From 1578465fa2726d4ff96fdc9d66cb3c6e1bb1c298 Mon Sep 17 00:00:00 2001 From: Munyoki Kilyungi Date: Fri, 26 May 2023 08:36:42 +0300 Subject: Remove some metadata from the probeset dump Signed-off-by: Munyoki Kilyungi --- examples/dump-probeset.scm | 43 ------------------------------------------- 1 file changed, 43 deletions(-) (limited to 'examples') diff --git a/examples/dump-probeset.scm b/examples/dump-probeset.scm index 8e809a5..a3eaa05 100755 --- a/examples/dump-probeset.scm +++ b/examples/dump-probeset.scm @@ -63,12 +63,7 @@ (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:unigene (field ProbeSet UniGeneId)) - (set gn:strandProbe (field ProbeSet Strand_Probe)) - (set gn:strandGene (field ProbeSet Strand_Gene)) (set gn:omim (ontology 'omim: (field ProbeSet OMIM))) - (set gn:comments (sanitize-rdf-string (field ProbeSet comments))) - (set gn:targetRegion (field ProbeSet Probe_set_target_region)) (set gn:specificity (annotate-field (field ("IFNULL(ProbeSet.Probe_set_specificity, '')" Probe_set_specificity)) '^^xsd:double)) @@ -82,56 +77,18 @@ (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:flag (field ProbeSet flag)) (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)) (set gn:RefSeq_TranscriptId (ontology 'nuccore: (field ProbeSet RefSeq_TranscriptId))) - (set gn:ENSEMBLGeneId (string-trim-both - (field ProbeSet ENSEMBLGeneId))) (set gn:Chr_mm8 (field ("IFNULL(ProbeSet.Chr_mm8, '')" Chr_mm8))) (set gn:Mb_mm8 (field ("IFNULL(ProbeSet.Mb_mm8, '')" Mb_mm8))) - (set gn:probeSetBlatMbStart_mm8 - (annotate-field - (field ("IFNULL(ProbeSet.Probe_set_Blat_Mb_start_mm8, '')" Probe_set_Blat_Mb_start_mm8)) - '^^xsd:double)) - (set gn:probeSetBlatMbEnd_mm8 - (annotate-field - (field ("IFNULL(ProbeSet.Probe_set_Blat_Mb_end_mm8, '')" Probe_set_Blat_Mb_end_mm8)) - '^^xsd:double)) - (set gn:homoloGeneID (ontology - 'homologene: - (field ProbeSet HomoloGeneID))) - (set gn:biotype_ENS (field ProbeSet Biotype_ENS)) - (set gn:proteinName (field ProbeSet ProteinName)) (set gn:uniProtReference (ontology 'uniprot: (field ProbeSet UniProtID))) - (set gn:flybase_Id (field ProbeSet Flybase_Id)) - (set gn:RGD_ID (field ("IFNULL(ProbeSet.RGD_ID, '')" RGD_ID))) - (set gn:hgnc (ontology - 'hgnc: (field ProbeSet HGNC_ID))) - (set gn:HMDB_ID (field ProbeSet HMDB_ID)) - (set gn:confidence (field ("IFNULL(ProbeSet.Confidence, '')" Confidence))) - (set gn:chebi_ID (ontology - 'chebi: - (field - ("IFNULL(ProbeSet.ChEBI_ID, '')" - ChEBI_ID)))) - (set gn:CASNumber (field ProbeSet CAS_number)) (set gn:PubChemID (ontology 'pubchem: (field ("IFNULL(ProbeSet.PubChem_ID, '')" PubChem_ID)))) - (set gn:chemSpiderID (field ("IFNULL(ProbeSet.ChemSpider_ID, '')" ChemSpider_ID))) - (set gn:uniiID (field ProbeSet UNII_ID)) - (set gn:ECNumber (field ProbeSet EC_number)) - (set gn:keggID (ontology 'kegg: - (field ProbeSet KEGG_ID))) - (set gn:molecularWeight (annotate-field (field ProbeSet Molecular_Weight) '^^xsd:double)) - (set gn:nugowikiID (field ("IFNULL(ProbeSet.Nugowiki_ID, '')" Nugowiki_ID))) - (set gn:type (field ProbeSet Type)) - (set gn:tissue (field ProbeSet Tissue)) (set gn:primaryName (field ProbeSet PrimaryName)) (set gn:secondaryNames (field ProbeSet SecondaryNames)) (set gn:peptideSequence (field ProbeSet PeptideSequence)))) -- cgit v1.2.3