Re: [Gmod-schema] redundancy in databases table

[Scott C. <ca...@cs...>]

Hi Jeff,

I hadn't really noticed these redundancies before.  Removing them should
not be a problem, I think.  The only problem I can see is GFF files that
use 'PFAM' for a dbxref name where the GFF3 bulk loader might expect to
find 'pfam', but the GBrowse adaptor shouldn't care at all.  Certainly,
they should be removed for the sake of consistency.  So, which should be
removed?

Scott


On Fri, 2006-07-28 at 12:03 -0600, Jeff Bowes wrote:
> Hi,
>=20
> In chado/load/etc/initialize.sql in the schema module there is some=20
> redundancy in the databases that get inserted into db.  I found this in=20
> both release 0.003 and the current CVS head.  For example: OMIM,=20
> Swisprot, Genbank protein, pfam have duplicate entries.  Can redundant=20
> versions of databases be deleted from this list or will this break=20
> something.  In particular,  will it break GBrowse using the chado adaptor=
.
>=20
> Thanks,
>=20
> Jeff
>=20
>=20
>=20
>=20
> insert into db (name, description) values ('GFF_source', 'A collection=20
> of sources (ie, column 2) from GFF files');
>=20
> insert into db (name, description) values ('GFF_source', 'A collection=20
> of sources (ie, column 2) from GFF files');
>=20
> insert into db (name) values ('ATCC');
>=20
> 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');
>=20
> 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');
>=20
> 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=20
> ('DB:affy:U133',(select contact_id from contact where name =3D=20
> 'null'),'Affymetrix=20
> U133','http://https://www.affymetrix.com/analysis/netaffx/fullrecord.affx=
?pk=3DHG-U133_PLUS_2:');
> --insert into db (name, contact_id, description, urlprefix) values=20
> ('DB:affy:U95',(select contact_id from contact where name =3D=20
> 'null'),'Affymetrix=20
> U95','http://https://www.affymetrix.com/analysis/netaffx/fullrecord.affx?=
pk=3DHG-U95AV2:');
>=20
> insert into db (name, description) values ('DB:GR','Gramene');
> insert into db (name, description, urlprefix) values=20
> ('DB:uniprot','UniProt/TrEMBL','http://us.expasy.org/cgi-bin/niceprot.pl?=
');
> insert into db (name, description, urlprefix) values=20
> ('DB:refseq:mrna','RefSeq=20
> mRNA','http://http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=3Dsearch&=
db=3Dnucleotide&dopt=3DGenBank&term=3D');
> insert into db (name, description, urlprefix) values=20
> ('DB:refseq:protein','RefSeq=20
> Protein','http://http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=3Dsear=
ch&db=3Dprotein&dopt=3DGenBank&term=3D');
> insert into db (name, description, urlprefix) values=20
> ('DB:unigene','Unigene','http://http://www.ncbi.nih.gov/entrez/query.fcgi=
?db=3Dunigene&cmd=3Dsearch&term=3D');
> insert into db (name, description, urlprefix) values=20
> ('DB:omim','OMIM','http://http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi=
?id=3D');
> insert into db (name, description, urlprefix) values=20
> ('DB:locuslink','LocusLink','http://http://www.ncbi.nlm.nih.gov/LocusLink=
/LocRpt.cgi?l=3D');
> insert into db (name, description, urlprefix) values=20
> ('DB:genbank:mrna','GenBank=20
> mRNA','http://http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=3Dsearch&=
db=3Dnucleotide&dopt=3DGenBank&term=3D');
> insert into db (name, description, urlprefix) values=20
> ('DB:genbank:protein','GenBank=20
> Protein','http://http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=3Dsear=
ch&db=3Dprotein&dopt=3DGenBank&term=3D');
> insert into db (name, description, urlprefix) values=20
> ('DB:swissprot:display','SwissProt','http://http://us.expasy.org/cgi-bin/=
niceprot.pl?');
> insert into db (name, description, urlprefix) values=20
> ('DB:pfam','Pfam','http://http://www.sanger.ac.uk/cgi-bin/Pfam/dql.pl?que=
ry=3D');
> tp://www.sanger.ac.uk/cgi-bin/Pfam/dql.pl?query=3D');
>=20
>=20
> --=20
> Jeff Bowes M.Sc.
> DBA/Technical Architect, Xenbase
> Department of Biological Sciences
> University of Calgary
> Calgary, Alberta T2N 1N4
> CANADA
> Tel: (403) 220-2824=20
> Fax: (403) 284-4707
>=20
>=20
>=20
>=20
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--=20
------------------------------------------------------------------------
Scott Cain, Ph. D.                                         ca...@cs...
GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
Cold Spring Harbor Laboratory