diff --git a/misc-scripts/xref_mapping/table.sql b/misc-scripts/xref_mapping/table.sql index d2772300e70ed70391ecac5f0e3feab7ac2d3674..0316529d5afb2f0d27bee9cb8b2fa1518c6a0c0f 100755 --- a/misc-scripts/xref_mapping/table.sql +++ b/misc-scripts/xref_mapping/table.sql @@ -10,6 +10,7 @@ CREATE TABLE xref ( xref_id int unsigned not null auto_increment, accession varchar(255) not null, label varchar(255), + description varchar(255), source_id int unsigned not null, species_id int unsigned not null, @@ -76,16 +77,21 @@ CREATE TABLE source ( # Sources to fetch data from # Note currently now UniProt/SwissProt data for fugu, anopheles, c.briggsae or chicken. -INSERT INTO source VALUES (1, 'UniProtSwissProt_homo_sapiens', 'ftp://ftp.ebi.ac.uk/pub/databases/SPproteomes/swissprot_files/proteomes/9606.SPC', '', now(), now(), 1); -INSERT INTO source VALUES (2, 'UniProtSwissProt_mus_musculus', 'ftp://ftp.ebi.ac.uk/pub/databases/SPproteomes/swissprot_files/proteomes/10090.SPC', '', now(), now(), 1); -INSERT INTO source VALUES (3, 'UniProtSwissProt_rattus_norvegicus', 'ftp://ftp.ebi.ac.uk/pub/databases/SPproteomes/swissprot_files/proteomes/10116.SPC', '', now(), now(), 1); -INSERT INTO source VALUES (4, 'UniProtSwissProt_drosophilla_melanogaster', 'ftp://ftp.ebi.ac.uk/pub/databases/SPproteomes/swissprot_files/proteomes/7227.SPC', '', now(), now(), 1); -INSERT INTO source VALUES (5, 'UniProtSwissProt_caenorhabditis_elegans', 'ftp://ftp.ebi.ac.uk/pub/databases/SPproteomes/swissprot_files/proteomes/6239.SPC', '', now(), now(), 1); -#INSERT INTO source VALUES (6, 'UniProtSwissProt_gallus_gallus', 'ftp://ftp.ebi.ac.uk/pub/databases/SPproteomes/swissprot_files/proteomes/9031.SPC', '', now(), now(), 1); -INSERT INTO source VALUES (7, 'UniProtSwissProt_pan_troglodytes', 'ftp://ftp.ebi.ac.uk/pub/databases/SPproteomes/swissprot_files/proteomes/9598.SPC', '', now(), now(), 1); +INSERT INTO source (name, url, checksum, file_modified_date, upload_date, release) VALUES ('UniProtSwissProt', 'ftp://ftp.ebi.ac.uk/pub/databases/SPproteomes/swissprot_files/proteomes/9606.SPC', '', now(), now(), 1); +INSERT INTO source (name, url, checksum, file_modified_date, upload_date, release) VALUES ('UniProtSwissProt', 'ftp://ftp.ebi.ac.uk/pub/databases/SPproteomes/swissprot_files/proteomes/10090.SPC', '', now(), now(), 1); +INSERT INTO source (name, url, checksum, file_modified_date, upload_date, release) VALUES ('UniProtSwissProt', 'ftp://ftp.ebi.ac.uk/pub/databases/SPproteomes/swissprot_files/proteomes/10116.SPC', '', now(), now(), 1); +INSERT INTO source (name, url, checksum, file_modified_date, upload_date, release) VALUES ('UniProtSwissProt', 'ftp://ftp.ebi.ac.uk/pub/databases/SPproteomes/swissprot_files/proteomes/7227.SPC', '', now(), now(), 1); +INSERT INTO source (name, url, checksum, file_modified_date, upload_date, release) VALUES ('UniProtSwissProt', 'ftp://ftp.ebi.ac.uk/pub/databases/SPproteomes/swissprot_files/proteomes/6239.SPC', '', now(), now(), 1); +##INSERT INTO source (name, url, checksum, file_modified_date, upload_date, release) VALUES ('UniProtSwissProt', 'ftp://ftp.ebi.ac.uk/pub/databases/SPproteomes/swissprot_files/proteomes/9031.SPC', '', now(), now(), 1); +INSERT INTO source (name, url, checksum, file_modified_date, upload_date, release) VALUES ('UniProtSwissProt', 'ftp://ftp.ebi.ac.uk/pub/databases/SPproteomes/swissprot_files/proteomes/9598.SPC', '', now(), now(), 1); + +# RefSeq - release/ and cumulative/ directories +INSERT INTO source (name, url, checksum, file_modified_date, upload_date, release) VALUES ('RefSeq', 'ftp://ftp.ncbi.nih.gov/refseq/release/vertebrate_mammalian/vertebrate_mammalian1.protein.faa.gz', '', now(), now(), 1); +INSERT INTO source (name, url, checksum, file_modified_date, upload_date, release) VALUES ('RefSeq', 'ftp://ftp.ncbi.nih.gov/refseq/release/vertebrate_mammalian/vertebrate_mammalian1.rna.fna.gz', '', now(), now(), 1); + # Other sources - used to create dependent xrefs, but not to upload from -INSERT INTO source VALUES (100, 'EMBL', null, null, null, null, null); +INSERT INTO source (name, url, checksum, file_modified_date, upload_date, release) VALUES ('EMBL', null, null, null, null, null); ################################################################################