diff options
| -rw-r--r-- | gn3/api/metadata.py | 64 |
1 files changed, 31 insertions, 33 deletions
diff --git a/gn3/api/metadata.py b/gn3/api/metadata.py index 2ae615b..24cbf11 100644 --- a/gn3/api/metadata.py +++ b/gn3/api/metadata.py @@ -37,21 +37,26 @@ DATASET_CONTEXT = { "foaf": "http://xmlns.com/foaf/0.1/", "geoSeriesId": "gnt:hasGeoSeriesId", "gnt": "http://genenetwork.org/term/", - "inbredSet": "ex:belongsToInbredSet", - "info": "ex:info", + "inbredSet": "gnt:belongsToGroup", "label": "rdfs:label", "normalization": "gnt:usesNormalization", + "platformInfo": "gnt:hasPlatformInfo", "notes": "gnt:hasNotes", "organization": "foaf:Organization", - "platform": "ex:platform", "prefLabel": "skos:prefLabel", + "citation": "dct:isReferencedBy", + "platform": "gnt:gnt:usePlatform", + "GoTree": "gnt:hasGoTreeValue", "processingInfo": "gnt:hasDataProcessingInfo", "rdfs": "http://www.w3.org/2000/01/rdf-schema#", "skos": "http://www.w3.org/2004/02/skos/core#", "specifics": "gnt:hasContentInfo", - "tissue": "ex:tissue", "title": "dct:title", "xkos": "http://rdf-vocabulary.ddialliance.org/xkos#", + "tissueInfo": "gnt:hasTissueInfo", + "tissue": "gnt:hasTissue", + "contactWebUrl": "foaf:homepage", + "contactName": "foaf:name", } SEARCH_CONTEXT = { @@ -139,34 +144,27 @@ def datasets(name): $prefix CONSTRUCT { - ?dataset ?predicate ?term ; - rdf:type dcat:Dataset ; - rdfs:label ?datasetName ; - dct:identifier ?accesionId ; - ex:belongsToInbredSet ?inbredSetName ; - gnt:usesNormalization ?normalizationLabel ; - dcat:contactPoint ?investigatorName ; - xkos:classifiedUnder ?altName ; - gnt:hasContentInfo ?contentInfo ; - dct:creator ?contributors ; - ex:platform ?platform ; - ex:tissue ?tissue . + ?dataset ?predicate ?term . + ?inbredSet rdfs:label ?inbredSetName . ?platform ?platformPred ?platformObject ; - ex:info ?platformInfo . - ?tissue rdfs:label ?tissueName ; - rdf:type gnc:tissue ; - ex:info ?tissueInfo . + gnt:hasPlatformInfo ?platformInfo . + ?normalization ?normalizationPred ?normalizationObj . + ?tissue ?tissuePred ?tissueObj ; + gnt:hasTissueInfo ?tissueInfo . + ?investigator foaf:name ?investigatorName ; + foaf:homepage ?homepage . + ?type skos:prefLabel ?altName . } WHERE { ?dataset rdf:type dcat:Dataset ; - xkos:classifiedUnder ?inbredSet ; - rdfs:label ?datasetName ; + ?predicate ?term ; (rdfs:label|dct:identifier|skos:prefLabel) "$name" . - OPTIONAL { ?dataset dct:identifier ?accesionId . } . - OPTIONAL { ?dataset dct:creator ?contributors . } . - OPTIONAL { ?dataset gnt:hasContentInfo ?contentInfo . } . + FILTER (!regex(str(?predicate), '(hasTissueInfo)', 'i')) . + FILTER (!regex(str(?predicate), '(usesNormalization)', 'i')) . + FILTER (!regex(str(?predicate), '(platformInfo)', 'i')) . OPTIONAL { ?inbredSet ^skos:member gnc:Set ; - rdfs:label ?inbredSetName . + ^gnt:belongsToGroup ?dataset ; + rdfs:label ?inbredSetName . } . OPTIONAL { ?type ^xkos:classifiedUnder ?dataset ; @@ -174,25 +172,25 @@ CONSTRUCT { skos:prefLabel ?altName . } . OPTIONAL { - ?normalization ^gnt:usesNormalization ?dataset ; - rdfs:label ?normalizationLabel . - } . - OPTIONAL { ?investigator foaf:name ?investigatorName ; + foaf:homepage ?homepage ; ^dcat:contactPoint ?dataset . } . OPTIONAL { ?platform ^gnt:usesPlatform ?dataset ; ?platformPred ?platformObject . } . + OPTIONAL { + ?normalization ^gnt:usesNormalization ?dataset ; + ?normalizationPred ?normalizationObj . + } OPTIONAL { ?dataset gnt:hasPlatformInfo ?platformInfo . } . OPTIONAL { ?dataset gnt:hasTissueInfo ?tissueInfo . } . OPTIONAL { ?dataset gnt:hasTissue ?tissue . - ?tissue rdfs:label ?tissueName . + ?tissue rdfs:label ?tissueName ; + ?tissuePred ?tissueObj . } . - FILTER (!regex(str(?predicate), '(classifiedUnder|usesNormalization|contactPoint|hasPlatformInfo|tissueInfo)', 'i')) . - FILTER (!regex(str(?platformPred), '(classifiedUnder|geoSeriesId|hasGoTreeValue)', 'i')) . }""").substitute(prefix=RDF_PREFIXES, name=name) _context = { "@context": BASE_CONTEXT | DATASET_CONTEXT, |