diff --git a/misc-scripts/xref_mapping/sql/populate_metadata.sql b/misc-scripts/xref_mapping/sql/populate_metadata.sql index 07af3e56cddc3931e218d85c83527516c2d45488..a4713a9dfbe01518d91b90744c5ee66d0368213c 100644 --- a/misc-scripts/xref_mapping/sql/populate_metadata.sql +++ b/misc-scripts/xref_mapping/sql/populate_metadata.sql @@ -33,9 +33,15 @@ INSERT INTO species (species_id, taxonomy_id, name, aliases) VALUES (7165,180454 INSERT INTO species (species_id, taxonomy_id, name, aliases) VALUES (13616,13616, 'monodelphis_domestica', 'mono,opossum,possum,monodelphis,monodelphisdomestica'); INSERT INTO species (species_id, taxonomy_id, name, aliases) VALUES (9544, 9544, 'macaca_mulatta', 'rmacaque, rhesus, rhesus macaque, macaque'); +INSERT INTO species (species_id, taxonomy_id, name, aliases) VALUES (9785, 9785, 'loxodonta_africana', 'elephant,lafricana,loxodontaafricana'); +INSERT INTO species (species_id, taxonomy_id, name, aliases) VALUES (9361, 9361, 'dasypus_novemcinctus', 'armadillo,dnovemcinctus,dasypusnovemcinctus'); +INSERT INTO species (species_id, taxonomy_id, name, aliases) VALUES (9986, 9986, 'oryctolagus_cuniculus', 'rabbit,ocuniculus,oryctolaguscuniculus'); +INSERT INTO species (species_id, taxonomy_id, name, aliases) VALUES (9371, 9371, 'echinops_telfairi', 'tenrec,etelfairi,echinopstelfairi'); +INSERT INTO species (species_id, taxonomy_id, name, aliases) VALUES (9685, 9685, 'felis_catus', 'cat,fcatus,feliscatus,moggy,tiddles'); INSERT INTO species (species_id, taxonomy_id, name, aliases) VALUES (7159, 7159, 'aedes_aegypti', 'aedes,aedesaegypti,aaegypti'); + ################################################################################ # SOURCES - types of data we can read @@ -1378,4 +1384,84 @@ INSERT INTO source_url (source_id, species_id, url, file_modified_date, upload_d INSERT INTO source_url (source_id, species_id, url, file_modified_date, upload_date, parser) VALUES\ (1300, 9544,'ftp://ftp.ebi.ac.uk/pub/databases/interpro/interpro.xml.gz', now(), now(), "InterproParser"); -################################################################################ +##------------------------------------------------------------------------------ +##### elephant + +## Uniprot +INSERT INTO source_url (source_id, species_id, url, file_modified_date, upload_date, parser) VALUES\ + (1, 9785, 'ftp://ftp.ebi.ac.uk/pub/databases/uniprot/knowledgebase/uniprot_sprot.dat.gz', now(), now(), "UniProtParser"); +INSERT INTO source_url (source_id, species_id, url, file_modified_date, upload_date, parser) VALUES\ + (2, 9785, 'ftp://ftp.ebi.ac.uk/pub/databases/uniprot/knowledgebase/uniprot_trembl.dat.gz', now(), now(), "UniProtParser"); +INSERT INTO source_url (source_id, species_id, url, checksum, file_modified_date, upload_date, parser) VALUES (3000, 9785, 'ftp://ftp.ebi.ac.uk/pub/databases/uniprot/knowledgebase/uniprot_sprot_varsplic.fasta.gz', '', now(), now(), "UniProtVarSplicParser"); + +## GO +INSERT INTO source_url (source_id, species_id, url, file_modified_date, upload_date, parser) VALUES (1070, 9785,'ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/UNIPROT/gene_association.goa_uniprot.gz', now(), now(), "GOParser"); + +## Interpro +INSERT INTO source_url (source_id, species_id, url, file_modified_date, upload_date, parser) VALUES (1300, 9785,'ftp://ftp.ebi.ac.uk/pub/databases/interpro/interpro.xml.gz', now(), now(), "InterproParser"); + +##------------------------------------------------------------------------------ +##### armadillo + +## Uniprot +INSERT INTO source_url (source_id, species_id, url, file_modified_date, upload_date, parser) VALUES\ + (1, 9361, 'ftp://ftp.ebi.ac.uk/pub/databases/uniprot/knowledgebase/uniprot_sprot.dat.gz', now(), now(), "UniProtParser"); +INSERT INTO source_url (source_id, species_id, url, file_modified_date, upload_date, parser) VALUES\ + (2, 9361, 'ftp://ftp.ebi.ac.uk/pub/databases/uniprot/knowledgebase/uniprot_trembl.dat.gz', now(), now(), "UniProtParser"); +INSERT INTO source_url (source_id, species_id, url, checksum, file_modified_date, upload_date, parser) VALUES (3000, 9361, 'ftp://ftp.ebi.ac.uk/pub/databases/uniprot/knowledgebase/uniprot_sprot_varsplic.fasta.gz', '', now(), now(), "UniProtVarSplicParser"); + +## GO +INSERT INTO source_url (source_id, species_id, url, file_modified_date, upload_date, parser) VALUES (1070, 9361,'ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/UNIPROT/gene_association.goa_uniprot.gz', now(), now(), "GOParser"); + +## Interpro +INSERT INTO source_url (source_id, species_id, url, file_modified_date, upload_date, parser) VALUES (1300, 9361,'ftp://ftp.ebi.ac.uk/pub/databases/interpro/interpro.xml.gz', now(), now(), "InterproParser"); + +##------------------------------------------------------------------------------ +##### rabbit + +## Uniprot +INSERT INTO source_url (source_id, species_id, url, file_modified_date, upload_date, parser) VALUES\ + (1, 9986, 'ftp://ftp.ebi.ac.uk/pub/databases/uniprot/knowledgebase/uniprot_sprot.dat.gz', now(), now(), "UniProtParser"); +INSERT INTO source_url (source_id, species_id, url, file_modified_date, upload_date, parser) VALUES\ + (2, 9986, 'ftp://ftp.ebi.ac.uk/pub/databases/uniprot/knowledgebase/uniprot_trembl.dat.gz', now(), now(), "UniProtParser"); +INSERT INTO source_url (source_id, species_id, url, checksum, file_modified_date, upload_date, parser) VALUES (3000, 9986, 'ftp://ftp.ebi.ac.uk/pub/databases/uniprot/knowledgebase/uniprot_sprot_varsplic.fasta.gz', '', now(), now(), "UniProtVarSplicParser"); + +## GO +INSERT INTO source_url (source_id, species_id, url, file_modified_date, upload_date, parser) VALUES (1070, 9986,'ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/UNIPROT/gene_association.goa_uniprot.gz', now(), now(), "GOParser"); + +## Interpro +INSERT INTO source_url (source_id, species_id, url, file_modified_date, upload_date, parser) VALUES (1300, 9986,'ftp://ftp.ebi.ac.uk/pub/databases/interpro/interpro.xml.gz', now(), now(), "InterproParser"); + +##------------------------------------------------------------------------------ +##### tenrec + +## Uniprot +INSERT INTO source_url (source_id, species_id, url, file_modified_date, upload_date, parser) VALUES\ + (1, 9371, 'ftp://ftp.ebi.ac.uk/pub/databases/uniprot/knowledgebase/uniprot_sprot.dat.gz', now(), now(), "UniProtParser"); +INSERT INTO source_url (source_id, species_id, url, file_modified_date, upload_date, parser) VALUES\ + (2, 9371, 'ftp://ftp.ebi.ac.uk/pub/databases/uniprot/knowledgebase/uniprot_trembl.dat.gz', now(), now(), "UniProtParser"); +INSERT INTO source_url (source_id, species_id, url, checksum, file_modified_date, upload_date, parser) VALUES (3000, 9371, 'ftp://ftp.ebi.ac.uk/pub/databases/uniprot/knowledgebase/uniprot_sprot_varsplic.fasta.gz', '', now(), now(), "UniProtVarSplicParser"); + +## GO +INSERT INTO source_url (source_id, species_id, url, file_modified_date, upload_date, parser) VALUES (1070, 9371,'ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/UNIPROT/gene_association.goa_uniprot.gz', now(), now(), "GOParser"); + +## Interpro +INSERT INTO source_url (source_id, species_id, url, file_modified_date, upload_date, parser) VALUES (1300, 9371,'ftp://ftp.ebi.ac.uk/pub/databases/interpro/interpro.xml.gz', now(), now(), "InterproParser"); + +##------------------------------------------------------------------------------ +##### cat + +## Uniprot +INSERT INTO source_url (source_id, species_id, url, file_modified_date, upload_date, parser) VALUES\ + (1, 9685, 'ftp://ftp.ebi.ac.uk/pub/databases/uniprot/knowledgebase/uniprot_sprot.dat.gz', now(), now(), "UniProtParser"); +INSERT INTO source_url (source_id, species_id, url, file_modified_date, upload_date, parser) VALUES\ + (2, 9685, 'ftp://ftp.ebi.ac.uk/pub/databases/uniprot/knowledgebase/uniprot_trembl.dat.gz', now(), now(), "UniProtParser"); +INSERT INTO source_url (source_id, species_id, url, checksum, file_modified_date, upload_date, parser) VALUES (3000, 9685, 'ftp://ftp.ebi.ac.uk/pub/databases/uniprot/knowledgebase/uniprot_sprot_varsplic.fasta.gz', '', now(), now(), "UniProtVarSplicParser"); + +## GO +INSERT INTO source_url (source_id, species_id, url, file_modified_date, upload_date, parser) VALUES (1070, 9685,'ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/UNIPROT/gene_association.goa_uniprot.gz', now(), now(), "GOParser"); + +## Interpro +INSERT INTO source_url (source_id, species_id, url, file_modified_date, upload_date, parser) VALUES (1300, 9685,'ftp://ftp.ebi.ac.uk/pub/databases/interpro/interpro.xml.gz', now(), now(), "InterproParser"); + +##------------------------------------------------------------------------------