gmod-schema Mailing List for Generic Model Organism Database Project

Hi Chris,
The chado-xml document is under the XORT page:
 http://www.gmod.org/node/115
It is the first page that turns up when you search the gmod site for
chado-xml, though that page uses an iframe that used to link into the
schema cvs at SourceForge, which was a broken link. It now points to a
local checkout of the schema cvs, so the broken link problem should be
taken care of.
That said, what I would really like is if Chado-XML-overview.html could
be created as a html fragment (with no html, head or stylesheet tags) so
that I could do a php include to get it inline. If I did that, then the
content of the page would get indexed by drupal (the gmod.org content
manager) and would be searchable. I don't know anything about AsciiDoc;
do you think that is doable?
Thanks,
Scott
On Sat, 2006年07月29日 at 13:03 -0700, chris mungall wrote:
> They used to be here:
>=20
> http://www.gmod.org/schema/chado-xml
>=20
> There's a number of external web pages that link to here
>=20
> It should just be a matter of pointing at gmod/schema/chado/chado-xml =20
> in cvs. I'd do this myself but I don't really understand the =20
> reorganisation of the gmod website...
>=20
>=20
> -------------------------------------------------------------------------
> Take Surveys. Earn Cash. Influence the Future of IT
> Join SourceForge.net's Techsay panel and you'll get the chance to share y=
our
> opinions on IT & business topics through brief surveys -- and earn cash
> http://www.techsay.com/default.php?page=3Djoin.php&p=3Dsourceforge&CID=3D=
DEVDEV
> _______________________________________________
> Gmod-schema mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-schema
--=20
------------------------------------------------------------------------
Scott Cain, Ph. D. ca...@cs...
GMOD Coordinator (http://www.gmod.org/) 216-392-3087
Cold Spring Harbor Laboratory

They used to be here:
http://www.gmod.org/schema/chado-xml
There's a number of external web pages that link to here
It should just be a matter of pointing at gmod/schema/chado/chado-xml 
in cvs. I'd do this myself but I don't really understand the 
reorganisation of the gmod website...

On Fri, 2006年07月28日 at 14:25 -0500, Don Gilbert wrote:
> Scott,
>=20
> I believe common usage is these database name abbreviations are
> case insensitive. I.e., people tend to use varying case, but
> they should be unique either way; all uppercase is common
> for the acronyms, some are CamelCased. Pfam is the way Pfam folks
> use it.=20
Yes, I was thinking along the same lines--that the bulk loader should
handle dbxrefs in a case insensitve manner. Shouldn't be too hard to
add.
>=20
> On this same subject, why is there the, to me, redundant or non-standard =
'DB:'=20
> prefix on these database names? That is confusing to software as well as=
 not
> common usage as far as I know. Also, I end up with chado db table name f=
ields
> full of both 'DB:somedb' and 'somedb' due to this.
I don't really know. It must have been a decision made back in the dark
ages; I'm not wedded to it unless there is a good reason for it.
>=20
> -- Don
>=20
--=20
------------------------------------------------------------------------
Scott Cain, Ph. D. cai...@gm...
GMOD Coordinator (http://www.gmod.org/) 216-392-3087
Cold Spring Harbor Laboratory

Scott,
I believe common usage is these database name abbreviations are
case insensitive. I.e., people tend to use varying case, but
they should be unique either way; all uppercase is common
for the acronyms, some are CamelCased. Pfam is the way Pfam folks
use it. 
On this same subject, why is there the, to me, redundant or non-standard 'DB:' 
prefix on these database names? That is confusing to software as well as not
common usage as far as I know. Also, I end up with chado db table name fields
full of both 'DB:somedb' and 'somedb' due to this.
-- Don

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年07月28日 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
> -------------------------------------------------------------------------
> Take Surveys. Earn Cash. Influence the Future of IT
> Join SourceForge.net's Techsay panel and you'll get the chance to share y=
our
> opinions on IT & business topics through brief surveys -- and earn cash
> http://www.techsay.com/default.php?page=3Djoin.php&p=3Dsourceforge&CID=3D=
DEVDEV
> _______________________________________________
> Gmod-schema mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-schema
--=20
------------------------------------------------------------------------
Scott Cain, Ph. D. ca...@cs...
GMOD Coordinator (http://www.gmod.org/) 216-392-3087
Cold Spring Harbor Laboratory

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

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Thanks for the help guys. Much appreciated.
Cheers!
On 7/21/06, chris mungall <cj...@fr...> wrote:
>
>
> This is indeed correct, I have changed the godb-chado bridge to use
> this call
>
> SELECT cvterm_id,name FROM cvterm WHERE NOT EXISTS (SELECT DISTINCT
> subject_id FROM cvterm_relationship WHERE subject_id=cvterm_id) AND
> is_obsolete = 0 AND is_relationshiptype = 0;
>
> On Jul 20, 2006, at 12:13 PM, Hilmar Lapp wrote:
>
> > some RDBMS may execute this faster if written as NOT EXISTS
> > (depending on optimizer, it may choose to rewrite as an outer join
> > that can use an index; NOT IN will typically use a full table scan).
> >
> > sorry if this is confusing just ignore, the NOT IN will do fine in
> > many cases ...
> >
> > On Jul 20, 2006, at 1:28 PM, chris mungall wrote:
> >
> >>
> >> Like this (from godb-bridge):
> >>
> >> SELECT * FROM cvterm WHERE cvterm_id NOT IN (SELECT DISTINCT
> >> subject_id FROM cvterm_relationship) AND is_obsolete = 0 AND
> >> is_relationshiptype = 0
> >>
> >> On Jul 20, 2006, at 1:39 AM, Kevin Manansala wrote:
> >>
> >>> Good day,
> >>>
> >>> I would like to know how to identify root cvterms of a cv in the
> >>> Chado schema?
> >>>
> >>> Thank you very much in advance.
> >>>
> >>> Cheers!
> >>>
> >>> --
> >>> Kevin L. Manansala
> >>> BS Computer Science
> >>> UP Diliman
> >>>
> >>> "I'm the best there is at what I do!" - wolverine
> >>> --------------------------------------------------------------------
> >>> --
> >>> ---
> >>> Take Surveys. Earn Cash. Influence the Future of IT
> >>> Join SourceForge.net's Techsay panel and you'll get the chance to
> >>> share your
> >>> opinions on IT & business topics through brief surveys -- and earn
> >>> cash
> >>> http://www.techsay.com/default.php?
> >>> page=join.php&p=sourceforge&CID=DEVDEV______________________________
> >>> __
> >>> _______________
> >>> Gmod-schema mailing list
> >>> Gmo...@li...
> >>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
> >>
> >>
> >> ---------------------------------------------------------------------
> >> ----
> >> Take Surveys. Earn Cash. Influence the Future of IT
> >> Join SourceForge.net's Techsay panel and you'll get the chance to
> >> share your
> >> opinions on IT & business topics through brief surveys -- and earn
> >> cash
> >> http://www.techsay.com/default.php?
> >> page=join.php&p=sourceforge&CID=DEVDEV
> >> _______________________________________________
> >> Gmod-schema mailing list
> >> Gmo...@li...
> >> https://lists.sourceforge.net/lists/listinfo/gmod-schema
> >>
> >
> > --
> > ===========================================================
> > : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net :
> > ===========================================================
> >
> >
> >
> >
> >
> >
>
>
-- 
Kevin L. Manansala
BS Computer Science
UP Diliman
"I'm the best there is at what I do!" - wolverine

This is indeed correct, I have changed the godb-chado bridge to use 
this call
SELECT cvterm_id,name FROM cvterm WHERE NOT EXISTS (SELECT DISTINCT 
subject_id FROM cvterm_relationship WHERE subject_id=cvterm_id) AND 
is_obsolete = 0 AND is_relationshiptype = 0;
On Jul 20, 2006, at 12:13 PM, Hilmar Lapp wrote:
> some RDBMS may execute this faster if written as NOT EXISTS 
> (depending on optimizer, it may choose to rewrite as an outer join 
> that can use an index; NOT IN will typically use a full table scan).
>
> sorry if this is confusing just ignore, the NOT IN will do fine in 
> many cases ...
>
> On Jul 20, 2006, at 1:28 PM, chris mungall wrote:
>
>>
>> Like this (from godb-bridge):
>>
>> SELECT * FROM cvterm WHERE cvterm_id NOT IN (SELECT DISTINCT
>> subject_id FROM cvterm_relationship) AND is_obsolete = 0 AND
>> is_relationshiptype = 0
>>
>> On Jul 20, 2006, at 1:39 AM, Kevin Manansala wrote:
>>
>>> Good day,
>>>
>>> I would like to know how to identify root cvterms of a cv in the
>>> Chado schema?
>>>
>>> Thank you very much in advance.
>>>
>>> Cheers!
>>>
>>> -- 
>>> Kevin L. Manansala
>>> BS Computer Science
>>> UP Diliman
>>>
>>> "I'm the best there is at what I do!" - wolverine
>>> -------------------------------------------------------------------- 
>>> --
>>> ---
>>> Take Surveys. Earn Cash. Influence the Future of IT
>>> Join SourceForge.net's Techsay panel and you'll get the chance to
>>> share your
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>>
>>
>> --------------------------------------------------------------------- 
>> ----
>> Take Surveys. Earn Cash. Influence the Future of IT
>> Join SourceForge.net's Techsay panel and you'll get the chance to 
>> share your
>> opinions on IT & business topics through brief surveys -- and earn 
>> cash
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>> page=join.php&p=sourceforge&CID=DEVDEV
>> _______________________________________________
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>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>
>
> -- 
> ===========================================================
> : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net :
> ===========================================================
>
>
>
>
>
>

some RDBMS may execute this faster if written as NOT EXISTS 
(depending on optimizer, it may choose to rewrite as an outer join 
that can use an index; NOT IN will typically use a full table scan).
sorry if this is confusing just ignore, the NOT IN will do fine in 
many cases ...
On Jul 20, 2006, at 1:28 PM, chris mungall wrote:
>
> Like this (from godb-bridge):
>
> SELECT * FROM cvterm WHERE cvterm_id NOT IN (SELECT DISTINCT
> subject_id FROM cvterm_relationship) AND is_obsolete = 0 AND
> is_relationshiptype = 0
>
> On Jul 20, 2006, at 1:39 AM, Kevin Manansala wrote:
>
>> Good day,
>>
>> I would like to know how to identify root cvterms of a cv in the
>> Chado schema?
>>
>> Thank you very much in advance.
>>
>> Cheers!
>>
>> -- 
>> Kevin L. Manansala
>> BS Computer Science
>> UP Diliman
>>
>> "I'm the best there is at what I do!" - wolverine
>> --------------------------------------------------------------------- 
>> -
>> ---
>> Take Surveys. Earn Cash. Influence the Future of IT
>> Join SourceForge.net's Techsay panel and you'll get the chance to
>> share your
>> opinions on IT & business topics through brief surveys -- and earn
>> cash
>> http://www.techsay.com/default.php?
>> page=join.php&p=sourceforge&CID=DEVDEV_______________________________ 
>> _
>> _______________
>> Gmod-schema mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>
>
> ---------------------------------------------------------------------- 
> ---
> Take Surveys. Earn Cash. Influence the Future of IT
> Join SourceForge.net's Techsay panel and you'll get the chance to 
> share your
> opinions on IT & business topics through brief surveys -- and earn 
> cash
> http://www.techsay.com/default.php? 
> page=join.php&p=sourceforge&CID=DEVDEV
> _______________________________________________
> Gmod-schema mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>
-- 
===========================================================
: Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net :
===========================================================

Like this (from godb-bridge):
SELECT * FROM cvterm WHERE cvterm_id NOT IN (SELECT DISTINCT 
subject_id FROM cvterm_relationship) AND is_obsolete = 0 AND 
is_relationshiptype = 0
On Jul 20, 2006, at 1:39 AM, Kevin Manansala wrote:
> Good day,
>
> I would like to know how to identify root cvterms of a cv in the 
> Chado schema?
>
> Thank you very much in advance.
>
> Cheers!
>
> -- 
> Kevin L. Manansala
> BS Computer Science
> UP Diliman
>
> "I'm the best there is at what I do!" - wolverine
> ---------------------------------------------------------------------- 
> ---
> Take Surveys. Earn Cash. Influence the Future of IT
> Join SourceForge.net's Techsay panel and you'll get the chance to 
> share your
> opinions on IT & business topics through brief surveys -- and earn 
> cash
> http://www.techsay.com/default.php? 
> page=join.php&p=sourceforge&CID=DEVDEV________________________________ 
> _______________
> Gmod-schema mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-schema

Good day,
I would like to know how to identify root cvterms of a cv in the Chado
schema?
Thank you very much in advance.
Cheers!
-- 
Kevin L. Manansala
BS Computer Science
UP Diliman
"I'm the best there is at what I do!" - wolverine

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It may be that just changing your password on the SourceForge website
will be sufficient to allow access to the cvs repository, however, you
should probably be using ssh keys anyway...
Here is the announcement from SourceForge:
 https://sourceforge.net/forum/forum.php?forum_id=3D591370
Scott
On Fri, 2006年07月14日 at 15:54 -0400, Scott Cain wrote:
> Hello,
>=20
> At some time in the last few days (I'm not sure when, since they haven't
> announced it), SourceForge began requiring ssh keys to access the cvs
> server, and disallowing the use of plain passwords. In order to commit,
> update or checkout and GMOD cvs repositories, therefore, you will need
> to set up an ssh key. Please see=20
>=20
> http://sourceforge.net/docs/F02/en/
>=20
> for information from SourceForge for setting up the key. Sorry for any
> inconvenience.
>=20
> Scott
>=20
> -------------------------------------------------------------------------
> Using Tomcat but need to do more? Need to support web services, security?
> Get stuff done quickly with pre-integrated technology to make your job ea=
sier
> Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronim=
o
> http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D120709&bid=3D263057&dat=
=3D121642
> _______________________________________________
> Gmod-gbrowse mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
--=20
------------------------------------------------------------------------
Scott Cain, Ph. D. ca...@cs...
GMOD Coordinator (http://www.gmod.org/) 216-392-3087
Cold Spring Harbor Laboratory

Hello,
At some time in the last few days (I'm not sure when, since they haven't
announced it), SourceForge began requiring ssh keys to access the cvs
server, and disallowing the use of plain passwords. In order to commit,
update or checkout and GMOD cvs repositories, therefore, you will need
to set up an ssh key. Please see=20
 http://sourceforge.net/docs/F02/en/
for information from SourceForge for setting up the key. Sorry for any
inconvenience.
Scott
--=20
------------------------------------------------------------------------
Scott Cain, Ph. D. ca...@cs...
GMOD Coordinator (http://www.gmod.org/) 216-392-3087
Cold Spring Harbor Laboratory

Naama,
The bioperl scripts includes one for genbank to gff3 (found this in gmod INSTALL doc):
 GFF3 can also be generated via a script provided with bioperl,
 bp_genbank2gff.pl:
 $ bp_genbank2gff.pl --stdout --file <genbank file> > <gff file>
 Note the redirection of standard out. Note that this method
 for generating GFF3 files is not completely satisfactory and
 development is ongoing to provide better translation.
-- Don

Thanks fro your reply!
What about a GenBank to gff3 file converter? Is there anything available 
from GMOD?
Scott Cain wrote:
>Hi Naama,
>
>The pub module only very lightly used right now; I don't know if FlyBase
>has loaded their pub data into chado, Dave or Pinglei?
>
>Even if they have, I imagine they are using custom scripts to load the
>data.
>
>Scott
>
>
>On Wed, 2006年07月05日 at 16:16 -0400, Naama Menda wrote:
> 
>
>>Hi,
>>
>>Is there a GMOD tool for bulk loading publication data into CHADO's pub 
>>module?
>>
>>I'd also like to load data from a GenBank file into the sequence module, 
>>but I only found gmod_fasta2gff3.pl.
>>The problem is fasta files do not contain many of the fields that exist 
>>in the .gb file.
>>Is there an available script for converting genbank format directly to 
>>gff3?
>>
>>Thanks!
>>
>>-Naama
>>
>>
>>
>>Using Tomcat but need to do more? Need to support web services, security?
>>Get stuff done quickly with pre-integrated technology to make your job easier
>>Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo
>>http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642
>>_______________________________________________
>>Gmod-schema mailing list
>>Gmo...@li...
>>https://lists.sourceforge.net/lists/listinfo/gmod-schema
>> 
>>

Ah, right. In schema/chado/load/bin there is a file called
new_bulk_load_gff3.PLS. To create the loader, execute the command `perl
new_bulk_load_gff3.PLS`, which is what will get done during the make
process (after the name is changed).
More problematic, though, is the wormbase file. There are several
issues:
 - it's too big. Unless you have a server with an insane amount of
ram, the loader will end up crashing as it runs out of memory. I
typically separate GFF files by reference sequences (or srcfeature in
chado-ese). That may still result in files that are too large--they
should be a few 100K lines a piece to be safe. (For reference, my 2G
server can process files with around 600K lines.)
 - there are no lines for the chromosomes. Unless you are loading
those first from a separate file, you need GFF lines for each chromosome
before you reference a feature on it.
 - I can't tell if parent features always come before their children,
but that is a potential problem.
 - Computational results are mixed with curated annotations. When
loading, you have to specify whether the file contains computational
results or not, and it can be only one or the other (see the docs for
prepping the database to accept computational results and commandline
args for loading).
I am working a GFF preprocessor that will take care of many of these
aspects, but up until now, I've been handling these things with quicky
perl scripts.
Scott
On Tue, 2006年07月11日 at 10:39 +0100, Anthony Rogers wrote:
> Scott Cain wrote:
> > Hi Ant,
> >
> > It looks to me like you are trying to us gmod_load_gff3.pl, which I
> > haven't tested and is very likely not working (as you seem to have foun=
d
> > out). Try gmod_new_bulk_load_gff3.pl (which will have its name changed
> > later this week to gmod_bulk_load_gff3.pl).
> >
> > Related to that, I'll be curious about how the loading goes. The last
> > time I looked at wormbase GFF, it looked to me like it wasn't sorted th=
e
> > way that the loader will like. It is on my list of things to write a
> > GFF3 preprocesser so that the loader will like it.
> > =20
> Hi Scott,
> Where do I find gmod_new_bulk_load_gff3.pl ? when I do a CVS update the=20
> gmod_bulk_load_gff3.pl script is still unchanged from May 16th
>=20
> Payan, in Lincoln's group, has generated a new GFF3 version of WormBase=20
> data which I've been trying to use. Its available at . . .
> http://dev.wormbase.org/~canaran/gff3_download_2006年06月27日/elegansWS159.gf=
f3.08.sorted.gz
>=20
> Ant
> > Nevertheless, I will try to fix the Class::DBI errors that are occurrin=
g
> > in your output below, since the recently released modware relies on it.
> >
> > Scott
> >
> >
> > On Fri, 2006年07月07日 at 12:15 +0100, Anthony Rogers wrote:
> > =20
> >> I've come back to my CHADO adventure and Im stuck on this error with t=
he=20
> >> gff loader
> >>
> >> perl new_gff_loader.pl --gfffile /wormsrv2/GMOD/DOWNLOADS/mini.gff3=20
> >> -organism worm --srcdb wormbase
> >> .
> >> .
> >> .
> >> 7.4 pg_catalog. gencode
> >> 7.4 pg_catalog. gencode_codon_aa
> >> Use of uninitialized value in split at=20
> >> /nfs/disk100/wormpub/lib/perl5/site_perl/5.8.7/Class/DBI/Pg.pm line 10=
8.
> >> gencode_codon_aa has no primary key at ../../lib/Bio/GMOD/Load/GFF.pm=20
> >> line 5
> >> Compilation failed in require at ../../lib/Bio/GMOD/Load/GFF.pm line 5=
.
> >> BEGIN failed--compilation aborted at ../../lib/Bio/GMOD/Load/GFF.pm li=
ne 5.
> >> Compilation failed in require at new_gff_loader.pl line 8.
> >> BEGIN failed--compilation aborted at new_gff_loader.pl line 8.
> >>
> >> look familiar ?
> >> This obviously happens in compilation so it cant be data. There must =
be=20
> >> something wrong in the database.
> >>
> >> Any help appreciated . .
> >> Ant
> >>
> >> =20
>=20
>=20
--=20
------------------------------------------------------------------------
Scott Cain, Ph. D. ca...@cs...
GMOD Coordinator (http://www.gmod.org/) 216-392-3087
Cold Spring Harbor Laboratory

Hi Naama,
The pub module only very lightly used right now; I don't know if FlyBase
has loaded their pub data into chado, Dave or Pinglei?
Even if they have, I imagine they are using custom scripts to load the
data.
Scott
On Wed, 2006年07月05日 at 16:16 -0400, Naama Menda wrote:
> Hi,
>=20
> Is there a GMOD tool for bulk loading publication data into CHADO's pub=20
> module?
>=20
> I'd also like to load data from a GenBank file into the sequence module,=20
> but I only found gmod_fasta2gff3.pl.
> The problem is fasta files do not contain many of the fields that exist=20
> in the .gb file.
> Is there an available script for converting genbank format directly to=20
> gff3?
>=20
> Thanks!
>=20
> -Naama
>=20
>=20
>=20
> Using Tomcat but need to do more? Need to support web services, security?
> Get stuff done quickly with pre-integrated technology to make your job ea=
sier
> Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronim=
o
> http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D120709&bid=3D263057&dat=
=3D121642
> _______________________________________________
> Gmod-schema mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-schema
--=20
------------------------------------------------------------------------
Scott Cain, Ph. D. ca...@cs...
GMOD Coordinator (http://www.gmod.org/) 216-392-3087
Cold Spring Harbor Laboratory

(also cc'ed to the schema list, which has a much larger reader base.)
Hi Sophia,
Sorry for the delay; I just got back from an extended trip to through
the Carolinas :-)
The sequence identifiers can definitely correspond to ID tags, since
that is how I typically load chromosome sequences. It should also work
for Target tags too, though I don't recall testing that off the top of
my head.
About your last question, the short answer is no. Why wouldn't you put
that in the fasta section?
Scott
On Wed, 2006年07月05日 at 16:27 -0600, Sofia Robb wrote:
> Hello,
>=20
> I use my GFF3 with gmod_bulk_load.pl.
>=20
> If I want to add sequences to my gff3 I know that I can add the=20
> following to the bottom of my GFF3 file.
>=20
> ##fasta
> >seq1
> >seq2
>=20
> My question is, what do the >seq1 and >seq2 need to correspond to in the=20
> GFF3 file? can it be ID=3D, or does it have to be Target=3D as is seen i=
n=20
> the documentation?
>=20
> Also, is there a Tag that i can add to the last column of the gff in=20
> which I can indicate short sequences as Values which will end up in=20
> residues field in the feature table?
>=20
> Thanks,
> Sofia
>=20
> Using Tomcat but need to do more? Need to support web services, security?
> Get stuff done quickly with pre-integrated technology to make your job ea=
sier
> Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronim=
o
> http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D120709&bid=3D263057&dat=
=3D121642
> _______________________________________________
> Gmod-chado-seq-ad mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-chado-seq-ad
--=20
------------------------------------------------------------------------
Scott Cain, Ph. D. ca...@cs...
GMOD Coordinator (http://www.gmod.org/) 216-392-3087
Cold Spring Harbor Laboratory

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Hi,
Is there a GMOD tool for bulk loading publication data into CHADO's pub 
module?
I'd also like to load data from a GenBank file into the sequence module, 
but I only found gmod_fasta2gff3.pl.
The problem is fasta files do not contain many of the fields that exist 
in the .gb file.
Is there an available script for converting genbank format directly to 
gff3?
Thanks!
-Naama