diff options
| -rwxr-xr-x | examples/dump-species-metadata.scm | 57 |
1 files changed, 19 insertions, 38 deletions
diff --git a/examples/dump-species-metadata.scm b/examples/dump-species-metadata.scm index 2937c80..4ea9ce7 100755 --- a/examples/dump-species-metadata.scm +++ b/examples/dump-species-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-species @@ -34,11 +31,11 @@ (set gn:displayName (field Species MenuName)) (set gn:binomialName (field Species FullName)) (set gn:family (field Species Family)) - (set gn:organism (ontology 'ncbiTaxon: (field Species TaxonomyId))))) + (set gn:organism (ontology 'taxon: (field Species TaxonomyId))))) (define-dump dump-strain (tables (Strain - (join Species "ON Strain.SpeciesId = Species.SpeciesId"))) + (left-join Species "ON Strain.SpeciesId = Species.SpeciesId"))) (schema-triples (gn:strainOfSpecies rdfs:domain gn:strain) (gn:strainOfSpecies rdfs:range gn:species) @@ -106,36 +103,20 @@ -(call-with-target-database - %connection-settings - (lambda (db) - (with-output-to-file (string-append %dump-directory "dump-species-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 "ncbiTaxon:" "<https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=>") - (prefix "uniprot:" "<http://purl.uniprot.org/uniprot/>") - (prefix "up:" "<http://purl.uniprot.org/core/>") - (prefix "xsd:" "<http://www.w3.org/2001/XMLSchema#>") - (newline) - (dump-species db) - (dump-strain db) - (dump-mapping-method db) - (dump-inbred-set db) - (dump-avg-method db)) - #:encoding "utf8"))) +(dump-with-documentation + (name "Species 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/>") + ("taxon:" "<http://purl.uniprot.org/taxonomy/>"))) + (inputs + (dump-species + dump-strain + dump-mapping-method + dump-avg-method)) + (outputs + (#:documentation "docs/dump-species-metadata.md" + #:rdf "./verified-data/dump-species-metadata.ttl"))) |