From 9bafebc914c183c57ee38011bacd6f77a2a1f1bb Mon Sep 17 00:00:00 2001
From: Munyoki Kilyungi
Date: Mon, 29 May 2023 14:29:44 +0300
Subject: Delete unused prefixes

Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
---
 examples/dump-dataset-metadata.scm |  8 ------
 examples/dump-genotype.scm         |  8 ------
 examples/dump-probeset.scm         | 55 ++++++++------------------------------
 examples/dump-probesetfreeze.scm   |  8 ------
 4 files changed, 11 insertions(+), 68 deletions(-)

diff --git a/examples/dump-dataset-metadata.scm b/examples/dump-dataset-metadata.scm
index 9d575df..76eaeb1 100755
--- a/examples/dump-dataset-metadata.scm
+++ b/examples/dump-dataset-metadata.scm
@@ -185,20 +185,12 @@
  (lambda (db)
    (with-output-to-file (string-append %dump-directory "dump-info-pages.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#>")
diff --git a/examples/dump-genotype.scm b/examples/dump-genotype.scm
index 53d101b..6da3630 100755
--- a/examples/dump-genotype.scm
+++ b/examples/dump-genotype.scm
@@ -93,20 +93,12 @@
  (lambda (db)
    (with-output-to-file (string-append %dump-directory "dump-genotype.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#>")
diff --git a/examples/dump-probeset.scm b/examples/dump-probeset.scm
index bbf5d8d..c28f7dd 100755
--- a/examples/dump-probeset.scm
+++ b/examples/dump-probeset.scm
@@ -48,44 +48,19 @@
     (multiset gn:alias (map string-trim-both
                             (string-split (sanitize-rdf-string (field ProbeSet alias))
                                           #\;)))
+    (set gn:unigene (field ProbeSet UniGeneId))
     (set gn:generif (ontology 'generif: (field ProbeSet GeneId)))
-    (set gn:genbank (ontology 'nuccore: (field ProbeSet GenbankId)))
-    (set gn:snp (field ("IFNULL(ProbeSet.SNP, '')" SNP)))
-    (set gn:blatSeq (string-trim-both (field ProbeSet BlatSeq)))
-    (set gn:targetSeq (field ProbeSet TargetSeq))
-    (set gn:omim (ontology 'omim: (field ProbeSet OMIM)))
-    (set gn:specificity (annotate-field
-                         (field ("IFNULL(ProbeSet.Probe_set_specificity, '')" Probe_set_specificity))
-                         '^^xsd:double))
-    (set gn:blatScore (annotate-field
-                       (field ("IFNULL(ProbeSet.Probe_set_BLAT_score, '')" Probe_set_BLAT_score))
-                       '^^xsd:double))
-    (set gn:blatMbStart (annotate-field
-                         (field ("IFNULL(ProbeSet.Probe_set_Blat_Mb_start, '')" Probe_set_Blat_Mb_start))
-                         '^^xsd:double))
-    (set gn:blatMbend (annotate-field
-                       (field ("IFNULL(ProbeSet.Probe_set_Blat_Mb_end, '')" Probe_set_Blat_Mb_end))
-                       '^^xsd:double))
-    (set gn:strand (field ProbeSet Probe_set_strand))
-    (set gn:chrNum (field ("IFNULL(ProbeSet.chr_num, '')" chr_num)))
-    (set gn:nameNum (field ("IFNULL(ProbeSet.name_num, '')" name_num)))
-    (set gn:RefSeq_TranscriptId (ontology 'nuccore: (field ProbeSet RefSeq_TranscriptId)))
-    (set gn:Chr_mm8 (field ("IFNULL(ProbeSet.Chr_mm8, '')" Chr_mm8)))
-    (set gn:Mb_mm8 (field ("IFNULL(ProbeSet.Mb_mm8, '')" Mb_mm8)))
+    (set gn:genbank (field ProbeSet GenbankId))
+    (set gn:blatSeq (sanitize-rdf-string
+                     (string-trim-both (field ProbeSet BlatSeq))))
+    (set gn:targetSeq (sanitize-rdf-string (field ProbeSet TargetSeq)))
+    (set gn:omim
+         (ontology
+          'omim:
+          (field ("IF(ProbeSet.OMIM REGEXP '^-?[0-9]+$' > 0, ProbeSet.OMIM, '')" OMIM))))
+    (set gn:RefSeq_TranscriptId (field ProbeSet RefSeq_TranscriptId))
     (set gn:uniProtReference (ontology 'uniprot:
-                                       (field ProbeSet UniProtID)))
-    (set gn:PubChemID (ontology
-                       'pubchem:
-                       (field
-                        ("IFNULL(ProbeSet.PubChem_ID, '')"
-                         PubChem_ID))))
-    (multiset gn:tissue (map string-trim-both
-                        (string-split
-                         (field ("IFNULL(ProbeSet.Tissue, '')" Tissue))
-                         #\,)))
-    (set gn:primaryName (field ProbeSet PrimaryName))
-    (set gn:secondaryNames (field ProbeSet SecondaryNames))
-    (set gn:peptideSequence (field ProbeSet PeptideSequence))))
+                                        (field ProbeSet UniProtID)))))
 
 
 
@@ -94,20 +69,12 @@
  (lambda (db)
    (with-output-to-file (string-append %dump-directory "dump-probeset.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#>")
diff --git a/examples/dump-probesetfreeze.scm b/examples/dump-probesetfreeze.scm
index b238851..e1fe572 100755
--- a/examples/dump-probesetfreeze.scm
+++ b/examples/dump-probesetfreeze.scm
@@ -64,20 +64,12 @@
  (lambda (db)
    (with-output-to-file (string-append %dump-directory "dump-probesetfreeze.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#>")
-- 
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