diff options
Diffstat (limited to 'examples/generif.scm')
| -rwxr-xr-x | examples/generif.scm | 31 |
1 files changed, 9 insertions, 22 deletions
diff --git a/examples/generif.scm b/examples/generif.scm index c4b70ae..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" @@ -47,7 +36,7 @@ GROUP BY GeneRIF.Id, GeneRIF.versionId, GeneRIF.symbol") '(("'" . "\\'")))))) (set rdf:type 'gnc:gn_wiki_entry) (set gnt:symbol (field GeneRIF symbol)) - (set gnt:belongs_to_species (string->identifier "" (remap-species-identifiers (field Species Fullname)))) + (set gnt:has_species (string->identifier "" (remap-species-identifiers (field Species Fullname)))) (set dct:created (string->symbol (format #f "~s^^xsd:datetime " @@ -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" @@ -119,7 +106,7 @@ GROUP BY GeneRIF.Id, GeneRIF.versionId, GeneRIF.symbol") (string-append (format #f "gnc:ncbi_wiki_entry ;\n") (format #f "\trdfs:label ~a ;\n" comment) - (format #f "\tgnt:belongs_to_species ~a ;\n" species) + (format #f "\tgnt:has_species ~a ;\n" species) (format #f "\tgnt:symbol ~s ;\n" symbol) (format #f "\tgnt:has_gene_id generif:~a ;\n" gene-id) (match taxon-id @@ -157,7 +144,7 @@ GROUP BY GeneRIF.Id, GeneRIF.versionId, GeneRIF.symbol") ("gnc:" "<http://rdf.genenetwork.org/v1/category/>") ("gnt:" "<http://rdf.genenetwork.org/v1/term/>") ("dct:" "<http://purl.org/dc/terms/>") - ("foaf:" "<http://xmlns.com/foaf/0.1/>") + ("foaf:" "<http://xmlns.com/foaf/0.1/#term_>") ("pubmed:" "<http://rdf.ncbi.nlm.nih.gov/pubmed/>") ("taxon:" "<https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=>") ("generif:" "<http://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=Graphics&list_uids=>") |