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| author | Munyoki Kilyungi | 2023-06-05 22:35:49 +0300 |
|---|---|---|
| committer | BonfaceKilz | 2023-06-12 19:06:36 +0300 |
| commit | aabe2fcc6b9e48269b0051bf115093d974d10065 (patch) | |
| tree | 03901ac02c35ed9ed1a0b82946af741f6530d529 /examples/dump-generif.scm | |
| parent | 87a0616ab9ca1e2a32348e243e96f06a1bb6e204 (diff) | |
| download | gn-transform-databases-aabe2fcc6b9e48269b0051bf115093d974d10065.tar.gz | |
Use NCBI taxonomy browser instead of uniprot
NCBI presents data in a user friendly way from the taxid. To get the same data from uniprot, you need a unique identify which requires an extra query to retrieve. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
Diffstat (limited to 'examples/dump-generif.scm')
| -rwxr-xr-x | examples/dump-generif.scm | 4 |
1 files changed, 2 insertions, 2 deletions
diff --git a/examples/dump-generif.scm b/examples/dump-generif.scm index 083490f..b546f42 100755 --- a/examples/dump-generif.scm +++ b/examples/dump-generif.scm @@ -36,7 +36,7 @@ (string-split (field ("GROUP_CONCAT(DISTINCT Species.SpeciesName)" species)) #\,)) - (multiset gn:taxId (map (cut ontology 'taxon: <>) + (multiset gn:taxId (map (cut ontology 'ncbiTaxon: <>) (string-split (field ("GROUP_CONCAT(DISTINCT TaxID)" taxId)) #\,))))) @@ -139,7 +139,7 @@ (prefix "dct:" "<http://purl.org/dc/terms/>") (prefix "pubmed:" "<http://rdf.ncbi.nlm.nih.gov/pubmed/>") (prefix "up:" "<http://purl.uniprot.org/core/>") - (prefix "taxon:" "<http://purl.uniprot.org/taxonomy/>") + (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#>") |