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```#+ summary: Get the genomic location of a feature identified by ID (e.g., gene, exon/intron, transcript or marker). #+ tags: #+ - Get the genomic location of a feature #+ defaults: #+ - featureid: "'Solyc01g005000.2'" PREFIX rdf: PREFIX rdfs: PREFIX owl: PREFIX dcterms: PREFIX obo: PREFIX faldo: PREFIX so: PREFIX bif: SELECT ?feature_id ?feature_name (?begin_lb AS ?chrom) ?begin_pos ?end_pos ?taxon_id FROM FROM FROM FROM WHERE { ?feature a ?feature_type ; dcterms:identifier ?feature_id ; faldo:location ?loc . ?loc faldo:begin ?begin ; faldo:end ?end . ?begin faldo:position ?begin_pos ; faldo:reference ?begin_ref . ?begin_ref rdfs:label ?begin_lb ; ^so:has_part/so:genome_of/dcterms:identifier ?taxon_id . ?end faldo:position ?end_pos ; faldo:reference ?end_ref . ?end_ref rdfs:label ?end_lb . ?feature_type a owl:Class ; rdfs:label ?feature_name . ?feature_id bif:contains ?_featureid . FILTER(?begin_lb = ?end_lb) }```

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  • ```#+ summary: Get the genomic location of a feature identified by ID (e.g., gene, exon/intron, transcript or marker). #+ tags: #+ - Get the genomic location of a feature #+ defaults: #+ - featureid: "'Solyc01g005000.2'" PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX dcterms: <http://purl.org/dc/terms/> PREFIX obo: <http://purl.obolibrary.org/obo/> PREFIX faldo: <http://biohackathon.org/resource/faldo#> PREFIX so: <http://purl.obolibrary.org/obo/so#> PREFIX bif: <bif:> SELECT ?feature_id ?feature_name (?begin_lb AS ?chrom) ?begin_pos ?end_pos ?taxon_id FROM <http://solgenomics.net/genome/Solanum_tuberosum> FROM <http://solgenomics.net/genome/Solanum_lycopersicum> FROM <http://solgenomics.net/genome/Solanum_pennellii> FROM <http://purl.obolibrary.org/obo/so.owl> WHERE { ?feature a ?feature_type ; dcterms:identifier ?feature_id ; faldo:location ?loc . ?loc faldo:begin ?begin ; faldo:end ?end . ?begin faldo:position ?begin_pos ; faldo:reference ?begin_ref . ?begin_ref rdfs:label ?begin_lb ; ^so:has_part/so:genome_of/dcterms:identifier ?taxon_id . ?end faldo:position ?end_pos ; faldo:reference ?end_ref . ?end_ref rdfs:label ?end_lb . ?feature_type a owl:Class ; rdfs:label ?feature_name . ?feature_id bif:contains ?_featureid . FILTER(?begin_lb = ?end_lb) }```
described by
description
  • Get the genomic location of a feature identified by ID (e.g., gene, exon/intron, transcript or marker).
target
topic
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