diff options
Diffstat (limited to 'examples/dump-generif.scm')
| -rwxr-xr-x | examples/dump-generif.scm | 102 |
1 files changed, 46 insertions, 56 deletions
diff --git a/examples/dump-generif.scm b/examples/dump-generif.scm index b546f42..0689f57 100755 --- a/examples/dump-generif.scm +++ b/examples/dump-generif.scm @@ -16,9 +16,6 @@ (call-with-input-file (list-ref (command-line) 1) read)) -(define %dump-directory - (list-ref (command-line) 2)) - (define-dump dump-genewiki-symbols @@ -26,17 +23,17 @@ (left-join Species "USING (SpeciesId)")) "GROUP BY GeneId ORDER BY BINARY symbol") (schema-triples - (gn:symbol rdfs:domain gn:geneWikiEntry) - (gn:wikiEntryOfSpecies rdfs:range gn:species) - (gn:taxid rdfs:domain gn:geneWikiEntry)) + (gnt:symbol rdfs:domain gn-term:geneWikiEntry) + (gnt:wikiEntryOfSpecies rdfs:range gn:species) + (gnt:taxid rdfs:domain gn-term:geneWikiEntry)) (triples (ontology 'generif: (field GeneRIF_BASIC GeneId)) - (multiset gn:symbol (string-split (field ("GROUP_CONCAT(DISTINCT symbol)" symbol)) + (multiset gnt:symbol (string-split (field ("GROUP_CONCAT(DISTINCT symbol)" symbol)) #\,)) - (multiset gn:wikiEntryOfSpecies + (multiset gnt:wikiEntryOfSpecies (string-split (field ("GROUP_CONCAT(DISTINCT Species.SpeciesName)" species)) #\,)) - (multiset gn:taxId (map (cut ontology 'ncbiTaxon: <>) + (multiset gnt:taxId (map (cut ontology 'ncbiTaxon: <>) (string-split (field ("GROUP_CONCAT(DISTINCT TaxID)" taxId)) #\,))))) @@ -48,16 +45,16 @@ (left-join GeneCategory "ON GeneRIFXRef.GeneCategoryId = GeneCategory.Id")) "WHERE GeneRIF.display > 0 AND GeneRIF.VersionId = 0 GROUP BY GeneRIF.symbol") (schema-triples - (gn:geneWikiEntry a rdfs:Class) - (gn:geneWikiEntry a owl:Class) - (gn:geneWikiEntry rdfs:comment "Represents GeneRIF Entries") - (gn:geneCategory rdfs:domain gn:geneWikiEntry) - (gn:geneWikiEntryOfGn rdfs:domain gn:geneWikiEntry) - (gn:geneWikiEntry rdfs:domain gn:geneWikiEntry)) + (gnt:geneWikiEntry a rdfs:Class) + (gnt:geneWikiEntry a owl:Class) + (gnt:geneWikiEntry rdfs:comment "Represents GeneRIF Entries") + (gnt:geneCategory rdfs:domain gn:geneWikiEntry) + (gnt:geneWikiEntryOfGn rdfs:domain gn:geneWikiEntry) + (gnt:geneWikiEntry rdfs:domain gn:geneWikiEntry)) (triples (let ([geneid (field GeneRIF_BASIC GeneId)]) (if (eq? geneid 0) - (ontology 'gn:anonSymbol_ + (ontology 'gnt:anonSymbol_ (field GeneRIF symbol)) (ontology 'generif: geneid))) @@ -65,14 +62,14 @@ (if (string-null? (field ("IFNULL(GeneRIF_BASIC.GeneId, '')" geneWikiEntryP))) "" 'gn:geneWikiEntry)) - (set gn:wikiEntryOfSpecies - (field Species SpeciesName)) + (set gnt:wikiEntryOfSpecies + (string->binomial-name (field Species FullName))) ;; This only dumps symbols not present in the GeneRIF_BASIC table - (set gn:symbol (let ([geneid (field GeneRIF_BASIC GeneId)]) + (set gnt:symbol (let ([geneid (field GeneRIF_BASIC GeneId)]) (if (eq? geneid 0) (field GeneRIF symbol) ""))) - (multiset gn:geneWikiEntryOfGn + (multiset gnt:geneWikiEntryOfGn (let* ([entries (sanitize-rdf-string (field @@ -83,7 +80,7 @@ (match-lambda ((genecategory pmid email text createtime weburl) (blank-node - (set gn:geneCategory genecategory) + (set gnt:geneCategory genecategory) (multiset dct:source (map (lambda (el) (if (string-null? el) "" @@ -94,7 +91,7 @@ 'pre "" 'post)) - (set gn:geneWikiEntry + (set gnt:geneWikiEntry (annotate-field text '^^xsd:string)) (set dct:created (annotate-field createtime @@ -108,12 +105,12 @@ (tables (GeneRIF_BASIC) "GROUP BY GeneId, comment, createtime") (schema-triples - (gn:geneWikiEntryofNCBI rdfs:domain gn:geneWikiEntry)) + (gnt:geneWikiEntryofNCBI rdfs:domain gn:geneWikiEntry)) (triples (ontology 'generif: (field GeneRIF_BASIC GeneId)) - (set gn:geneWikiEntryOfNCBI + (set gnt:geneWikiEntryOfNCBI (blank-node - (set gn:geneWikiEntry + (set gnt:geneWikiEntry (annotate-field (field GeneRIF_BASIC comment) '^^xsd:string)) (multiset dct:source (map (lambda (el) (if (string-null? el) @@ -127,34 +124,27 @@ -(call-with-target-database - %connection-settings - (lambda (db) - (with-output-to-file (string-append %dump-directory "dump-generif.ttl") - (lambda () - (prefix "rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>") - (prefix "rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>") - (prefix "foaf:" "<http://xmlns.com/foaf/0.1/>") - (prefix "gn:" "<http://genenetwork.org/>") - (prefix "dct:" "<http://purl.org/dc/terms/>") - (prefix "pubmed:" "<http://rdf.ncbi.nlm.nih.gov/pubmed/>") - (prefix "up:" "<http://purl.uniprot.org/core/>") - (prefix "ncbiTaxon:" "<https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=>") - (prefix "generif:" "<http://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=Graphics&list_uids=>") - (prefix "xsd:" "<http://www.w3.org/2001/XMLSchema#>") - (prefix "owl:" "<http://www.w3.org/2002/07/owl#>") - (prefix "phenotype:" "<http://genenetwork.org/phenotype/>") - (prefix "molecularTrait:" "<http://genenetwork.org/molecular-trait/>") - (prefix "nuccore:" "<https://www.ncbi.nlm.nih.gov/nuccore/>") - (prefix "omim:" "<https://www.omim.org/entry/>") - (prefix "pubchem:" "<https://pubchem.ncbi.nlm.nih.gov/>") - (prefix "uniprot:" "<http://purl.uniprot.org/uniprot/>") - (prefix "hgnc:" "<http://bio2rdf.org/hgnc:>") - (prefix "homologene:" "<https://bio2rdf.org/homologene:>") - (prefix "chebi:" "<http://purl.obolibrary.org/obo/CHEBI_>") - (prefix "kegg:" "<http://bio2rdf.org/ns/kegg#>") - (newline) - (dump-genewiki-symbols db) - (dump-gn-genewiki-entries db) - (dump-ncbi-genewiki-entries db)) - #:encoding "utf8"))) +(dump-with-documentation + (name "GeneRIF Metadata") + (connection %connection-settings) + (table-metadata? #f) + (prefixes + '(("rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>") + ("rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>") + ("gn:" "<http://genenetwork.org/id/>") + ("gnc:" "<http://genenetwork.org/category/>") + ("gnt:" "<http://genenetwork.org/term/>") + ("dct:" "<http://purl.org/dc/terms/>") + ("pubmed:" "<http://rdf.ncbi.nlm.nih.gov/pubmed/>") + ("ncbiTaxon:" "<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=>") + ("xsd:" "<http://www.w3.org/2001/XMLSchema#>") + ("owl:" "<http://www.w3.org/2002/07/owl#>"))) + (inputs + (list ;; dump-genewiki-symbols + dump-gn-genewiki-entries + ;; dump-ncbi-genewiki-entries + )) + (outputs + '(#:documentation "./docs/dump-generif.md" + #:rdf "./verified-data/dump-generif.ttl"))) |