diff options
| -rwxr-xr-x | examples/dump-probeset-metadata.scm | 65 |
1 files changed, 24 insertions, 41 deletions
diff --git a/examples/dump-probeset-metadata.scm b/examples/dump-probeset-metadata.scm index b0c4853..6da1eb0 100755 --- a/examples/dump-probeset-metadata.scm +++ b/examples/dump-probeset-metadata.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-probeset-metadata (tables (ProbeSetXRef @@ -27,14 +24,14 @@ "WHERE ProbeSetFreeze.public > 0 AND ProbeSetFreeze.confidentiality < 1") (schema-triples (gn:probesetData rdfs:range gn:probeset) - (gn:hasProbeset rdfs:range rdfs:Literal)) + (gn-term:hasProbeset rdfs:range rdfs:Literal)) (triples (string->identifier "probesetData" (field ("CONCAT(ProbeSetFreeze.Name,':',IFNULL(ProbeSet.Name, ProbeSet.Id))" ProbeSetName))) (set rdf:type 'gn:probesetData) - (set gn:hasProbeset + (set gn-term:hasProbeset (ontology 'probeset: (regexp-substitute/global @@ -42,66 +39,52 @@ (field ("IFNULL(ProbeSet.Name, ProbeSet.Id)" name)) 'pre "_" 'post))) - (set gn:probesetOfDataset + (set gn-term:probesetOfDataset (ontology 'probeset: (regexp-substitute/global #f "[^A-Za-z0-9:]" (field ProbeSetFreeze Name) 'pre "_" 'post))) - (set gn:mean + (set gn-term:mean (annotate-field (field ("IFNULL(ProbeSetXRef.mean, '')" mean)) '^^xsd:double)) - (set gn:se + (set gn-term:se (annotate-field (field ("IFNULL(ProbeSetXRef.se, '')" se)) '^^xsd:double)) - (set gn:locus (field ProbeSetXRef Locus)) + (set gn-term:locus (field ProbeSetXRef Locus)) (set gn:LRS (annotate-field (field ("IFNULL(ProbeSetXRef.LRS, '')" LRS)) '^^xsd:double)) - (set gn:pValue + (set gn-term:pValue (annotate-field (field ("IFNULL(ProbeSetXRef.pValue, '')" pValue)) '^^xsd:double)) - (set gn:additive + (set gn-term:additive (annotate-field (field ("IFNULL(ProbeSetXRef.additive, '')" additive)) '^^xsd:double)) - (set gn:h2 + (set gn-term:h2 (annotate-field (field ("IFNULL(ProbeSetXRef.h2, '')" h2)) '^^xsd:float)))) -(call-with-target-database - %connection-settings - (lambda (db) - (with-output-to-file (string-append %dump-directory "dump-probeset-metadata.ttl") - (lambda () - (prefix "chebi:" "<http://purl.obolibrary.org/obo/CHEBI_>") - (prefix "dct:" "<http://purl.org/dc/terms/>") - (prefix "foaf:" "<http://xmlns.com/foaf/0.1/>") - (prefix "generif:" "<http://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=Graphics&list_uids=>") - (prefix "gn:" "<http://genenetwork.org/>") - (prefix "hgnc:" "<http://bio2rdf.org/hgnc:>") - (prefix "homologene:" "<https://bio2rdf.org/homologene:>") - (prefix "kegg:" "<http://bio2rdf.org/ns/kegg#>") - (prefix "molecularTrait:" "<http://genenetwork.org/molecular-trait/>") - (prefix "nuccore:" "<https://www.ncbi.nlm.nih.gov/nuccore/>") - (prefix "omim:" "<https://www.omim.org/entry/>") - (prefix "owl:" "<http://www.w3.org/2002/07/owl#>") - (prefix "phenotype:" "<http://genenetwork.org/phenotype/>") - (prefix "pubchem:" "<https://pubchem.ncbi.nlm.nih.gov/>") - (prefix "pubmed:" "<http://rdf.ncbi.nlm.nih.gov/pubmed/>") - (prefix "rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>") - (prefix "rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>") - (prefix "uniprot:" "<http://purl.uniprot.org/uniprot/>") - (prefix "up:" "<http://purl.uniprot.org/core/>") - (prefix "xsd:" "<http://www.w3.org/2001/XMLSchema#>") - (prefix "probeset:" "<http://genenetwork.org/probeset/>") - (newline) - (dump-probeset-metadata db)) - #:encoding "utf8"))) +(dump-with-documentation + (name "Probeset Metadata") + (connection %connection-settings) + (table-metadata? #f) + (prefixes + '(("gn:" "<http://genenetwork.org/id/>") + ("gn-term:" "<http://genenetwork.org/id/>") + ("rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>") + ("rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>") + ("xsd:" "<http://www.w3.org/2001/XMLSchema#>"))) + (inputs + (list dump-probeset-metadata)) + (outputs + '(#:documentation "./docs/dump-probeset-metadata.md" + #:rdf "./verified-data/dump-probeset-metadata.ttl"))) |