From c3127599d06270acf85a5738c22913d079c38355 Mon Sep 17 00:00:00 2001 From: Munyoki Kilyungi Date: Mon, 11 Dec 2023 15:00:16 +0300 Subject: Remove some resource links from ProbeSet RDF transform. Signed-off-by: Munyoki Kilyungi --- examples/probeset.scm | 209 +------------------------------------------------- 1 file changed, 2 insertions(+), 207 deletions(-) diff --git a/examples/probeset.scm b/examples/probeset.scm index eeb2dcc..d214117 100755 --- a/examples/probeset.scm +++ b/examples/probeset.scm @@ -14,16 +14,9 @@ (define-transformer probeset (tables (ProbeSet (left-join GeneChip "ON GeneChip.Id = ProbeSet.ChipId") - (left-join GeneList "ON GeneList.GeneID = ProbeSet.GeneId") - (left-join GeneList_rn33 "ON GeneList.geneSymbol = ProbeSet.Symbol") - (left-join Species "ON GeneChip.SpeciesId = Species.Id"))) + (left-join Species "ON GeneChip.SpeciesId = Species.Id")) + "WHERE ProbeSet.Name IS NOT NULL") (schema-triples - (gnc:pantherLink rdf:type gnc:ResourceLink) - (gnc:pantherLink rdfs:label "PANTHER") - (gnc:pantherLink rdfs:comments "Gene and protein data resources from Celera-ABI") - (gnc:gnt:NCBIGeneLink rdfs:Class gnc:ResourceLink) - (gnc:gnt:NCBIGeneLink rdfs:label "Gene") - (gnc:gnt:NCBIGeneLink rdfs:comments "Info from NCBI Entrez Gene") (gnc:omimLink rdfs:Class gnc:ResourceLink) (gnc:omimLink rdfs:label "OMIM") (gnc:omimLink rdfs:comments "Summary from On Mendelion Inheritance in Man") @@ -33,33 +26,6 @@ (gnc:uniprotLink rdfs:Class gnc:ResourceLink) (gnc:uniprotLink rdfs:label "UniProt") (gnc:uniprotLink rdfs:comments "UniProt") - (gnc:stringLink rdfs:Class gnc:ResourceLink) - (gnc:stringLink rdfs:label "STRING") - (gnc:stringLink rdfs:comments "Protein interactions: known and inferred") - (gnc:gtexLink rdfs:Class gnc:ResourceLink) - (gnc:gtexLink rdfs:label "GTEx Portal") - (gnc:gtexLink rdfs:comments "GTEx Portal") - (gnc:ebiGwasLink rdfs:Class gnc:ResourceLink) - (gnc:ebiGwasLink rdfs:label "EBI GWAS") - (gnc:ebiGwasLink rdfs:comments "EBI GWAS") - (gnc:genemaniaLink rdfs:Class gnc:ResourceLink) - (gnc:genemaniaLink rdfs:label "GeneMANIA") - (gnc:genemaniaLink rdfs:comments "GeneMANIA") - (gnc:gemmaLink rdfs:Class gnc:ResourceLink) - (gnc:gemmaLink rdfs:label "Gemma") - (gnc:gemmaLink rdfs:comments "Meta-analysis of gene expression data") - (gnc:biogpsLink rdfs:Class gnc:ResourceLink) - (gnc:biogpsLink rdfs:label "BioGPS") - (gnc:biogpsLink rdfs:comments "Expression across many tissues and cell types") - (gnc:abaLink rdfs:Class gnc:ResourceLink) - (gnc:abaLink rdfs:label "ABA") - (gnc:abaLink rdfs:comments "Allen Brain Atlas") - (gnc:ucsRefSeqLink rdfs:Class gnc:ResourceLink) - (gnc:ucsRefSeqLink rdfs:label "Info from UCSC Genome Browser") - (gnc:ucsRefSeqLink rdfs:comments "UCSC") - (gnc:proteinAtlasLink rdfs:Class gnc:ResourceLink) - (gnc:proteinAtlasLink rdfs:label "Protein Atlas") - (gnc:proteinAtlasLink rdfs:comments "Human Protein Atlas") (gnt:hasChip a owl:ObjectProperty) (gnt:hasChip rdfs:domain gnc:Probeset) (gnt:hasTargetId a owl:ObjectProperty) @@ -148,17 +114,6 @@ ((string=? "-" strand-probe) " on the minus strand") (else ""))))))) - ;; NCBI Gene Link - (set dct:references - (let ((geneId (field ProbeSet GeneId))) - (if (not (string-blank? geneId)) - (string->symbol - (format #f - "<~0@*~a~1@*~a> .~%<~0@*~a~1@*~a> ~2@*~a" - "http://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=Graphics&list_uids=" - geneId - "a gnc:NCBIGeneLink")) - ""))) ;; OMIM Link (set dct:references (let ((omim (field ProbeSet OMIM))) @@ -192,166 +147,6 @@ uniprot "a gnc:uniprotLink")) ""))) - ;; STRING Link - (set dct:references - (let ((symbol (field ProbeSet Symbol))) - (if (not (string-blank? symbol)) - (string->symbol - (format #f - "<~0@*~a~1@*~a> .~%<~0@*~a~1@*~a> ~2@*~a" - "http://string-db.org/newstring_cgi/show_network_section.pl?identifier=" - symbol - "a gnc:stringLink")) - ""))) - ;; GTEX link - (set dct:references - (let ((symbol (field ProbeSet Symbol))) - (if (not (string-blank? symbol)) - (string->symbol - (format #f - "<~0@*~a~1@*~a> .~%<~0@*~a~1@*~a> ~2@*~a" - "https://www.gtexportal.org/home/gene/" - (string-trim-both symbol) - "a gnc:gtexLink")) - ""))) - ;; EBI GWAS Link - (set dct:references - (let ((symbol (field ProbeSet Symbol))) - (if (not (string-blank? symbol)) - (string->symbol - (format #f - "<~0@*~a~1@*~a> .~%<~0@*~a~1@*~a> ~2@*~a" - "https://www.ebi.ac.uk/gwas/search?query=" - (string-trim-both symbol) - "a gnc:ebiGwasLink")) - ""))) - ;; Protein Atlas Link - (set dct:references - (let ((symbol (field ProbeSet Symbol))) - (if (not (string-blank? symbol)) - (string->symbol - (format #f - "<~0@*~a~1@*~a> .~%<~0@*~a~1@*~a> ~2@*~a" - "http://www.proteinatlas.org/search/" - (string-trim-both symbol) - "a gnc:proteinAtlasLink")) - ""))) - ;; UCS Link - (set dct:references - (let* ((symbol (field ProbeSet Symbol)) - (species (field Species Name)) - (db (if (string=? species "mouse") - "mm10" "rn7")) - (transcriptId (field ProbeSet RefSeq_TranscriptId)) - (kgId (field GeneList_rn33 kgId)) - (transcriptStart - (if (string=? species "mouse") - (field ("(GeneList.txStart * 1000000)" TranscriptStartMm10)) - (field ("(GeneList_rn33.txStart * 1000000)" TranscriptStartRn7)))) - (chromosome - (if (string=? species "mouse") - (field GeneList Chromosome) - (field GeneList_rn33 Chromosome))) - (transcriptEnd - (if (string=? species "mouse") - (field ("(GeneList.txEnd * 1000000)" TranscriptEndMm10)) - (field ("(GeneList_rn33.txEnd * 1000000)" TranscriptEndRn7)))) - (url (format - #f - "http://genome.cse.ucsc.edu/cgi-bin/hgTracks?db=~a&hgg_gene=" - db))) - (if (and (not (string-blank? symbol)) - (not (string-blank? transcriptId)) - (number? transcriptStart) - (number? transcriptEnd) - (not (string-blank? chromosome)) - (or (string=? species "mouse") - (string=? species "rat"))) - (string->symbol - (format #f - "<~0@*~a~1@*~a&hgg_chrom=chr~2@*~a&hgg_start=~3@*~a&hgg_end=~4@*~a> .~%<~0@*~a~1@*~a&hgg_chrom=chr~2@*~a&hgg_start=~3@*~a&hgg_end=~4@*~a> ~2@*~a" - url - transcriptId - chromosome - transcriptStart - transcriptEnd - "a gnc:ucsRefSeqLink" - )) - ""))) - ;; PANTHER link - (set dct:references - (let ((symbol (field ProbeSet Symbol))) - (if (not (string-blank? symbol)) - (string->symbol - (format #f - "<~0@*~a~1@*~a> .~%<~0@*~a~1@*~a> ~2@*~a" - "http://www.pantherdb.org/genes/geneList.do?searchType=basic&fieldName=all&organism=all&listType=1&fieldValue=" - (string-trim-both symbol) - "a gnc:PantherLink")) - ""))) - ;; A GeneManiaLink - (set dct:references - (let ((symbol (field ProbeSet GeneId)) - (species (lower-case-and-replace-spaces - (field Species FullName)))) - (if (and (not (string-blank? symbol)) - (not (string-blank? species)) - (or - (string=? species "mus-musculus") - (string=? species "rattus-norvegicus") - (string=? species "homo-sapiens"))) - (string->symbol - (format #f "<~0@*~a/~1@*~a/~2@*~a> .~%<~0@*~a/~1@*~a/~2@*~a> ~3@*~a" - "https://genemania.org/search" species (string-trim-both symbol) - "a gnc:genemaniaLink")) - ""))) - ;; ABA Link - (set dct:references - (let ((symbol (field ProbeSet Symbol)) - (geneId (field ProbeSet GeneId)) - (species (field Species name))) - (if (and (not (string-blank? symbol)) - (not (string-blank? species)) - (or (string=? species "human") - (string=? species "mouse"))) - (string->symbol - (format #f "<~0@*~a> .~%<~0@*~a> ~2@*~a" - "http://mouse.brain-map.org/search/show?search_type=gene&search_term=" - "a " - (if (string=? species "mouse") - (string-trim-both symbol) - geneId))) - ""))) - ;; Gemma Link - (set dct:references - (let ((geneId (field ProbeSet GeneId))) - (if (not (string-blank? geneId)) - (string->symbol - (format #f - "<~0@*~a~1@*~a> .~%<~0@*~a~1@*~a> ~2@*~a" - "http://www.chibi.ubc.ca/Gemma/gene/showGene.html?ncbiid=" - geneId - "a gnc:gemmaLink")) - ""))) - ;; BioGPS Link - (set dct:references - (let ((geneId (field ProbeSet GeneId)) - (species (field Species Name))) - (if (and (not (string-blank? geneId)) - (not (string-blank? species)) - (or - (string=? species "mouse") - (string=? species "rat") - (string=? species "humans"))) - (string->symbol - (format #f - "<~0@*~a~1@*~a~2@*~a~3@*~a> .~%<~0@*~a~1@*~a~2@*~a~3@*~a> ~4@*~a ; ~5@*~a" - "http://biogps.org/?org=" - species - "#goto=genereport&id=" - geneId - "a gnc:ResourceLink")) - ""))) (set gnt:strandProbe (field ProbeSet Strand_Probe)) (set gnt:hasSpecificity -- cgit v1.2.3