From 8076e5c096d709e707927b1bad7090063dc68ce0 Mon Sep 17 00:00:00 2001
From: Munyoki Kilyungi
Date: Tue, 23 May 2023 15:46:48 +0300
Subject: Remove unnecessary fields from probeset dump
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
---
examples/dump-probeset.scm | 48 +++++++++++++++++++++-------------------------
1 file changed, 22 insertions(+), 26 deletions(-)
(limited to 'examples')
diff --git a/examples/dump-probeset.scm b/examples/dump-probeset.scm
index d1ea2ae..0b37514 100755
--- a/examples/dump-probeset.scm
+++ b/examples/dump-probeset.scm
@@ -35,12 +35,17 @@
(left-join GeneChip "ON GeneChip.Id = ProbeSet.ChipId")))
(schema-triples
(gn:name rdfs:range rdfs:Literal))
- (triples (ontology 'gn:probeset_ (field ("IFNULL(ProbeSet.Name, ProbeSet.Id)"
- name)))
+ (triples (ontology
+ 'probeset:
+ (field ("IFNULL(ProbeSet.Name, ProbeSet.Id)"
+ name)))
(set gn:probesetOfDataset
- (string->identifier
- "dataset"
- (field ProbeSetFreeze Name)))
+ (ontology
+ 'probeset:
+ (regexp-substitute/global
+ #f "[^A-Za-z0-9:]"
+ (field ProbeSetFreeze Name)
+ 'pre "_" 'post)))
(set gn:mean (annotate-field (field ("IFNULL(ProbeSetXRef.mean, '')" mean))
'^^xsd:double))
(set gn:se (annotate-field (field ("IFNULL(ProbeSetXRef.se, '')" se))
@@ -60,8 +65,6 @@
(set gn:description (field ProbeSet description))
(set gn:chr (field ProbeSet Chr))
(set gn:mb (annotate-field (field ("IFNULL(ProbeSet.Mb, '')" Mb)) '^^xsd:double))
- (set gn:chr_2016 (field ProbeSet Chr_2016))
- (set gn:mb_2016 (annotate-field (field ("IFNULL(ProbeSet.Mb_2016, '')" Mb_2016)) '^^xsd:double))
(set gn:alias (string-trim-both (field ProbeSet alias)))
(set gn:generif (ontology 'generif: (field ProbeSet GeneId)))
(set gn:genbank (ontology 'nuccore: (field ProbeSet GenbankId)))
@@ -86,21 +89,8 @@
(set gn:blatMbend (annotate-field
(field ("IFNULL(ProbeSet.Probe_set_Blat_Mb_end, '')" Probe_set_Blat_Mb_end))
'^^xsd:double))
- (set gn:blatMbStart2016
- (annotate-field
- (field ("IFNULL(ProbeSet.Probe_set_Blat_Mb_start_2016, '')" Probe_set_Blat_Mb_start_2016)) '^^xsd:double))
- (set gn:blatMbend2016
- (annotate-field
- (field ("IFNULL(ProbeSet.Probe_set_Blat_Mb_end_2016, '')" Probe_set_Blat_Mb_end_2016)) '^^xsd:double))
(set gn:strand (field ProbeSet Probe_set_strand))
- (set gn:noteByRW (field ProbeSet Probe_set_Note_by_RW))
(set gn:flag (field ProbeSet flag))
- (set gn:symbolH (field ProbeSet Symbol_H))
- (set gn:descriptionH (field ProbeSet Description_H))
- (set gn:chromosomeH (field ProbeSet chromosome_H))
- (set gn:mbH (annotate-field (field ProbeSet MB_H) '^^xsd:double))
- (set gn:aliasH (field ProbeSet alias_H))
- (set gn:geneIdH (field ProbeSet GeneId_H))
(set gn:chrNum (field ("IFNULL(ProbeSet.chr_num, '')" chr_num)))
(set gn:nameNum (field ("IFNULL(ProbeSet.name_num, '')" name_num)))
(set gn:probeTargetDescription (field ProbeSet Probe_Target_Description))
@@ -157,16 +147,21 @@
;; Molecular Traits are also referred to as ProbeSets
(define-dump dump-probesetfreeze
(tables (ProbeSetFreeze
+ (left-join InfoFiles "ON InfoFiles.InfoPageName = ProbeSetFreeze.Name")
(left-join ProbeFreeze "USING (ProbeFreezeId)")
(left-join AvgMethod "ON AvgMethod.AvgMethodId = ProbeSetFreeze.AvgID")
(left-join InbredSet "ON ProbeFreeze.InbredSetId=InbredSet.Id")
(left-join Tissue "USING (TissueId)"))
- "WHERE ProbeSetFreeze.public > 0 GROUP BY ProbeFreeze.Id")
+ "WHERE ProbeSetFreeze.public > 0 AND InfoFiles.InfoPageName IS NULL GROUP BY ProbeFreeze.Id")
(schema-triples
- (gn:molecularTrait rdfs:range rdfs:Literal))
+ (gn:avgMethod rdfs:range rdfs:Literal)
+ (gn:dataScale rdfs:range rdfs:Literal))
(triples
- (string->identifier "dataset" (field ProbeSetFreeze Name))
- (set rdf:type 'gn:dataset)
+ (ontology 'probeset:
+ (regexp-substitute/global #f "[^A-Za-z0-9:]"
+ (field ProbeSetFreeze Name)
+ 'pre "_" 'post))
+ (set rdf:type 'gn:probesetDataset)
(set gn:avgMethod (string->identifier "avgmethod" (field AvgMethod Name)))
(set gn:fullName (field ProbeSetFreeze FullName))
(set gn:shortName (field ProbeSetFreeze ShortName))
@@ -206,8 +201,9 @@
(prefix "uniprot:" "<http://purl.uniprot.org/uniprot/>")
(prefix "up:" "<http://purl.uniprot.org/core/>")
(prefix "xsd:" "<http://www.w3.org/2001/XMLSchema#>")
+ (prefix "probeset:" "<http://genenetwork.org/probeset/>")
(newline)
(dump-gene-chip db)
- (dump-probeset db)
- (dump-probesetfreeze db))
+ (dump-probesetfreeze db)
+ (dump-probeset db))
#:encoding "utf8")))
--
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