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```#+ summary: Get annotations from SGN, Ensembl and UniProt given a gene ID. #+ tags: #+ - Get annotations given a gene #+ defaults: #+ - geneid: "'Solyc01g00500*'" PREFIX rdf: PREFIX rdfs: PREFIX owl: PREFIX dcterms: PREFIX dc: PREFIX skos: PREFIX uniprot: PREFIX so: PREFIX go: PREFIX Gene: PREFIX ensembl: PREFIX bif: SELECT ?gene_id ?gene_name ?transcript_id ?sgn_des ?uniprot_acc ?uniprot_reviewed ?uniprot_existence (GROUP_CONCAT(DISTINCT(?uniprot_des); separator=", ") AS ?uniprot_des) (REPLACE(GROUP_CONCAT(DISTINCT(CONCAT(?go_id, ' [', ?go_term, ']')); separator="; "), ' \\[\\]', '') AS ?uniprot_goa) FROM FROM FROM FROM FROM FROM FROM FROM FROM WHERE { ?gene a Gene: ; dcterms:identifier ?gene_id ; so:transcribed_to ?transcript . ?transcript rdfs:comment ?sgn_des ; dcterms:identifier ?transcript_id . OPTIONAL { ?transcript owl:sameAs/so:translates_to ?ensembl_prot . ?ensembl_prot ensembl:CHECKSUM|ensembl:SEQUENCE_MATCH ?uniprot . ?uniprot dc:identifier ?uniprot_acc ; dc:description ?uniprot_des ; uniprot:existence/rdfs:label ?uniprot_existence ; uniprot:reviewed ?uniprot_reviewed . OPTIONAL { ?uniprot uniprot:encodedBy/skos:prefLabel ?gene_name. } OPTIONAL { ?go ^uniprot:classifiedWith ?uniprot ; go:id ?go_id OPTIONAL { ?go rdfs:label ?go_term } } } ?gene_id bif:contains ?_geneid } GROUP BY ?gene_id ?gene_name ?transcript_id ?sgn_des ?uniprot_acc ?uniprot_reviewed ?uniprot_existence ```

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  • ```#+ summary: Get annotations from SGN, Ensembl and UniProt given a gene ID. #+ tags: #+ - Get annotations given a gene #+ defaults: #+ - geneid: "'Solyc01g00500*'" 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 dc: <http://purl.org/dc/elements/1.1/> PREFIX skos: <http://www.w3.org/2004/02/skos/core#> PREFIX uniprot: <http://purl.uniprot.org/core/> PREFIX so: <http://purl.obolibrary.org/obo/so#> PREFIX go: <http://www.geneontology.org/formats/oboInOwl#> PREFIX Gene: <http://purl.obolibrary.org/obo/SO_0001217> PREFIX ensembl: <http://rdf.ebi.ac.uk/terms/ensembl/> PREFIX bif: <bif:> SELECT ?gene_id ?gene_name ?transcript_id ?sgn_des ?uniprot_acc ?uniprot_reviewed ?uniprot_existence (GROUP_CONCAT(DISTINCT(?uniprot_des); separator=", ") AS ?uniprot_des) (REPLACE(GROUP_CONCAT(DISTINCT(CONCAT(?go_id, ' [', ?go_term, ']')); separator="; "), ' \\[\\]', '') AS ?uniprot_goa) FROM <http://solgenomics.net/genome/Solanum_lycopersicum> FROM <http://solgenomics.net/genome/Solanum_pennellii> FROM <http://solgenomics.net/genome/Solanum_tuberosum> FROM <http://plants.ensembl.org/Solanum_lycopersicum> FROM <http://plants.ensembl.org/Solanum_tuberosum> FROM <http://www.uniprot.org/proteomes/Solanum_lycopersicum> FROM <http://www.uniprot.org/proteomes/Solanum_tuberosum> FROM <http://purl.obolibrary.org/obo/go.owl> FROM <http://purl.uniprot.org/core/> WHERE { ?gene a Gene: ; dcterms:identifier ?gene_id ; so:transcribed_to ?transcript . ?transcript rdfs:comment ?sgn_des ; dcterms:identifier ?transcript_id . OPTIONAL { ?transcript owl:sameAs/so:translates_to ?ensembl_prot . ?ensembl_prot ensembl:CHECKSUM|ensembl:SEQUENCE_MATCH ?uniprot . ?uniprot dc:identifier ?uniprot_acc ; dc:description ?uniprot_des ; uniprot:existence/rdfs:label ?uniprot_existence ; uniprot:reviewed ?uniprot_reviewed . OPTIONAL { ?uniprot uniprot:encodedBy/skos:prefLabel ?gene_name. } OPTIONAL { ?go ^uniprot:classifiedWith ?uniprot ; go:id ?go_id OPTIONAL { ?go rdfs:label ?go_term } } } ?gene_id bif:contains ?_geneid } GROUP BY ?gene_id ?gene_name ?transcript_id ?sgn_des ?uniprot_acc ?uniprot_reviewed ?uniprot_existence ```
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  • Get annotations from SGN, Ensembl and UniProt given a gene ID.
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