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author | Munyoki Kilyungi | 2023-05-15 21:20:50 +0300 |
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committer | BonfaceKilz | 2023-05-26 08:40:22 +0300 |
commit | afaa6b096ec0df7055faafbe7f89917f734b3897 (patch) | |
tree | 2c16dc1550468018e14bd4407b5344f895b90331 /examples/dump-tissue.scm | |
parent | 79975a5dc78daa03b43d37b3fe636265c148abc0 (diff) | |
download | gn-transform-databases-afaa6b096ec0df7055faafbe7f89917f734b3897.tar.gz |
Replace dump.scm with separete dumps for several tables
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
Diffstat (limited to 'examples/dump-tissue.scm')
-rwxr-xr-x | examples/dump-tissue.scm | 66 |
1 files changed, 66 insertions, 0 deletions
diff --git a/examples/dump-tissue.scm b/examples/dump-tissue.scm new file mode 100755 index 0000000..3d55383 --- /dev/null +++ b/examples/dump-tissue.scm @@ -0,0 +1,66 @@ +#! /usr/bin/env guile +!# + +(use-modules (srfi srfi-1) + (srfi srfi-26) + (ice-9 match) + (ice-9 regex) + (dump strings) + (dump sql) + (dump triples) + (dump special-forms)) + + + +(define %connection-settings + (call-with-input-file (list-ref (command-line) 1) + read)) + +(define %dump-directory + (list-ref (command-line) 2)) + + + +(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)) + (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)))) + + + +(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 "taxon:" "<http://purl.uniprot.org/taxonomy/>") + (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"))) |