[Gmod-schema] redundancy in databases table

[Jeff B. <bo...@uc...>]

Hi,

In chado/load/etc/initialize.sql in the schema module there is some 
redundancy in the databases that get inserted into db.  I found this in 
both release 0.003 and the current CVS head.  For example: OMIM, 
Swisprot, Genbank protein, pfam have duplicate entries.  Can redundant 
versions of databases be deleted from this list or will this break 
something.  In particular,  will it break GBrowse using the chado adaptor.

Thanks,

Jeff




insert into db (name, description) values ('GFF_source', 'A collection 
of sources (ie, column 2) from GFF files');

insert into db (name, description) values ('GFF_source', 'A collection 
of sources (ie, column 2) from GFF files');

insert into db (name) values ('ATCC');

insert into db (name) values ('DB:refseq');
insert into db (name) values ('DB:genbank');
insert into db (name) values ('DB:EMBL');
insert into db (name) values ('DB:TIGR');
insert into db (name) values ('DB:ucsc');
insert into db (name) values ('DB:ucla');
insert into db (name) values ('DB:SGD');

insert into db (name) values ('DB:PFAM');
insert into db (name) values ('DB:SUPERFAMILY');
insert into db (name) values ('DB:PROFILE');
insert into db (name) values ('DB:PRODOM');
insert into db (name) values ('DB:PRINTS');
insert into db (name) values ('DB:SMART');
insert into db (name) values ('DB:TIGRFAMs');
insert into db (name) values ('DB:PIR');

insert into db (name) values ('DB:Affymetrix_U133');
insert into db (name) values ('DB:Affymetrix_U133PLUS');
insert into db (name) values ('DB:Affymetrix_U95');
insert into db (name) values ('DB:LocusLink');
insert into db (name) values ('DB:RefSeq_protein');
insert into db (name) values ('DB:GenBank_protein');
insert into db (name) values ('DB:OMIM');
insert into db (name) values ('DB:Swiss');
insert into db (name) values ('DB:RefSNP');
insert into db (name) values ('DB:TSC');
--insert into db (name, contact_id, description, urlprefix) values 
('DB:affy:U133',(select contact_id from contact where name = 
'null'),'Affymetrix 
U133','http://https://www.affymetrix.com/analysis/netaffx/fullrecord.affx?pk=HG-U133_PLUS_2:');
--insert into db (name, contact_id, description, urlprefix) values 
('DB:affy:U95',(select contact_id from contact where name = 
'null'),'Affymetrix 
U95','http://https://www.affymetrix.com/analysis/netaffx/fullrecord.affx?pk=HG-U95AV2:');

insert into db (name, description) values ('DB:GR','Gramene');
insert into db (name, description, urlprefix) values 
('DB:uniprot','UniProt/TrEMBL','http://us.expasy.org/cgi-bin/niceprot.pl?');
insert into db (name, description, urlprefix) values 
('DB:refseq:mrna','RefSeq 
mRNA','http://http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=search&db=nucleotide&dopt=GenBank&term=');
insert into db (name, description, urlprefix) values 
('DB:refseq:protein','RefSeq 
Protein','http://http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=search&db=protein&dopt=GenBank&term=');
insert into db (name, description, urlprefix) values 
('DB:unigene','Unigene','http://http://www.ncbi.nih.gov/entrez/query.fcgi?db=unigene&cmd=search&term=');
insert into db (name, description, urlprefix) values 
('DB:omim','OMIM','http://http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=');
insert into db (name, description, urlprefix) values 
('DB:locuslink','LocusLink','http://http://www.ncbi.nlm.nih.gov/LocusLink/LocRpt.cgi?l=');
insert into db (name, description, urlprefix) values 
('DB:genbank:mrna','GenBank 
mRNA','http://http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=search&db=nucleotide&dopt=GenBank&term=');
insert into db (name, description, urlprefix) values 
('DB:genbank:protein','GenBank 
Protein','http://http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=search&db=protein&dopt=GenBank&term=');
insert into db (name, description, urlprefix) values 
('DB:swissprot:display','SwissProt','http://http://us.expasy.org/cgi-bin/niceprot.pl?');
insert into db (name, description, urlprefix) values 
('DB:pfam','Pfam','http://http://www.sanger.ac.uk/cgi-bin/Pfam/dql.pl?query=');
tp://www.sanger.ac.uk/cgi-bin/Pfam/dql.pl?query=');


-- 
Jeff Bowes M.Sc.
DBA/Technical Architect, Xenbase
Department of Biological Sciences
University of Calgary
Calgary, Alberta T2N 1N4
CANADA
Tel: (403) 220-2824 
Fax: (403) 284-4707