From aabe2fcc6b9e48269b0051bf115093d974d10065 Mon Sep 17 00:00:00 2001
From: Munyoki Kilyungi
Date: Mon, 5 Jun 2023 22:35:49 +0300
Subject: 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>
---
 examples/dump-dataset-metadata.scm  | 1 -
 examples/dump-generif.scm           | 4 ++--
 examples/dump-genotype.scm          | 1 -
 examples/dump-phenotype.scm         | 1 -
 examples/dump-probeset-metadata.scm | 1 -
 examples/dump-probeset.scm          | 1 -
 examples/dump-probesetfreeze.scm    | 1 -
 examples/dump-publication.scm       | 1 -
 examples/dump-species-metadata.scm  | 4 ++--
 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#>")
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