{"__v":7,"_id":"5739b31a9042980e00ad1b97","category":{"project":"5735936aafab441700723a50","version":"5735936aafab441700723a53","_id":"5735e5d9e4824c3400aa1f23","__v":0,"sync":{"url":"","isSync":false},"reference":false,"createdAt":"2016-05-13T14:34:01.858Z","from_sync":false,"order":9,"slug":"configuration-options-core-import","title":"Configuration Options (Core Import)"},"parentDoc":null,"project":"5735936aafab441700723a50","user":"573592b84b0ab120000b7d44","version":{"__v":12,"_id":"5735936aafab441700723a53","project":"5735936aafab441700723a50","createdAt":"2016-05-13T08:42:18.615Z","releaseDate":"2016-05-13T08:42:18.615Z","categories":["5735936aafab441700723a54","5735a32931a73b1700887c94","5735b55beceb872200abbc6c","5735b56eb667601700d3bd6f","5735b9ba4b0ab120000b7dd4","5735b9c94b0ab120000b7dd5","5735cb131f16241700c8a0f7","5735e5c4e4824c3400aa1f21","5735e5d9e4824c3400aa1f23","5735e5f2ec67f6290013ac72","573ecfe0804f901700a9dfc7","573f276c7eeb8b190094ca7d"],"is_deprecated":false,"is_hidden":false,"is_beta":false,"is_stable":false,"codename":"","version_clean":"1.0.0","version":"1.0"},"updates":[],"next":{"pages":[],"description":""},"createdAt":"2016-05-16T11:46:34.728Z","link_external":false,"link_url":"","githubsync":"","sync_unique":"","hidden":false,"api":{"results":{"codes":[]},"settings":"","auth":"required","params":[],"url":""},"isReference":false,"order":9,"body":"```\n[GENE_NAMES]\n  GFF = [ 1 gene->Name /(.+)/ ]\n[TRANSCRIPT_NAMES]\n  GFF = [ 1 SELF->Name /(.+)/ ]\n```\nThese are used to set synonyms for each stable_id.  If multiple files are specified, each separate synonym will be added to the database.  In this case if the first number in the value array is 1, the first synonym from this source will be added to the database as a display_name, shown in preference to the stable_id.\n[block:callout]\n{\n  \"type\": \"warning\",\n  \"title\": \"[DBXREFS]\",\n  \"body\": \"Importing synonyms to an Ensembl database requires an xref so the import code here relies on a matching definition in [[DBXREFS]](doc:dbxrefs-core).  In the circumstance where the synonyms are not associated with any [[EXTERNAL_DBS]](doc:external_dbs-core), you will need to set an ``Internal`` xref with appropriate pattern, e.g. to load tRNA products as synonyms/display_names:\\n```\\n[TRANSCRIPT_NAMES]\\n  GFF = [ 1 SELF->product /(.+)/ ]\\n[DBXREFS]\\n  INTERNAL = [ 9999 Internal /^(tRNA.+)/ ]\\n```\"\n}\n[/block]","excerpt":"","slug":"_names-core","type":"basic","title":"[_NAMES]"}
``` [GENE_NAMES] GFF = [ 1 gene->Name /(.+)/ ] [TRANSCRIPT_NAMES] GFF = [ 1 SELF->Name /(.+)/ ] ``` These are used to set synonyms for each stable_id. If multiple files are specified, each separate synonym will be added to the database. In this case if the first number in the value array is 1, the first synonym from this source will be added to the database as a display_name, shown in preference to the stable_id. [block:callout] { "type": "warning", "title": "[DBXREFS]", "body": "Importing synonyms to an Ensembl database requires an xref so the import code here relies on a matching definition in [[DBXREFS]](doc:dbxrefs-core). In the circumstance where the synonyms are not associated with any [[EXTERNAL_DBS]](doc:external_dbs-core), you will need to set an ``Internal`` xref with appropriate pattern, e.g. to load tRNA products as synonyms/display_names:\n```\n[TRANSCRIPT_NAMES]\n GFF = [ 1 SELF->product /(.+)/ ]\n[DBXREFS]\n INTERNAL = [ 9999 Internal /^(tRNA.+)/ ]\n```" } [/block]