diff --git a/etc/chado_extra.sql b/etc/chado_extra.sql new file mode 100644 index 0000000000000000000000000000000000000000..37ead609850d13980a63e94db8b5b621a71fe369 --- /dev/null +++ b/etc/chado_extra.sql @@ -0,0 +1,65 @@ +-- +-- Add extra terms used by Artemis with Chado +-- + +-- +-- add term for evidence codes +-- +INSERT INTO dbxref + ( db_id, accession ) +VALUES + ( (SELECT db_id FROM db WHERE name = 'null'), 'Typically an evidence code' ); + +INSERT INTO cvterm + ( cv_id, name, dbxref_id ) +VALUES + ( (SELECT cv_id FROM cv WHERE name ='feature_property'), 'evidence', + (SELECT dbxref_id FROM dbxref WHERE accession='Typically an evidence code') ); + +-- +-- database used for controlled curation terms +-- +INSERT INTO db ( name ) VALUES ( 'CCGEN' ); + +-- +-- add terms for literature +-- +INSERT INTO cv + ( name, definition) +VALUES + ( 'genedb_literature', 'terms for literature' ); + +INSERT INTO dbxref + ( db_id, accession ) +VALUES + ( (SELECT db_id FROM db WHERE name = 'null'), 'unfetched literature type'); + +INSERT INTO dbxref + ( db_id, accession ) +VALUES + ( (SELECT db_id FROM db WHERE name = 'null'), 'journal literature type' ); + +INSERT INTO dbxref + ( db_id, accession ) +VALUES + ( (SELECT db_id FROM db WHERE name = 'null'), 'unknown literature type' ); + +INSERT INTO cvterm + ( cv_id, name, dbxref_id ) +VALUES + ( (SELECT cv_id FROM cv WHERE name = 'genedb_literature'), 'unfetched', + (SELECT dbxref_id FROM dbxref WHERE accession='unfetched literature type') ); + +INSERT INTO cvterm + ( cv_id, name, dbxref_id ) +VALUES + ( (SELECT cv_id FROM cv WHERE name = 'genedb_literature'), 'journal', + (SELECT dbxref_id FROM dbxref WHERE accession='journal literature type') ); + +INSERT INTO cvterm + ( cv_id, name, dbxref_id ) +VALUES + ( (SELECT cv_id FROM cv WHERE name = 'genedb_literature'), 'unknown', + (SELECT dbxref_id FROM dbxref WHERE accession='unknown literature type') ); + +