diff options
-rwxr-xr-x | examples/dump-dataset-metadata.scm | 1 | ||||
-rwxr-xr-x | examples/dump-generif.scm | 4 | ||||
-rwxr-xr-x | examples/dump-genotype.scm | 1 | ||||
-rwxr-xr-x | examples/dump-phenotype.scm | 1 | ||||
-rwxr-xr-x | examples/dump-probeset-metadata.scm | 1 | ||||
-rwxr-xr-x | examples/dump-probeset.scm | 1 | ||||
-rwxr-xr-x | examples/dump-probesetfreeze.scm | 1 | ||||
-rwxr-xr-x | examples/dump-publication.scm | 1 | ||||
-rwxr-xr-x | examples/dump-species-metadata.scm | 4 | ||||
-rwxr-xr-x | examples/dump-tissue.scm | 1 |
10 files changed, 4 insertions, 12 deletions
diff --git a/examples/dump-dataset-metadata.scm b/examples/dump-dataset-metadata.scm index aad2331..afbec75 100755 --- a/examples/dump-dataset-metadata.scm +++ b/examples/dump-dataset-metadata.scm @@ -229,7 +229,6 @@ (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#>") 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#>") diff --git a/examples/dump-genotype.scm b/examples/dump-genotype.scm index 6da3630..1be1d34 100755 --- a/examples/dump-genotype.scm +++ b/examples/dump-genotype.scm @@ -102,7 +102,6 @@ (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#>") diff --git a/examples/dump-phenotype.scm b/examples/dump-phenotype.scm index d7d940f..a493fa2 100755 --- a/examples/dump-phenotype.scm +++ b/examples/dump-phenotype.scm @@ -129,7 +129,6 @@ (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#>") diff --git a/examples/dump-probeset-metadata.scm b/examples/dump-probeset-metadata.scm index b3f4165..b0c4853 100755 --- a/examples/dump-probeset-metadata.scm +++ b/examples/dump-probeset-metadata.scm @@ -98,7 +98,6 @@ (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#>") diff --git a/examples/dump-probeset.scm b/examples/dump-probeset.scm index 730e914..6b1b7a8 100755 --- a/examples/dump-probeset.scm +++ b/examples/dump-probeset.scm @@ -75,7 +75,6 @@ (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#>") diff --git a/examples/dump-probesetfreeze.scm b/examples/dump-probesetfreeze.scm index fb46120..605e415 100755 --- a/examples/dump-probesetfreeze.scm +++ b/examples/dump-probesetfreeze.scm @@ -74,7 +74,6 @@ (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#>") diff --git a/examples/dump-publication.scm b/examples/dump-publication.scm index b0b35b6..e4c57ad 100755 --- a/examples/dump-publication.scm +++ b/examples/dump-publication.scm @@ -82,7 +82,6 @@ (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#>") diff --git a/examples/dump-species-metadata.scm b/examples/dump-species-metadata.scm index ed4113c..2937c80 100755 --- a/examples/dump-species-metadata.scm +++ b/examples/dump-species-metadata.scm @@ -34,7 +34,7 @@ (set gn:displayName (field Species MenuName)) (set gn:binomialName (field Species FullName)) (set gn:family (field Species Family)) - (set up:organism (ontology 'taxon: (field Species TaxonomyId))))) + (set gn:organism (ontology 'ncbiTaxon: (field Species TaxonomyId))))) (define-dump dump-strain (tables (Strain @@ -128,7 +128,7 @@ (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 "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#>") diff --git a/examples/dump-tissue.scm b/examples/dump-tissue.scm index 3d55383..b1104ab 100755 --- a/examples/dump-tissue.scm +++ b/examples/dump-tissue.scm @@ -57,7 +57,6 @@ (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#>") |