,
rdfs:subPropertyOf,
skos:broadMatch,
skos:closeMatch,
skos:exactMatch,
skos:narrowMatch,
skos:relatedMatch
)
)
}
```

### qc-proxy-merge-missing-preferred.sparql

```
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
prefix owl: <http://www.w3.org/2002/07/owl#>
prefix oboInOwl: <http://www.geneontology.org/formats/oboInOwl#>
prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>
SELECT DISTINCT ?entity ?property ?value WHERE {
?entity rdfs:subClassOf+ <http://purl.obolibrary.org/obo/MONDO_0000001> .
?entity oboInOwl:hasDbXref ?xref .
?entity oboInOwl:hasDbXref ?xref2 .
?xref_anno a owl:Axiom ;
owl:annotatedSource ?entity ;
owl:annotatedProperty oboInOwl:hasDbXref ;
owl:annotatedTarget ?xref ;
oboInOwl:source ?source1 .
?xref_anno2 a owl:Axiom ;
owl:annotatedSource ?entity ;
owl:annotatedProperty oboInOwl:hasDbXref ;
owl:annotatedTarget ?xref2 ;
oboInOwl:source ?source2 .
FILTER(STRSTARTS(STR(?xref),"DOID") || STRSTARTS(STR(?xref),"Orphanet") || STRSTARTS(STR(?xref),"OMIM"))
FILTER(str(?xref2)!=str(?xref))
FILTER(STRBEFORE(str(?xref),":") = STRBEFORE(str(?xref2),":"))
FILTER NOT EXISTS {
?xref_anno oboInOwl:source ?source11 .
FILTER ((str(?source11)="MONDO:preferredExternal"))
}
FILTER NOT EXISTS {
?xref_anno2 oboInOwl:source ?source21 .
FILTER ((str(?source21)="MONDO:preferredExternal"))
}
FILTER ((str(?source1)="MONDO:equivalentTo") || (str(?source1)="MONDO:equivalentObsolete"))
FILTER ((str(?source2)="MONDO:equivalentTo") || (str(?source2)="MONDO:equivalentObsolete"))
FILTER ((str(?source1)="MONDO:equivalentTo") && (str(?source2)="MONDO:equivalentTo"))
FILTER ((str(?source1)="MONDO:equivalentObsolete") && (str(?source2)="MONDO:equivalentObsolete"))
FILTER (isIRI(?entity) && STRSTARTS(str(?entity), "http://purl.obolibrary.org/obo/MONDO_"))
BIND(?xref as ?property)
BIND(?xref2 as ?value)
}
```
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