diff options
Diffstat (limited to 'examples')
| -rwxr-xr-x | examples/classification.scm | 2 | ||||
| -rwxr-xr-x | examples/generif.scm | 25 | ||||
| -rwxr-xr-x | examples/genotype.scm | 2 | ||||
| -rwxr-xr-x | examples/ontology.scm | 54 | ||||
| -rwxr-xr-x | examples/phenotype.scm | 10 |
5 files changed, 66 insertions, 27 deletions
diff --git a/examples/classification.scm b/examples/classification.scm index 130bec8..d44fe5d 100755 --- a/examples/classification.scm +++ b/examples/classification.scm @@ -82,7 +82,7 @@ (set rdfs:label (field InbredSet FullName)) (set skos:prefLabel (field InbredSet Name InbredSetName)) (set gnt:genetic_type (field InbredSet GeneticType)) - (set dct:description (annotate-field (sanitize-rdf-string (field InbredSet description)) + (set dct:description (annotate-field (sanitize-rdf-string (field InbredSet Description)) '^^rdf:HTML)) (set gnt:uses_mapping_method (string->identifier "mapping_method" (field MappingMethod Name) #:separator "_")) diff --git a/examples/generif.scm b/examples/generif.scm index 3b794fa..a4a2e4b 100755 --- a/examples/generif.scm +++ b/examples/generif.scm @@ -22,17 +22,6 @@ (left-join GeneCategory "ON GeneRIFXRef.GeneCategoryId = GeneCategory.Id")) "WHERE GeneRIF.display > 0 AND GeneRIF.comment IS NOT NULL GROUP BY GeneRIF.Id, GeneRIF.versionId, GeneRIF.symbol") - (schema-triples - (gnc:gene_wiki_entry a rdfs:Class) - (gnc:gn_wiki_entry rdfs:subClassOf gnc:gene_wiki_entry) - (gnt:initial a owl:ObjectProperty) - (gnt:initial rdfs:domain gnc:gene_wiki_entry) - (gnt:initial skos:definition "Optional user or project code or your initials") - (gnt:reason a owl:ObjectProperty) - (gnt:reason rdfs:domain gnc:gene_wiki_entry) - (gnt:reason skos:definition "The reason why this resource was modified") - (gnc:gn_wiki_entry rdfs:comment "Represents GeneRIF Entries entered from GeneNetwork") - (gnt:gene_symbol rdfs:domain gnc:gn_wiki_entry)) (triples (string->identifier "wiki" (format #f "~a_~a" @@ -61,11 +50,12 @@ GROUP BY GeneRIF.Id, GeneRIF.versionId, GeneRIF.symbol") (format #f "pubmed:~a" (string-trim-both pmid)))))) (string-split (field GeneRIF PubMed_ID PMID) #\space))) - (set foaf:mbox - (match (sanitize-rdf-string (field GeneRIF email)) - ((? string-blank? mbox) "") - (mbox (string->symbol - (format #f "<~a>" mbox))))) + ;; Hide e-mail for now. + ;; (set foaf:mbox + ;; (match (sanitize-rdf-string (field GeneRIF email)) + ;; ((? string-blank? mbox) "") + ;; (mbox (string->symbol + ;; (format #f "<~a>" mbox))))) (set dct:identifier (annotate-field (format #f "~s" (field GeneRIF Id)) '^^xsd:integer)) (set foaf:homepage @@ -86,9 +76,6 @@ GROUP BY GeneRIF.Id, GeneRIF.versionId, GeneRIF.symbol") (define-transformer ncbi-genewiki-entries (tables (GeneRIF_BASIC (left-join Species "USING (SpeciesId)"))) - (schema-triples - (gnc:ncbi_wiki_entry rdfs:subClassOf gnc:gene_wiki_entry) - (gnc:ncbi_wiki_entry rdfs:comment "Represents GeneRIF Entries obtained from NCBI")) (triples (string->identifier "rif" (format #f "~a_~a_~a_~a" diff --git a/examples/genotype.scm b/examples/genotype.scm index 4a91b63..f2ba75f 100755 --- a/examples/genotype.scm +++ b/examples/genotype.scm @@ -24,7 +24,7 @@ (set skos:prefLabel (field Geno Name)) (set skos:altLabel (field Geno Marker_Name)) (set gnt:chr (field Geno Chr)) - (set gnt:mb (annotate-field (field Geno Mb) '^^xsd:doubleg)) + (set gnt:mb (annotate-field (field Geno Mb) '^^xsd:double)) (set gnt:sequence (field Geno Sequence)) (set gnt:source (field Geno Source)) (set rdfs:comment (field Geno Comments)))) diff --git a/examples/ontology.scm b/examples/ontology.scm index 724a75a..f2b54cc 100755 --- a/examples/ontology.scm +++ b/examples/ontology.scm @@ -269,4 +269,56 @@ (triple 'gnt:source 'rdfs:label "Source") (triple 'gnt:source 'rdfs:domain 'gnc:marker) (triple 'gnt:source 'rdfs:range 'rdfs:Literal) - (triple 'gnt:source 'rdfs:subPropertyOf 'sdmx-measure:obsValue)))) + (triple 'gnt:source 'rdfs:subPropertyOf 'sdmx-measure:obsValue) + + ;; Probesets + (triple 'gnc:probeset 'a 'owl:Class) + (triple 'gnc:probeset 'a 'skos:Concept) + (triple 'gnc:probeset 'rdfs:label "A probeset") + (triple 'gnt:has_target_id 'a 'owl:ObjectProperty) + (triple 'gnt:has_target_id 'rdfs:label "The target id for this probeset") + (triple 'gnt:has_target_id 'rdfs:domain 'gnc:probeset) + (triple 'gnt:symbol 'a 'owl:ObjectProperty) + (triple 'gnt:symbol 'rdfs:domain 'gnc:probeset) + (triple 'gnt:targets_region 'a 'owl:ObjectProperty) + (triple 'gnt:targets_region 'rdfs:label "The target region") + (triple 'gnt:targets_region 'rdfs:domain 'gnc:probeset) + (triple 'gnt:mb_mm8 'rdfs:domain 'gnc:probeset) + (triple 'gnt:has_specificity 'a 'owl:ObjectProperty) + (triple 'gnt:has_specificity 'rdfs:domain 'gnc:probeset) + (triple 'gnt:has_blat_score 'a 'owl:ObjectProperty) + (triple 'gnt:has_blat_score 'rdfs:domain 'gnc:probeset) + (triple 'gnt:has_blat_mb_start 'a 'owl:ObjectProperty) + (triple 'gnt:has_blat_mb_start 'rdfs:domain 'gnc:probeset) + (triple 'gnt:has_blat_mb_end 'a 'owl:ObjectProperty) + (triple 'gnt:has_blat_mb_end 'rdfs:domain 'gnc:probeset) + (triple 'gnt:has_blat_seq 'a 'owl:ObjectProperty) + (triple 'gnt:has_blat_seq 'rdfs:domain 'gnc:probeset) + (triple 'gnt:has_target_seq 'a 'owl:ObjectProperty) + (triple 'gnt:has_target_seq 'rdfs:domain 'gnc:probeset) + (triple 'gnt:has_homologene_id 'a 'owl:ObjectProperty) + (triple 'gnt:has_homologene_id 'rdfs:domain 'gnc:probeset) + (triple 'gnt:has_uniprot_id 'a 'owl:ObjectProperty) + (triple 'gnt:has_uniprot_id 'rdfs:domain 'gnc:probeset) + (triple 'gnt:has_pub_chem_id 'a 'owl:ObjectProperty) + (triple 'gnt:has_pub_chem_id 'rdfs:domain 'gnc:probeset) + (triple 'gnt:has_kegg_id 'a 'owl:ObjectProperty) + (triple 'gnt:has_kegg_id 'rdfs:domain 'gnc:probeset) + (triple 'gnt:has_omim_id 'a 'owl:ObjectProperty) + (triple 'gnt:has_omim_id 'rdfs:domain 'gnc:probeset) + (triple 'gnt:has_chebi_id 'a 'owl:ObjectProperty) + (triple 'gnt:has_chebi_id 'rdfs:domain 'gnc:probeset) + + ;; RIF + (triple 'gnc:gene_wiki_entry 'a 'rdfs:Class) + (triple 'gnc:gn_wiki_entry 'rdfs:subClassOf 'gnc:gene_wiki_entry) + (triple 'gnt:initial 'a 'owl:ObjectProperty) + (triple 'gnt:initial 'rdfs:domain 'gnc:gene_wiki_entry) + (triple 'gnt:initial 'skos:definition "Optional user or project code or your initials") + (triple 'gnt:reason 'a 'owl:ObjectProperty) + (triple 'gnt:reason 'rdfs:domain 'gnc:gene_wiki_entry) + (triple 'gnt:reason 'skos:definition "The reason why this resource was modified") + (triple 'gnc:gn_wiki_entry 'rdfs:comment "Represents GeneRIF Entries entered from GeneNetwork") + (triple 'gnt:gene_symbol 'rdfs:domain 'gnc:gn_wiki_entry) + (triple 'gnc:ncbi_wiki_entry 'rdfs:subClassOf 'gnc:gene_wiki_entry) + (triple 'gnc:ncbi_wiki_entry 'rdfs:comment "Represents GeneRIF Entries obtained from NCBI")))) diff --git a/examples/phenotype.scm b/examples/phenotype.scm index 834ff5a..c2564b6 100755 --- a/examples/phenotype.scm +++ b/examples/phenotype.scm @@ -84,13 +84,13 @@ (set rdf:type 'gnc:phenotype_trait) (set gnt:has_strain (string->identifier "set" (field InbredSet Name InbredSetName) #:separator "_")) (set owl:equivalentClass - (field ("CONCAT(IFNULL(InbredSet.InbredSetCode, PublishXRef.InbredSetId), '_', PublishXRef.Id)" - Phenotype))) + (field ("CONCAT(PublishFreeze.Name, '_', PublishXRef.Id)" + PublishFreeze))) (set dcat:distribution (string->symbol - (format #f "gnd:~a" + (format #f "gnd:~a.json" (field ("CONCAT(PublishFreeze.Name, '_', PublishXRef.Id)" - Phenotype)))) ) + PublishFreeze)))) ) (set dct:references (let ((pmid (field ("IF(Publication.PubMed_ID IS NULL, '', CONVERT(Publication.PubMed_Id, INT))" @@ -144,7 +144,7 @@ ("gn:" "<http://rdf.genenetwork.org/v1/id/>") ("owl:" "<http://www.w3.org/2002/07/owl#>") ("gnc:" "<http://rdf.genenetwork.org/v1/category/>") - ("gnd:" "<https://cd.genenetwork.org/lmdb/v1/data/traits/>") + ("gnd:" "<https://cd.genenetwork.org/api3/lmdb/v1/data/traits/>") ("gnt:" "<http://rdf.genenetwork.org/v1/term/>") ("sdmx-measure:" "<http://purl.org/linked-data/sdmx/2009/measure#>") ("skos:" "<http://www.w3.org/2004/02/skos/core#>") |