diff --git a/misc-scripts/xref_mapping/sql/populate_metadata.sql b/misc-scripts/xref_mapping/sql/populate_metadata.sql index 734133824ed18f52016836ea44448205cc443b6c..a4278773124417cffe7dccb7fe3e6c6e581658c0 100644 --- a/misc-scripts/xref_mapping/sql/populate_metadata.sql +++ b/misc-scripts/xref_mapping/sql/populate_metadata.sql @@ -58,13 +58,10 @@ INSERT INTO source VALUES (2000, 'CCDS', 1, 'Y', 4); ################################################################################ # Files to fetch data from -# -------------------------------------------------------------------------------- -# UniProt (SwissProt & SPTrEMBL) - -# Note currently no UniProt data for fugu, anopheles, c.briggsae or chicken. +# -------------------------------------------------------------------------------- -###HUMAN +### HUMAN ## uniprot INSERT INTO source_url (source_id, species_id, url, checksum, file_modified_date, upload_date, parser) VALUES (1, 9606,'ftp://ftp.ebi.ac.uk/pub/databases/SPproteomes/swissprot_files/proteomes/9606.SPC', '', now(), now(), "UniProtParser"); @@ -95,6 +92,7 @@ INSERT INTO source_url (source_id, species_id, url, checksum, file_modified_date ## UniGene ##INSERT INTO source_url (source_id, species_id, url, checksum, file_modified_date, upload_date, parser) VALUES (6, 9606,'ftp://ftp.ncbi.nih.gov/repository/UniGene/Hs.seq.uniq.gz ftp://ftp.ncbi.nih.gov/repository/UniGene/Hs.data.gz', '', now(), now(), "UniGeneParser"); +# -------------------------------------------------------------------------------- ###MOUSE ## uniprot @@ -115,10 +113,14 @@ INSERT INTO source_url (source_id, species_id, url, checksum, file_modified_date ## IPI INSERT INTO source_url (source_id, species_id, url, checksum, file_modified_date, upload_date, parser) VALUES (5, 10090,'ftp://ftp.ebi.ac.uk/pub/databases/IPI/current/ipi.MOUSE.fasta.gz', '', now(), now(), "IPIParser"); +## Interpro +INSERT INTO source_url (source_id, species_id, url, checksum, file_modified_date, upload_date, parser) VALUES (1300, 10090,'ftp://ftp.ebi.ac.uk/pub/databases/interpro/interpro.xml.gz', '', now(), now(), "InterproParser"); + ## UniGene ##INSERT INTO source_url (source_id, species_id, url, checksum, file_modified_date, upload_date, parser) VALUES (6, 10090,'ftp://ftp.ncbi.nih.gov/repository/UniGene/Mm.seq.uniq.gz ftp://ftp.ncbi.nih.gov/repository/UniGene/Mm.data.gz', '', now(), now(), "UniGeneParser"); -###RAT +# -------------------------------------------------------------------------------- +### RAT ## uniprot INSERT INTO source_url (source_id, species_id, url, checksum, file_modified_date, upload_date, parser) VALUES (1, 10116, 'ftp://ftp.ebi.ac.uk/pub/databases/SPproteomes/swissprot_files/proteomes/10116.SPC', '', now(), now(), "UniProtParser"); @@ -144,8 +146,9 @@ INSERT INTO source_url (source_id, species_id, url, checksum, file_modified_date ## UniGene ##INSERT INTO source_url (source_id, species_id, url, checksum, file_modified_date, upload_date, parser) VALUES (6, 10116,'ftp://ftp.ncbi.nih.gov/repository/UniGene/Rn.seq.uniq.gz ftp://ftp.ncbi.nih.gov/repository/UniGene/Rn.data.gz', '', now(), now(), "UniGeneParser"); +# -------------------------------------------------------------------------------- -###Zebrafish +### Zebrafish ## uniprot #until zebra fish has it's own .SPC file parse all. #INSERT INTO source_url (source_id, species_id, url, checksum, file_modified_date, upload_date, parser) VALUES (1, 7955, 'ftp://ftp.ebi.ac.uk/pub/databases/SPproteomes/swissprot_files/proteomes/7955.SPC', '', now(), now(), "UniProtParser"); @@ -154,7 +157,6 @@ INSERT INTO source_url (source_id, species_id, url, checksum, file_modified_date INSERT INTO source_url (source_id, species_id, url, checksum, file_modified_date, upload_date, parser) VALUES (1, 7955, 'ftp://ftp.ebi.ac.uk/pub/databases/uniprot/knowledgebase/uniprot_trembl.dat.gz', '', now(), now(), "UniProtParser"); - ## refseq INSERT INTO source_url (source_id, species_id, url, checksum, file_modified_date, upload_date, parser) VALUES (3, 7955,'ftp://ftp.ncbi.nih.gov/genomes/D_rerio/protein/protein.gbk.gz', '', now(), now(), "RefSeqGPFFParser"); @@ -170,10 +172,14 @@ INSERT INTO source_url (source_id, species_id, url, checksum, file_modified_date ## IPI INSERT INTO source_url (source_id, species_id, url, checksum, file_modified_date, upload_date, parser) VALUES (5, 7955,'ftp://ftp.ebi.ac.uk/pub/databases/IPI/current/ipi.BRARE.fasta.gz', '', now(), now(), "IPIParser"); +## Interpro +INSERT INTO source_url (source_id, species_id, url, checksum, file_modified_date, upload_date, parser) VALUES (1300, 7955,'ftp://ftp.ebi.ac.uk/pub/databases/interpro/interpro.xml.gz', '', now(), now(), "InterproParser"); + ## UniGene ##INSERT INTO source_url (source_id, species_id, url, checksum, file_modified_date, upload_date, parser) VALUES (6, 7955,'ftp://ftp.ncbi.nih.gov/repository/UniGene/Dr.seq.uniq.gz ftp://ftp.ncbi.nih.gov/repository/UniGene/Dr.data.gz', '', now(), now(), "UniGeneParser"); -###chicken +# -------------------------------------------------------------------------------- +### Chicken ## uniprot # no chicken specific file!!!! #INSERT INTO source_url (source_id, species_id, url, checksum, file_modified_date, upload_date, parser) VALUES (1, 9031, 'ftp://ftp.ebi.ac.uk/pub/databases/SPproteomes/swissprot_files/proteomes/9031.SPC', '', now(), now(), "UniProtParser"); @@ -191,12 +197,15 @@ INSERT INTO source_url (source_id, species_id, url, checksum, file_modified_date ## GO INSERT INTO source_url (source_id, species_id, url, checksum, file_modified_date, upload_date, parser) VALUES (1070, 9031,'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, checksum, file_modified_date, upload_date, parser) VALUES (1300, 9031,'ftp://ftp.ebi.ac.uk/pub/databases/interpro/interpro.xml.gz', '', now(), now(), "InterproParser"); + ## UniGene ##INSERT INTO source_url (source_id, species_id, url, checksum, file_modified_date, upload_date, parser) VALUES (6, 9031,'ftp://ftp.ncbi.nih.gov/repository/UniGene/Gga.seq.uniq.gz ftp://ftp.ncbi.nih.gov/repository/UniGene/Gga.data.gz', '', now(), now(), "UniGeneParser"); -###8364, 'xenopus_tropicalis' - -#uniprot +# -------------------------------------------------------------------------------- +### XENOPUS +# uniprot INSERT INTO source_url (source_id, species_id, url, checksum, file_modified_date, upload_date, parser) VALUES (1, 8364, 'ftp://ftp.ebi.ac.uk/pub/databases/uniprot/knowledgebase/uniprot_sprot.dat.gz', '', now(), now(), "UniProtParser"); #uniprot @@ -214,9 +223,14 @@ INSERT INTO source_url (source_id, species_id, url, checksum, file_modified_date INSERT INTO source_url (source_id, species_id, url, checksum, file_modified_date, upload_date, parser) VALUES (4, 8364,'ftp://ftp.ncbi.nih.gov/refseq/release/vertebrate_other/vertebrate_other2.rna.fna.gz', '', now(), now(), "RefSeqParser"); INSERT INTO source_url (source_id, species_id, url, checksum, file_modified_date, upload_date, parser) VALUES (4, 8364,'ftp://ftp.ncbi.nih.gov/refseq/release/vertebrate_other/vertebrate_other3.rna.fna.gz', '', now(), now(), "RefSeqParser"); +## Interpro +INSERT INTO source_url (source_id, species_id, url, checksum, file_modified_date, upload_date, parser) VALUES (1300, 8364,'ftp://ftp.ebi.ac.uk/pub/databases/interpro/interpro.xml.gz', '', now(), now(), "InterproParser"); + ## UniGene ##INSERT INTO source_url (source_id, species_id, url, checksum, file_modified_date, upload_date, parser) VALUES (6, 8364,'ftp://ftp.ncbi.nih.gov/repository/UniGene/Str.seq.uniq.gz ftp://ftp.ncbi.nih.gov/repository/UniGene/Str.data.gz', '', now(), now(), "UniGeneParser"); +# -------------------------------------------------------------------------------- + ### Dog INSERT INTO source_url (source_id, species_id, url, checksum, file_modified_date, upload_date, parser) VALUES (1, 9615, 'ftp://ftp.ebi.ac.uk/pub/databases/uniprot/knowledgebase/uniprot_sprot.dat.gz', '', now(), now(), "UniProtParser"); @@ -232,8 +246,15 @@ INSERT INTO source_url (source_id, species_id, url, checksum, file_modified_date ## GO INSERT INTO source_url (source_id, species_id, url, checksum, file_modified_date, upload_date, parser) VALUES (1070, 9615,'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, checksum, file_modified_date, upload_date, parser) VALUES (1300, 9615,'ftp://ftp.ebi.ac.uk/pub/databases/interpro/interpro.xml.gz', '', now(), now(), "InterproParser"); + ## UniGene ##INSERT INTO source_url (source_id, species_id, url, checksum, file_modified_date, upload_date, parser) VALUES (6, 9615,'ftp://ftp.ncbi.nih.gov/repository/UniGene/Cfa.seq.uniq.gz ftp://ftp.ncbi.nih.gov/repository/UniGene/Cfa.data.gz', '', now(), now(), "UniGeneParser"); +# -------------------------------------------------------------------------------- + + + ################################################################################