diff options
Diffstat (limited to 'examples')
| -rwxr-xr-x | examples/dump-tissue.scm | 57 |
1 files changed, 19 insertions, 38 deletions
diff --git a/examples/dump-tissue.scm b/examples/dump-tissue.scm index b1104ab..4998cff 100755 --- a/examples/dump-tissue.scm +++ b/examples/dump-tissue.scm @@ -13,53 +13,34 @@ (define %connection-settings - (call-with-input-file (list-ref (command-line) 1) - read)) - -(define %dump-directory - (list-ref (command-line) 2)) + (call-with-input-file (list-ref (command-line) 1) + read)) (define-dump dump-tissue - ;; The Name and TissueName fields seem to be identical. BIRN_lex_ID - ;; and BIRN_lex_Name are mostly NULL. - (tables (Tissue)) + ;; The Name and TissueName fields seem to be identical. BIRN_lex_ID + ;; and BIRN_lex_Name are mostly NULL. + (tables (Tissue)) (schema-triples (gn:name rdfs:range rdfs:Literal)) ;; Hopefully the Short_Name field is distinct and can be used as an ;; identifier. (triples (string->identifier "tissue" (field Tissue Short_Name)) - (set rdf:type 'gn:tissue) - (set gn:name (field Tissue Name)))) + (set rdf:type 'gn:tissue) + (set gn:name (field Tissue Name)))) -(call-with-target-database - %connection-settings - (lambda (db) - (with-output-to-file (string-append %dump-directory "dump-tissue.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#>") - (newline) - (dump-tissue db)) - #:encoding "utf8"))) +(dump-with-documentation + (name "Tissue 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/terms/>"))) + (inputs + (dump-tissue)) + (outputs + (#:documentation "./docs/dump-tissue.md" #:rdf "./verified-data/dump-tissue.ttl"))) |