Added description field to xref.

Modified INSERTs for source table to not have hard-coded source_id.

Started adding sources for RefSeq files.

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);
 
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