gmod-schema Mailing List for Generic Model Organism Database Project

Hi Chris,
Not surprisingly, I oversimplified too much (it isn't surprising since I
really don't know that much about GUS, other than what people have told
me). Take a look at how I changed it to see it is better:
 http://www.gmod.org/node/230
Thanks,
Scott
On Fri, 2006年09月29日 at 16:48 -0400, Chris Stoeckert wrote:
> Hi Scott,
> You wrote:
> > GUS is a relational database schema aimed at genomics data,
> >=20
> GUS is also aimed at functional genomics data with schemas for
> array-based, SAGE, and RT-PCR data (RAD), mass spec proteomics (Prot),
> experimental design and factors (Study). and regulatory interactions
> (TESS).=20
>=20
>=20
> GUS does encode information about the biology in the tables as you say
> but not simply for storage of sequence features. There are separate
> tables (and views) for sequence features and for the conceptual
> entities Gene, RNA. and Protein. These conceptual central dogma tables
> link together instances of sequence features representing the same
> "gene" (or RNA or protein).=20
>=20
>=20
> Cheers,
> Chris
>=20
> Chris Stoeckert, Ph.D.
>=20
> Research Associate Professor, Dept. of Genetics
>=20
> 1415 Blockley Hall, Center for Bioinformatics
>=20
> 423 Guardian Dr., University of Pennsylvania
>=20
> Philadelphia, PA 19104
>=20
> Ph: 215-573-4409 FAX: 215-573-3111
>=20
>=20
>=20
> On Sep 29, 2006, at 4:17 PM, Scott Cain wrote:
>=20
> > Hi,
> >=20
> >=20
> > Since I've gotten several questions about Chado vs GUS (a death
> > match :-) in the last few weeks, I decided to take a stab at
> > answering
> > it. Please feel free to comment on my answer:
> >=20
> >=20
> > http://www.gmod.org/node/230
> >=20
> >=20
> > Thanks,
> > Scott
> >=20
> >=20
> > --=20
> > -----------------------------------------------------------------------=
-
> > Scott Cain, Ph. D.
> > ca...@cs...
> > GMOD Coordinator (http://www.gmod.org/)
> > 216-392-3087
> > Cold Spring Harbor Laboratory
> > -----------------------------------------------------------------------=
--
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=3DDEVDEV_______________________________________________
> > Gmod-schema mailing list
> > Gmo...@li...
> > https://lists.sourceforge.net/lists/listinfo/gmod-schema
>=20
>=20
> -------------------------------------------------------------------------
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DEVDEV
> _______________________________________________ Gmod-schema mailing list =
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nfo/gmod-schema
--=20
------------------------------------------------------------------------
Scott Cain, Ph. D. ca...@cs...
GMOD Coordinator (http://www.gmod.org/) 216-392-3087
Cold Spring Harbor Laboratory

Hi Scott,
You wrote:
> GUS is a relational database schema aimed at genomics data,
GUS is also aimed at functional genomics data with schemas for array- 
based, SAGE, and RT-PCR data (RAD), mass spec proteomics (Prot), 
experimental design and factors (Study). and regulatory interactions 
(TESS).
GUS does encode information about the biology in the tables as you 
say but not simply for storage of sequence features. There are 
separate tables (and views) for sequence features and for the 
conceptual entities Gene, RNA. and Protein. These conceptual central 
dogma tables link together instances of sequence features 
representing the same "gene" (or RNA or protein).
Cheers,
Chris
Chris Stoeckert, Ph.D.
Research Associate Professor, Dept. of Genetics
1415 Blockley Hall, Center for Bioinformatics
423 Guardian Dr., University of Pennsylvania
Philadelphia, PA 19104
Ph: 215-573-4409 FAX: 215-573-3111
On Sep 29, 2006, at 4:17 PM, Scott Cain wrote:
> Hi,
>
> Since I've gotten several questions about Chado vs GUS (a death
> match :-) in the last few weeks, I decided to take a stab at answering
> it. Please feel free to comment on my answer:
>
> http://www.gmod.org/node/230
>
> Thanks,
> Scott
>
> -- 
> ---------------------------------------------------------------------- 
> --
> Scott Cain, Ph. D. 
> ca...@cs...
> GMOD Coordinator (http://www.gmod.org/) 
> 216-392-3087
> Cold Spring Harbor Laboratory
> ---------------------------------------------------------------------- 
> ---
> 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

Hello,
I sent an email about this to the list a few days ago, but it seems to
have been lost in the pipes of the Internets(TM). Due to several
questions recently about using Apollo with Chado, I created a simple
Chado database along with documenting all of the steps and starting
materials I used to create the database and put them on the website:
 http://www.gmod.org/node/227
Scott
--=20
------------------------------------------------------------------------
Scott Cain, Ph. D. ca...@cs...
GMOD Coordinator (http://www.gmod.org/) 216-392-3087
Cold Spring Harbor Laboratory

Hi,
Since I've gotten several questions about Chado vs GUS (a death
match :-) in the last few weeks, I decided to take a stab at answering
it. Please feel free to comment on my answer:
 http://www.gmod.org/node/230
Thanks,
Scott
--=20
------------------------------------------------------------------------
Scott Cain, Ph. D. ca...@cs...
GMOD Coordinator (http://www.gmod.org/) 216-392-3087
Cold Spring Harbor Laboratory

Pinglei Zhou wrote:
> Hi Henry,
> 
>> Hi, Pinglei,
>>
>> Thanks for your reply and explanation.
>>
>> I think the problem boils down to how a gene is represented as a
>> feature. As provided in the GFF3 specification, a single exon gene from
>> a prokaryotic organism can be represented as either
>>
>> ChrX . gene XXXX YYYY . + . ID=gene01;
>> ChrX . exon XXXX YYYY . + . Parent=gene01
>> ChrX . CDS XXXX YYYY . + . Parent=gene01
>>
>> or
>>
>> ChrX . gene XXXX YYYY . + . ID=gene01;
>> ChrX . CDS XXXX YYYY . + . Parent=gene01
>>
>> It's really hard to say which is more correct. So my question is: Is
>> there any way to configure apollo so that it can also recognize the
>> "two-level" genes?
> 
> I asked a few people around here, the answer is 'no', there is no way to recognize it now.
> 
Pinglei is right - apollo expects genes to be 3 levels: gene transcript exon.
Without these 3 levels it wouldnt be able to do alternative splicing, sorry its
intolerant of 2 levels. If you have single transcript genes you can just make
the gene the same as the transcript (or vice versa). Is it problematic to use
gff with the 3 levels?
Mark

Hi Henry,
 
>Hi, Pinglei,
>
>Thanks for your reply and explanation.
>
>I think the problem boils down to how a gene is represented as a
>feature. As provided in the GFF3 specification, a single exon gene from
>a prokaryotic organism can be represented as either
>
>ChrX . gene XXXX YYYY . + . ID=gene01;
>ChrX . exon XXXX YYYY . + . Parent=gene01
>ChrX . CDS XXXX YYYY . + . Parent=gene01
>
>or
>
>ChrX . gene XXXX YYYY . + . ID=gene01;
>ChrX . CDS XXXX YYYY . + . Parent=gene01
>
>It's really hard to say which is more correct. So my question is: Is
>there any way to configure apollo so that it can also recognize the
>"two-level" genes?
I asked a few people around here, the answer is 'no', there is no way to recognize it now.
>As for the problem with XORT. Here's the command I ran and the error
>message I got:
>
>[root@rip XML-XORT-0.003]# xort_dump.pl -d chado -p chado_test.xml -g
>examples/dumpspec_apollo_no_evidence.xml -f no_local_id -s module
>
>filename:/usr/local/gmod/conf/XORT/chado.properties
>
>filename:/usr/local/gmod/conf/XORT/chado.properties
>DBD::Pg::st execute failed: execute called with an unbound placeholder
>at /usr/lib/perl5/site_perl/5.8.5/XML/XORT/Util/DbUtil/DB.pm line 137,
><IN> line 2476.
>Unable to execute query: DBI::db=HASH(0x875ccd4)->errstr:select
>substr(residues, 2ドル+1, 3ドル-2ドル) from feature where feature_id=1ドル
I know the problem here. We typically have some other wrappers to work for FlyBase specific data, if you look inside the 
dumpspec_apollo_no_evidence.xml file, those 1,ドル 2ドル... require real data you feed to xort_dump, 1ドル for feature_id for the arm, 
2ドル for fmin of chrosomsome arm, 3ドル for fmax of chrosomosome, 4ドル for title, 5ドル for arm name. 
so you should call it like this:
xort_dump.pl -d chado -p chado_test.xml -g examples/dumpspec_apollo_no_evidence.xml -f no_local_id -s module -a "1000011 1 
1000 titlesomething 2L'
or use the attached apollo_chado.pl (you need to edit a little to reflect your implement, say whether you have abbreviation 
column for organism table in order to get organism_id etc.)
Sorry for the confusion, I will spend more to document XORT better.
pinglei
>I checked chado.properties file but didn't find any problems there. As a
>matter of fact, if I run 'xort_dump.pl -d chado', the script can spit
>out some sort of XML but not chado XML. So it seems to me database
>connection is not an issue here. I'm wondering if you know what else
>could be wrong?
>
>I'll apreciate your help.
>
>Thanks,
>
>Henry
>
> 
>
>-----Original Message-----
>From: Pinglei Zhou [mailto:zh...@mo...] 
>Sent: Thursday, September 28, 2006 6:38 AM
>To: cai...@gm...; HXI (Henry Xiang)
>Cc: gmo...@li...; ha...@mo...
>Subject: Re: [Gmod-schema] Apollo-Chado Integration
>
>Hi Scott, Henry,
>
>>On thing that occurred to me in reading your email that isn't laid out 
>>anywhere is that Apollo is somewhat (ok, very) finicky about the 
>>structure of gene annotations. It expects there to be a gene feature 
>>with one or more child transcript features with one or more child exon 
>>features, which is why the yeast GFF file won't work with it. I've 
>>occasionally toyed with the idea of modifying the GFF loader to detect 
>>instances of gene structures that Apollo won't like and then fixing 
>>them on the fly, but it is a difficult thing to do right on many
>levels.
>
>Not sure if this can help. FlyBase have many other feature types without
>the three-level structures (for instance, transposable_element). By edit
>the configure file, we are able to load and view the data.
>
> 
>>> the chado database, I've never been able to make a apollo-chado 
>>> "round-trip" via either XORT or jdbc connector. I tried 
>>> Saccharomyces
>
>Can you say more about the XORT problem ? We FlyBase daily use the XORT
>to round-trip the Apollo-chado, it works very well. 
>
>pinglei
>
>
>
>
>
>>> cerevisiae sample database from SGD and a trivial two-entry database 
>>> like this:
>>> 
>>> ##gff-version 3
>>> SJ1904 NZCA chromosome 1 4345449 . + .
>>> ID=SJ1904
>>> SJ1904 NZCA gene 506 1846 . + .
>>> ID=BLP00001
>>> ###
>>> ##FASTA
>>> >SJ1904
>>> cgaaagcctaatttcatttttcctcaattttagcttaaaagattttttt......
>>> 
>>> Both of them worked for "one-way trip", but none of them worked for 
>>> "round-trip". I sent my questions to both gmod schema and Apollo 
>>> mailing lists a month ago, but so far I only got one reply (which is
>>from you).
>>> 
>>> I think what I need most right now is
>>> a) someone who has the hands-on experience of gmod-apollo integration
>
>>> and is willing to show me the rope, or
>>> b) some working instance of gmod-apollo that I can "borrow" and 
>>> figure
>>
>>> out things by myself.
>>> 
>>> I'm just wondering if any of those options is possible. I'll 
>>> appreciate your inputs/advice/direction/guidance. :-)
>>> 
>>> Thanks,
>>> 
>>> Henry
>>> 
>>> -----Original Message-----
>>> From: Scott Cain [mailto:cai...@gm...]
>>> Sent: Thursday, September 21, 2006 10:33 AM
>>> To: HXI (Henry Xiang)
>>> Cc: gmo...@li...
>>> Subject: Re: [Gmod-schema] Apollo-Chado Integration
>>> 
>>> Hi Henry,
>>> 
>>> I am back from England and very nearly awake today :-)
>>> 
>>> So, some questions:
>>> 
>>> What version of gmod/chado are you using? Did you get a reasonably
>
>>> recent checkout from cvs?
>>> 
>>> What version of Apollo are you using?
>>> 
>>> I'm not exactly sure where the 'f.type_id = null' is coming from, but
>
>>> I agree that it doesn't make much sense.
>>> 
>>> Also, you can take a look at the updated doc I wrote on apollo and 
>>> chado at
>>> 
>>> http://gmod.cvs.sourceforge.net/*checkout*/gmod/schema/chado/README.A
>>> p
>>> ol
>>> lo.pod
>>> 
>>> It is still a little skimpy on details, but it is getting better.
>>> 
>>> Scott
>>> 
>>> 
>>> On Wed, 2006年09月13日 at 10:10 -0700, HXI (Henry Xiang) wrote:
>>> > Hi,
>>> > 
>>> > Has someone successfully done Apollo-Chado integration so that 
>>> > Apollo can directly talk to Chado database via jdbc? I desperatelly
>
>>> > need help
>>> 
>>> > from Apollo/Chado gurus.
>>> > 
>>> > I'm testing on a very simple Chado instance. When I searched for a 
>>> > gene with unique ID 'BLP00001', Apollo sent the following query
>>> > 
>>> > SELECT f.feature_id FROM feature f WHERE (f.uniquename = 
>>> > 'BLP00001' OR f.name = 'BLP00001') AND f.type_id = null
>>> > 
>>> > to chado database, and popped up an error message saying the gene 
>>> > can't be found.
>>> > 
>>> > In fact, the feature 'BLP00001' has the cv term 'gene' associated 
>>> > with
>>> 
>>> > it, and I verified it at the database level with the following SQL 
>>> > query
>>> > 
>>> > chado=# select f.uniquename, t.name from feature f, cvterm t where 
>>> > f.type_id = t.cvterm_id and f.uniquename = 'BLP00001'; uniquename 
>>> > |
>>
>>> > name
>>> > ------------+------
>>> > BLP00001 | gene
>>> > (1 row)
>>> > 
>>> > Besides, column 'type_id' of table 'feature' has 'NOT NULL'
>>> > constraint, so it doesn't make sense for Apollo to send query with 
>>> > type_id = null.
>>> > 
>>> > I'm wondering if someone came across the same problem before. How 
>>> > should I configure Apollo data adapter so that it can find the 
>>> > correct
>>> 
>>> > type_id for a feature?
>>> > 
>>> > Any assistance/advice will be highly appreciated.
>>> > 
>>> > Thanks a million!
>>> > 
>>> > Henry
>>> > 
>>> > PS: My chado-adapter.xml looks like this:
>>> > 
>>> > <?xml version="1.0" encoding="UTF-8"?>
>>> > <!-- This file is used to config chado database adapter --> 
>>> > <chado-adapter>
>>> > <chadoInstance id="referenceInstance" default="true">
>>> > 
>>> >
>>> <writebackXmlTemplateFile>transactionXMLTemplate.xml</writebackXmlTem
>>> p
>>> la
>>> teFile>
>>> > <featureCV>sequence</featureCV>
>>> > <polypeptideType>polypeptide</polypeptideType>
>>> > <relationshipCV>relationship</relationshipCV>
>>> > <propertyTypeCV>feature_property</propertyTypeCV>
>>> > <!-- default is part_of -->
>>> > <partOfCvTerm>part_of</partOfCvTerm>
>>> > <transProtRelationTerm>derives_from</transProtRelationTerm>
>>> > <searchHitsHaveFeatLocs>true</searchHitsHaveFeatLocs>
>>> > 
>>> > <clsName>apollo.dataadapter.chado.jdbc.FlybaseChadoInstance</clsNam
>>> > e
>>> > >
>>> > 
>>> > <oneLevelAnnotTypes>
>>> > <type>promoter</type>
>>> > <type>insertion site</type>
>>> > <type>transposable_element</type>
>>> > <type>transposable_element_insertion_site</type>
>>> > <type>remark</type>
>>> > <type>repeat_region</type> 
>>> > </oneLevelAnnotTypes>
>>> > 
>>> > <threeLevelAnnotTypes>
>>> > <type>gene</type>
>>> > <type>pseudogene</type>
>>> > <type>tRNA</type>
>>> > <type>snRNA</type>
>>> > <type>snoRNA</type>
>>> > <type>ncRNA</type>
>>> > <type>rRNA</type>
>>> > <type>miRNA</type>
>>> > </threeLevelAnnotTypes> 
>>> > 
>>> > </chadoInstance>
>>> > 
>>> > <chadoInstance id="riceInstance" default="true">
>>> > <inheritsInstance>referenceInstance</inheritsInstance>
>>> > <sequenceTypes>
>>> > <type>gene</type>
>>> > <type>
>>> > <name>chromosome</name>
>>> > <useStartAndEnd>true</useStartAndEnd>
>>> > <queryForValueList>true</queryForValueList>
>>> > <isTopLevel>true</isTopLevel>
>>> > </type>
>>> > </sequenceTypes>
>>> > 
>>> > 
>>> >
>>> <writebackXmlTemplateFile>transactionXMLTemplate_rice.xml</writebackX
>>> m
>>> lT
>>> emplateFile>
>>> > <featureCV>Sequence Ontology Feature Annotation</featureCV>
>>> > <relationshipCV>Relationship Ontology</relationshipCV>
>>> > <propertyTypeCV>autocreated</propertyTypeCV>
>>> > 
>>> > <genePredictionPrograms>
>>> > <program>FgenesH</program>
>>> > </genePredictionPrograms>
>>> > <searchHitPrograms>
>>> > <program>blat</program>
>>> > </searchHitPrograms> 
>>> > <searchHitsHaveFeatLocs>true</searchHitsHaveFeatLocs>
>>> > 
>>> > <clsName>apollo.dataadapter.chado.jdbc.RiceChadoInstance</clsName>
>>> > <oneLevelAnnotTypes>
>>> > <type>promoter</type>
>>> > <type>transposable_element</type>
>>> > <type>remark</type>
>>> > <type>repeat_region</type> 
>>> > </oneLevelAnnotTypes>
>>> > </chadoInstance>
>>> > 
>>> > <!-- Test chado database at rip.usca.nzcorp.net -->
>>> > <chadodb>
>>> > <name>Test chado database on rip</name>
>>> > 
>>> >
>><adapter>apollo.dataadapter.chado.jdbc.PostgresChadoAdapter</adapter>
>>> > <url>jdbc:postgresql://rip.usca.nzcorp.net:5432/chado</url>
>>> > <dbName>chado</dbName>
>>> > <dbUser>chado</dbUser>
>>> > <dbInstance>riceInstance</dbInstance>
>>> > <style>rice.style</style>
>>> > </chadodb>
>>> > </chado-adapter>
>>> > 
>>> > 
>>> > 
>>> > -------------------------------------------------------------------
>>> > -
>>> > --
>>> > --- 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=1
>>> > 2
>>> > 16
>>> > 42 _______________________________________________ Gmod-schema 
>>> > mailing
>>> 
>>> > list Gmo...@li... 
>>> > https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>> --
>>>
>>-----------------------------------------------------------------------
>>-
>>> Scott Cain, Ph. D.
>>cai...@gm...
>>> GMOD Coordinator (http://www.gmod.org/)
>>216-392-3087
>>> Cold Spring Harbor Laboratory
>>> 
>>--
>>-----------------------------------------------------------------------
>-
>>Scott Cain, Ph. D.
>cai...@gm...
>>GMOD Coordinator (http://www.gmod.org/)
>216-392-3087
>>Cold Spring Harbor Laboratory
>>
>>
>>-----------------------------------------------------------------------
>>-- 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=DEVD
>>EV _______________________________________________
>>Gmod-schema mailing list
>>Gmo...@li...
>>https://lists.sourceforge.net/lists/listinfo/gmod-schema
>

Hi, Pinglei,
Thanks for your reply and explanation.
I think the problem boils down to how a gene is represented as a
feature. As provided in the GFF3 specification, a single exon gene from
a prokaryotic organism can be represented as either
ChrX . gene XXXX YYYY . + . ID=3Dgene01;
ChrX . exon XXXX YYYY . + . Parent=3Dgene01
ChrX . CDS XXXX YYYY . + . Parent=3Dgene01
or
ChrX . gene XXXX YYYY . + . ID=3Dgene01;
ChrX . CDS XXXX YYYY . + . Parent=3Dgene01
It's really hard to say which is more correct. So my question is: Is
there any way to configure apollo so that it can also recognize the
"two-level" genes?
As for the problem with XORT. Here's the command I ran and the error
message I got:
[root@rip XML-XORT-0.003]# xort_dump.pl -d chado -p chado_test.xml -g
examples/dumpspec_apollo_no_evidence.xml -f no_local_id -s module
filename:/usr/local/gmod/conf/XORT/chado.properties
filename:/usr/local/gmod/conf/XORT/chado.properties
DBD::Pg::st execute failed: execute called with an unbound placeholder
at /usr/lib/perl5/site_perl/5.8.5/XML/XORT/Util/DbUtil/DB.pm line 137,
<IN> line 2476.
Unable to execute query: DBI::db=3DHASH(0x875ccd4)->errstr:select
substr(residues, 2ドル+1, 3ドル-2ドル) from feature where feature_id=3D1ドル
I checked chado.properties file but didn't find any problems there. As a
matter of fact, if I run 'xort_dump.pl -d chado', the script can spit
out some sort of XML but not chado XML. So it seems to me database
connection is not an issue here. I'm wondering if you know what else
could be wrong?
I'll apreciate your help.
Thanks,
Henry
=20
-----Original Message-----
From: Pinglei Zhou [mailto:zh...@mo...]=20
Sent: Thursday, September 28, 2006 6:38 AM
To: cai...@gm...; HXI (Henry Xiang)
Cc: gmo...@li...; ha...@mo...
Subject: Re: [Gmod-schema] Apollo-Chado Integration
Hi Scott, Henry,
>On thing that occurred to me in reading your email that isn't laid out=20
>anywhere is that Apollo is somewhat (ok, very) finicky about the=20
>structure of gene annotations. It expects there to be a gene feature=20
>with one or more child transcript features with one or more child exon=20
>features, which is why the yeast GFF file won't work with it. I've=20
>occasionally toyed with the idea of modifying the GFF loader to detect=20
>instances of gene structures that Apollo won't like and then fixing=20
>them on the fly, but it is a difficult thing to do right on many
levels.
Not sure if this can help. FlyBase have many other feature types without
the three-level structures (for instance, transposable_element). By edit
the configure file, we are able to load and view the data.
=20
>> the chado database, I've never been able to make a apollo-chado=20
>> "round-trip" via either XORT or jdbc connector. I tried =20
>> Saccharomyces
Can you say more about the XORT problem ? We FlyBase daily use the XORT
to round-trip the Apollo-chado, it works very well.=20
pinglei
>> cerevisiae sample database from SGD and a trivial two-entry database=20
>> like this:
>>=20
>> ##gff-version 3
>> SJ1904 NZCA chromosome 1 4345449 . + .
>> ID=3DSJ1904
>> SJ1904 NZCA gene 506 1846 . + .
>> ID=3DBLP00001
>> ###
>> ##FASTA
>> >SJ1904
>> cgaaagcctaatttcatttttcctcaattttagcttaaaagattttttt......
>> =20
>> Both of them worked for "one-way trip", but none of them worked for=20
>> "round-trip". I sent my questions to both gmod schema and Apollo=20
>> mailing lists a month ago, but so far I only got one reply (which is
>from you).
>>=20
>> I think what I need most right now is
>> a) someone who has the hands-on experience of gmod-apollo integration
>> and is willing to show me the rope, or
>> b) some working instance of gmod-apollo that I can "borrow" and=20
>> figure
>
>> out things by myself.
>>=20
>> I'm just wondering if any of those options is possible. I'll=20
>> appreciate your inputs/advice/direction/guidance. :-)
>>=20
>> Thanks,
>>=20
>> Henry
>> =20
>> -----Original Message-----
>> From: Scott Cain [mailto:cai...@gm...]
>> Sent: Thursday, September 21, 2006 10:33 AM
>> To: HXI (Henry Xiang)
>> Cc: gmo...@li...
>> Subject: Re: [Gmod-schema] Apollo-Chado Integration
>>=20
>> Hi Henry,
>>=20
>> I am back from England and very nearly awake today :-)
>>=20
>> So, some questions:
>>=20
>> What version of gmod/chado are you using? Did you get a reasonably
>> recent checkout from cvs?
>>=20
>> What version of Apollo are you using?
>>=20
>> I'm not exactly sure where the 'f.type_id =3D null' is coming from, =
but
>> I agree that it doesn't make much sense.
>>=20
>> Also, you can take a look at the updated doc I wrote on apollo and=20
>> chado at
>>=20
>> http://gmod.cvs.sourceforge.net/*checkout*/gmod/schema/chado/README.A
>> p
>> ol
>> lo.pod
>>=20
>> It is still a little skimpy on details, but it is getting better.
>>=20
>> Scott
>>=20
>>=20
>> On Wed, 2006年09月13日 at 10:10 -0700, HXI (Henry Xiang) wrote:
>> > Hi,
>> > =20
>> > Has someone successfully done Apollo-Chado integration so that=20
>> > Apollo can directly talk to Chado database via jdbc? I desperatelly
>> > need help
>>=20
>> > from Apollo/Chado gurus.
>> > =20
>> > I'm testing on a very simple Chado instance. When I searched for a=20
>> > gene with unique ID 'BLP00001', Apollo sent the following query
>> > =20
>> > SELECT f.feature_id FROM feature f WHERE (f.uniquename =3D=20
>> > 'BLP00001' OR f.name =3D 'BLP00001') AND f.type_id =3D null
>> > =20
>> > to chado database, and popped up an error message saying the gene=20
>> > can't be found.
>> > =20
>> > In fact, the feature 'BLP00001' has the cv term 'gene' associated=20
>> > with
>>=20
>> > it, and I verified it at the database level with the following SQL=20
>> > query
>> > =20
>> > chado=3D# select f.uniquename, t.name from feature f, cvterm t =
where=20
>> > f.type_id =3D t.cvterm_id and f.uniquename =3D 'BLP00001'; =
uniquename=20
>> > |
>
>> > name
>> > ------------+------
>> > BLP00001 | gene
>> > (1 row)
>> >=20
>> > Besides, column 'type_id' of table 'feature' has 'NOT NULL'
>> > constraint, so it doesn't make sense for Apollo to send query with=20
>> > type_id =3D null.
>> > =20
>> > I'm wondering if someone came across the same problem before. How=20
>> > should I configure Apollo data adapter so that it can find the=20
>> > correct
>>=20
>> > type_id for a feature?
>> > =20
>> > Any assistance/advice will be highly appreciated.
>> > =20
>> > Thanks a million!
>> > =20
>> > Henry
>> > =20
>> > PS: My chado-adapter.xml looks like this:
>> > =20
>> > <?xml version=3D"1.0" encoding=3D"UTF-8"?>
>> > <!-- This file is used to config chado database adapter -->=20
>> > <chado-adapter>
>> > <chadoInstance id=3D"referenceInstance" default=3D"true">
>> >=20
>> >
>> <writebackXmlTemplateFile>transactionXMLTemplate.xml</writebackXmlTem
>> p
>> la
>> teFile>
>> > <featureCV>sequence</featureCV>
>> > <polypeptideType>polypeptide</polypeptideType>
>> > <relationshipCV>relationship</relationshipCV>
>> > <propertyTypeCV>feature_property</propertyTypeCV>
>> > <!-- default is part_of -->
>> > <partOfCvTerm>part_of</partOfCvTerm>
>> > <transProtRelationTerm>derives_from</transProtRelationTerm>
>> > <searchHitsHaveFeatLocs>true</searchHitsHaveFeatLocs>
>> >=20
>> > <clsName>apollo.dataadapter.chado.jdbc.FlybaseChadoInstance</clsNam
>> > e
>> > >
>> > =20
>> > <oneLevelAnnotTypes>
>> > <type>promoter</type>
>> > <type>insertion site</type>
>> > <type>transposable_element</type>
>> > <type>transposable_element_insertion_site</type>
>> > <type>remark</type>
>> > <type>repeat_region</type>=20
>> > </oneLevelAnnotTypes>
>> > =20
>> > <threeLevelAnnotTypes>
>> > <type>gene</type>
>> > <type>pseudogene</type>
>> > <type>tRNA</type>
>> > <type>snRNA</type>
>> > <type>snoRNA</type>
>> > <type>ncRNA</type>
>> > <type>rRNA</type>
>> > <type>miRNA</type>
>> > </threeLevelAnnotTypes> =20
>> > =20
>> > </chadoInstance>
>> > =20
>> > <chadoInstance id=3D"riceInstance" default=3D"true">
>> > <inheritsInstance>referenceInstance</inheritsInstance>
>> > <sequenceTypes>
>> > <type>gene</type>
>> > <type>
>> > <name>chromosome</name>
>> > <useStartAndEnd>true</useStartAndEnd>
>> > <queryForValueList>true</queryForValueList>
>> > <isTopLevel>true</isTopLevel>
>> > </type>
>> > </sequenceTypes>
>> > =20
>> >=20
>> >
>> <writebackXmlTemplateFile>transactionXMLTemplate_rice.xml</writebackX
>> m
>> lT
>> emplateFile>
>> > <featureCV>Sequence Ontology Feature Annotation</featureCV>
>> > <relationshipCV>Relationship Ontology</relationshipCV>
>> > <propertyTypeCV>autocreated</propertyTypeCV>
>> > =20
>> > <genePredictionPrograms>
>> > <program>FgenesH</program>
>> > </genePredictionPrograms>
>> > <searchHitPrograms>
>> > <program>blat</program>
>> > </searchHitPrograms> =20
>> > <searchHitsHaveFeatLocs>true</searchHitsHaveFeatLocs>
>> >=20
>> > <clsName>apollo.dataadapter.chado.jdbc.RiceChadoInstance</clsName>
>> > <oneLevelAnnotTypes>
>> > <type>promoter</type>
>> > <type>transposable_element</type>
>> > <type>remark</type>
>> > <type>repeat_region</type>=20
>> > </oneLevelAnnotTypes>
>> > </chadoInstance>
>> > =20
>> > <!-- Test chado database at rip.usca.nzcorp.net -->
>> > <chadodb>
>> > <name>Test chado database on rip</name>
>> >=20
>> >
><adapter>apollo.dataadapter.chado.jdbc.PostgresChadoAdapter</adapter>
>> > <url>jdbc:postgresql://rip.usca.nzcorp.net:5432/chado</url>
>> > <dbName>chado</dbName>
>> > <dbUser>chado</dbUser>
>> > <dbInstance>riceInstance</dbInstance>
>> > <style>rice.style</style>
>> > </chadodb>
>> > </chado-adapter>
>> > =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=20
>> > job
>>=20
>> > easier Download IBM WebSphere Application Server v.1.0.1 based on=20
>> > Apache Geronimo
>> > =
http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D120709&bid=3D263057&dat=3D=
1
>> > 2
>> > 16
>> > 42 _______________________________________________ Gmod-schema=20
>> > mailing
>>=20
>> > list Gmo...@li...=20
>> > https://lists.sourceforge.net/lists/listinfo/gmod-schema
>> --
>>
>-----------------------------------------------------------------------
>-
>> Scott Cain, Ph. D.
>cai...@gm...
>> GMOD Coordinator (http://www.gmod.org/)
>216-392-3087
>> Cold Spring Harbor Laboratory
>>=20
>--
>-----------------------------------------------------------------------
-
>Scott Cain, Ph. D.
cai...@gm...
>GMOD Coordinator (http://www.gmod.org/)
216-392-3087
>Cold Spring Harbor Laboratory
>
>
>-----------------------------------------------------------------------
>-- Take Surveys. Earn Cash. Influence the Future of IT Join=20
>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=3Djoin.php&p=3Dsourceforge&CID=3D=
DEVD
>EV _______________________________________________
>Gmod-schema mailing list
>Gmo...@li...
>https://lists.sourceforge.net/lists/listinfo/gmod-schema

Hi Eric,
 
 
>The architecture working group is planning on a similar API bake off at the 
>next GMOD meeting. We are working on the details. Please sign up for the 
>gmod-architecture mailing list if you have not already, since that's where 
>most of this will be discussed. I will definitely be contacting you in the 
>future about this, thanks for volunteering!
I did sign up for the gomd-architecture. Lincoln brought up this topic again to 
emphasize the importance. We all like to see some progress in the near future.
pinglei
>At 08:58 AM 9/28/2006, Pinglei Zhou wrote:
>>Hi Scott,
>>
>> >I am in the process of planning the next GMOD meeting to take place in
>> >San Diego in January in conjunction with the Plant and Animal Genome
>> >meeting.
>>
>> >One of the activities I would like to consider for the GMOD meeting is a
>> >user interface 'bake off', where there would be a set of activities,
>> >like finding a list of genes expressed in a tissue of interest, and then
>> >a representative of each MOD would show how each task would be done via
>> >her MOD's UI. So, what I am looking for is this: a small list of
>> >suggested tasks that users typically need to do.
>>
>>I am working here to get some canned queries from our FlyBase uerss, will 
>>send
>>to you once done.
>>
>>Another important item Lincoln mentioned during our FlyBase project 
>>meeting is
>>the API. Since people already start to divert the Chado implementation, GMOD
>>should take the lead to work on the API, so those groups implement 
>>differently
>>from 'golden-standard' have responsible to provide their adaptor (so 
>>DISCOURAGE
>>different implementation) to public. I am willing to take the lead for 
>>FlyBase
>>API.
>>
>>
>>pinglei
>>
>>
>>
>>-------------------------------------------------------------------------
>>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
>
>============================================
>
>Eric Just
>e-...@no...
>dictyBase Programmer
>Center for Genetic Medicine
>Northwestern University
>http://dictybase.org
>
>============================================ 
>

Hi Pinglei,
The architecture working group is planning on a similar API bake off at the 
next GMOD meeting. We are working on the details. Please sign up for the 
gmod-architecture mailing list if you have not already, since that's where 
most of this will be discussed. I will definitely be contacting you in the 
future about this, thanks for volunteering!
Eric
At 08:58 AM 9/28/2006, Pinglei Zhou wrote:
>Hi Scott,
>
> >I am in the process of planning the next GMOD meeting to take place in
> >San Diego in January in conjunction with the Plant and Animal Genome
> >meeting.
>
> >One of the activities I would like to consider for the GMOD meeting is a
> >user interface 'bake off', where there would be a set of activities,
> >like finding a list of genes expressed in a tissue of interest, and then
> >a representative of each MOD would show how each task would be done via
> >her MOD's UI. So, what I am looking for is this: a small list of
> >suggested tasks that users typically need to do.
>
>I am working here to get some canned queries from our FlyBase uerss, will 
>send
>to you once done.
>
>Another important item Lincoln mentioned during our FlyBase project 
>meeting is
>the API. Since people already start to divert the Chado implementation, GMOD
>should take the lead to work on the API, so those groups implement 
>differently
>from 'golden-standard' have responsible to provide their adaptor (so 
>DISCOURAGE
>different implementation) to public. I am willing to take the lead for 
>FlyBase
>API.
>
>
>pinglei
>
>
>
>-------------------------------------------------------------------------
>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
============================================
Eric Just
e-...@no...
dictyBase Programmer
Center for Genetic Medicine
Northwestern University
http://dictybase.org
============================================ 

Hi Scott,
>I am in the process of planning the next GMOD meeting to take place in
>San Diego in January in conjunction with the Plant and Animal Genome
>meeting.
>One of the activities I would like to consider for the GMOD meeting is a
>user interface 'bake off', where there would be a set of activities,
>like finding a list of genes expressed in a tissue of interest, and then
>a representative of each MOD would show how each task would be done via
>her MOD's UI. So, what I am looking for is this: a small list of
>suggested tasks that users typically need to do.
I am working here to get some canned queries from our FlyBase uerss, will send 
to you once done.
Another important item Lincoln mentioned during our FlyBase project meeting is 
the API. Since people already start to divert the Chado implementation, GMOD 
should take the lead to work on the API, so those groups implement differently 
from 'golden-standard' have responsible to provide their adaptor (so DISCOURAGE 
different implementation) to public. I am willing to take the lead for FlyBase 
API.
pinglei

Hi Scott, Henry,
>On thing that occurred to me in reading your email that isn't laid out
>anywhere is that Apollo is somewhat (ok, very) finicky about the
>structure of gene annotations. It expects there to be a gene feature
>with one or more child transcript features with one or more child exon
>features, which is why the yeast GFF file won't work with it. I've
>occasionally toyed with the idea of modifying the GFF loader to detect
>instances of gene structures that Apollo won't like and then fixing them
>on the fly, but it is a difficult thing to do right on many levels.
Not sure if this can help. FlyBase have many other feature types without the three-level structures (for instance, 
transposable_element). By edit the configure file, we are able to load and view the data.
 
>> the chado database, I've never been able to make a apollo-chado 
>> "round-trip" via either XORT or jdbc connector. I tried Saccharomyces
Can you say more about the XORT problem ? We FlyBase daily use the XORT to round-trip the Apollo-chado, it works very well. 
pinglei
>> cerevisiae sample database from SGD and a trivial two-entry database 
>> like this:
>> 
>> ##gff-version 3
>> SJ1904 NZCA chromosome 1 4345449 . + .
>> ID=SJ1904
>> SJ1904 NZCA gene 506 1846 . + .
>> ID=BLP00001
>> ###
>> ##FASTA
>> >SJ1904
>> cgaaagcctaatttcatttttcctcaattttagcttaaaagattttttt......
>> 
>> Both of them worked for "one-way trip", but none of them worked for 
>> "round-trip". I sent my questions to both gmod schema and Apollo 
>> mailing lists a month ago, but so far I only got one reply (which is
>from you).
>> 
>> I think what I need most right now is
>> a) someone who has the hands-on experience of gmod-apollo integration 
>> and is willing to show me the rope, or
>> b) some working instance of gmod-apollo that I can "borrow" and figure
>
>> out things by myself.
>> 
>> I'm just wondering if any of those options is possible. I'll 
>> appreciate your inputs/advice/direction/guidance. :-)
>> 
>> Thanks,
>> 
>> Henry
>> 
>> -----Original Message-----
>> From: Scott Cain [mailto:cai...@gm...]
>> Sent: Thursday, September 21, 2006 10:33 AM
>> To: HXI (Henry Xiang)
>> Cc: gmo...@li...
>> Subject: Re: [Gmod-schema] Apollo-Chado Integration
>> 
>> Hi Henry,
>> 
>> I am back from England and very nearly awake today :-)
>> 
>> So, some questions:
>> 
>> What version of gmod/chado are you using? Did you get a reasonably 
>> recent checkout from cvs?
>> 
>> What version of Apollo are you using?
>> 
>> I'm not exactly sure where the 'f.type_id = null' is coming from, but 
>> I agree that it doesn't make much sense.
>> 
>> Also, you can take a look at the updated doc I wrote on apollo and 
>> chado at
>> 
>> http://gmod.cvs.sourceforge.net/*checkout*/gmod/schema/chado/README.Ap
>> ol
>> lo.pod
>> 
>> It is still a little skimpy on details, but it is getting better.
>> 
>> Scott
>> 
>> 
>> On Wed, 2006年09月13日 at 10:10 -0700, HXI (Henry Xiang) wrote:
>> > Hi,
>> > 
>> > Has someone successfully done Apollo-Chado integration so that 
>> > Apollo can directly talk to Chado database via jdbc? I desperatelly 
>> > need help
>> 
>> > from Apollo/Chado gurus.
>> > 
>> > I'm testing on a very simple Chado instance. When I searched for a 
>> > gene with unique ID 'BLP00001', Apollo sent the following query
>> > 
>> > SELECT f.feature_id FROM feature f WHERE (f.uniquename = 
>> > 'BLP00001' OR f.name = 'BLP00001') AND f.type_id = null
>> > 
>> > to chado database, and popped up an error message saying the gene 
>> > can't be found.
>> > 
>> > In fact, the feature 'BLP00001' has the cv term 'gene' associated 
>> > with
>> 
>> > it, and I verified it at the database level with the following SQL 
>> > query
>> > 
>> > chado=# select f.uniquename, t.name from feature f, cvterm t where 
>> > f.type_id = t.cvterm_id and f.uniquename = 'BLP00001'; uniquename |
>
>> > name
>> > ------------+------
>> > BLP00001 | gene
>> > (1 row)
>> > 
>> > Besides, column 'type_id' of table 'feature' has 'NOT NULL'
>> > constraint, so it doesn't make sense for Apollo to send query with 
>> > type_id = null.
>> > 
>> > I'm wondering if someone came across the same problem before. How 
>> > should I configure Apollo data adapter so that it can find the 
>> > correct
>> 
>> > type_id for a feature?
>> > 
>> > Any assistance/advice will be highly appreciated.
>> > 
>> > Thanks a million!
>> > 
>> > Henry
>> > 
>> > PS: My chado-adapter.xml looks like this:
>> > 
>> > <?xml version="1.0" encoding="UTF-8"?>
>> > <!-- This file is used to config chado database adapter --> 
>> > <chado-adapter>
>> > <chadoInstance id="referenceInstance" default="true">
>> > 
>> >
>> <writebackXmlTemplateFile>transactionXMLTemplate.xml</writebackXmlTemp
>> la
>> teFile>
>> > <featureCV>sequence</featureCV>
>> > <polypeptideType>polypeptide</polypeptideType>
>> > <relationshipCV>relationship</relationshipCV>
>> > <propertyTypeCV>feature_property</propertyTypeCV>
>> > <!-- default is part_of -->
>> > <partOfCvTerm>part_of</partOfCvTerm>
>> > <transProtRelationTerm>derives_from</transProtRelationTerm>
>> > <searchHitsHaveFeatLocs>true</searchHitsHaveFeatLocs>
>> > 
>> > <clsName>apollo.dataadapter.chado.jdbc.FlybaseChadoInstance</clsName
>> > >
>> > 
>> > <oneLevelAnnotTypes>
>> > <type>promoter</type>
>> > <type>insertion site</type>
>> > <type>transposable_element</type>
>> > <type>transposable_element_insertion_site</type>
>> > <type>remark</type>
>> > <type>repeat_region</type> 
>> > </oneLevelAnnotTypes>
>> > 
>> > <threeLevelAnnotTypes>
>> > <type>gene</type>
>> > <type>pseudogene</type>
>> > <type>tRNA</type>
>> > <type>snRNA</type>
>> > <type>snoRNA</type>
>> > <type>ncRNA</type>
>> > <type>rRNA</type>
>> > <type>miRNA</type>
>> > </threeLevelAnnotTypes> 
>> > 
>> > </chadoInstance>
>> > 
>> > <chadoInstance id="riceInstance" default="true">
>> > <inheritsInstance>referenceInstance</inheritsInstance>
>> > <sequenceTypes>
>> > <type>gene</type>
>> > <type>
>> > <name>chromosome</name>
>> > <useStartAndEnd>true</useStartAndEnd>
>> > <queryForValueList>true</queryForValueList>
>> > <isTopLevel>true</isTopLevel>
>> > </type>
>> > </sequenceTypes>
>> > 
>> > 
>> >
>> <writebackXmlTemplateFile>transactionXMLTemplate_rice.xml</writebackXm
>> lT
>> emplateFile>
>> > <featureCV>Sequence Ontology Feature Annotation</featureCV>
>> > <relationshipCV>Relationship Ontology</relationshipCV>
>> > <propertyTypeCV>autocreated</propertyTypeCV>
>> > 
>> > <genePredictionPrograms>
>> > <program>FgenesH</program>
>> > </genePredictionPrograms>
>> > <searchHitPrograms>
>> > <program>blat</program>
>> > </searchHitPrograms> 
>> > <searchHitsHaveFeatLocs>true</searchHitsHaveFeatLocs>
>> > 
>> > <clsName>apollo.dataadapter.chado.jdbc.RiceChadoInstance</clsName>
>> > <oneLevelAnnotTypes>
>> > <type>promoter</type>
>> > <type>transposable_element</type>
>> > <type>remark</type>
>> > <type>repeat_region</type> 
>> > </oneLevelAnnotTypes>
>> > </chadoInstance>
>> > 
>> > <!-- Test chado database at rip.usca.nzcorp.net -->
>> > <chadodb>
>> > <name>Test chado database on rip</name>
>> > 
>> >
><adapter>apollo.dataadapter.chado.jdbc.PostgresChadoAdapter</adapter>
>> > <url>jdbc:postgresql://rip.usca.nzcorp.net:5432/chado</url>
>> > <dbName>chado</dbName>
>> > <dbUser>chado</dbUser>
>> > <dbInstance>riceInstance</dbInstance>
>> > <style>rice.style</style>
>> > </chadodb>
>> > </chado-adapter>
>> > 
>> > 
>> > 
>> > --------------------------------------------------------------------
>> > --
>> > --- 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=12
>> > 16
>> > 42 _______________________________________________ Gmod-schema 
>> > mailing
>> 
>> > list Gmo...@li... 
>> > https://lists.sourceforge.net/lists/listinfo/gmod-schema
>> --
>>
>------------------------------------------------------------------------
>> Scott Cain, Ph. D.
>cai...@gm...
>> GMOD Coordinator (http://www.gmod.org/)
>216-392-3087
>> Cold Spring Harbor Laboratory
>> 
>--
>------------------------------------------------------------------------
>Scott Cain, Ph. D. cai...@gm...
>GMOD Coordinator (http://www.gmod.org/) 216-392-3087
>Cold Spring Harbor Laboratory
>
>
>-------------------------------------------------------------------------
>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

Hello,
I am in the process of planning the next GMOD meeting to take place in
San Diego in January in conjunction with the Plant and Animal Genome
meeting.
One of the activities I would like to consider for the GMOD meeting is a
user interface 'bake off', where there would be a set of activities,
like finding a list of genes expressed in a tissue of interest, and then
a representative of each MOD would show how each task would be done via
her MOD's UI. So, what I am looking for is this: a small list of
suggested tasks that users typically need to do.
Thanks much,
Scott
--=20
------------------------------------------------------------------------
Scott Cain, Ph. D. ca...@cs...
GMOD Coordinator (http://www.gmod.org/) 216-392-3087
Cold Spring Harbor Laboratory

Hi, Scott,
Thanks for your effort to put things together. I'll expect to see your
sample GFF and find out how to satisfy the finickiness of Apollo. :-)
Henry
-----Original Message-----
From: Scott Cain [mailto:cai...@gm...]=20
Sent: Monday, September 25, 2006 9:54 AM
To: HXI (Henry Xiang)
Cc: gmod schema
Subject: RE: [Gmod-schema] Apollo-Chado Integration
Hi Henry,
I cc'ed this back to the schema mailing list so my answer can be
archived...
Some sample GFF that I load and subsequently can edit with Apollo is a
very good idea. I'll see if I can work something up today. A dump of a
chado database would also be a good idea, so I'll try to do that too.
On thing that occurred to me in reading your email that isn't laid out
anywhere is that Apollo is somewhat (ok, very) finicky about the
structure of gene annotations. It expects there to be a gene feature
with one or more child transcript features with one or more child exon
features, which is why the yeast GFF file won't work with it. I've
occasionally toyed with the idea of modifying the GFF loader to detect
instances of gene structures that Apollo won't like and then fixing them
on the fly, but it is a difficult thing to do right on many levels.
Scott
On Mon, 2006年09月25日 at 09:42 -0700, HXI (Henry Xiang) wrote:
> Hi, Scott,
>=20
> Thank you so much for the reply. I hope you're getting better with=20
> your jetlag.
>=20
> To answer your questions: I'm using the newest version of gmod/chado=20
> checked out from cvs just two weeks ago, and I'm using Apollo 1.6.5,=20
> which I think is also the newest version.
>=20
> To be perfectly honest, I read ALL of the human readable docs in the=20
> source tree. However, it seems that I'm still missing something=20
> somewhere. :-) As a matter of fact, although I'm successful in loading
> the chado database, I've never been able to make a apollo-chado=20
> "round-trip" via either XORT or jdbc connector. I tried Saccharomyces
> cerevisiae sample database from SGD and a trivial two-entry database=20
> like this:
>=20
> ##gff-version 3
> SJ1904 NZCA chromosome 1 4345449 . + .
> ID=3DSJ1904
> SJ1904 NZCA gene 506 1846 . + .
> ID=3DBLP00001
> ###
> ##FASTA
> >SJ1904
> cgaaagcctaatttcatttttcctcaattttagcttaaaagattttttt......
> =20
> Both of them worked for "one-way trip", but none of them worked for=20
> "round-trip". I sent my questions to both gmod schema and Apollo=20
> mailing lists a month ago, but so far I only got one reply (which is
from you).
>=20
> I think what I need most right now is
> a) someone who has the hands-on experience of gmod-apollo integration=20
> and is willing to show me the rope, or
> b) some working instance of gmod-apollo that I can "borrow" and figure
> out things by myself.
>=20
> I'm just wondering if any of those options is possible. I'll=20
> appreciate your inputs/advice/direction/guidance. :-)
>=20
> Thanks,
>=20
> Henry
> =20
> -----Original Message-----
> From: Scott Cain [mailto:cai...@gm...]
> Sent: Thursday, September 21, 2006 10:33 AM
> To: HXI (Henry Xiang)
> Cc: gmo...@li...
> Subject: Re: [Gmod-schema] Apollo-Chado Integration
>=20
> Hi Henry,
>=20
> I am back from England and very nearly awake today :-)
>=20
> So, some questions:
>=20
> What version of gmod/chado are you using? Did you get a reasonably=20
> recent checkout from cvs?
>=20
> What version of Apollo are you using?
>=20
> I'm not exactly sure where the 'f.type_id =3D null' is coming from, =
but=20
> I agree that it doesn't make much sense.
>=20
> Also, you can take a look at the updated doc I wrote on apollo and=20
> chado at
>=20
> http://gmod.cvs.sourceforge.net/*checkout*/gmod/schema/chado/README.Ap
> ol
> lo.pod
>=20
> It is still a little skimpy on details, but it is getting better.
>=20
> Scott
>=20
>=20
> On Wed, 2006年09月13日 at 10:10 -0700, HXI (Henry Xiang) wrote:
> > Hi,
> > =20
> > Has someone successfully done Apollo-Chado integration so that=20
> > Apollo can directly talk to Chado database via jdbc? I desperatelly=20
> > need help
>=20
> > from Apollo/Chado gurus.
> > =20
> > I'm testing on a very simple Chado instance. When I searched for a=20
> > gene with unique ID 'BLP00001', Apollo sent the following query
> > =20
> > SELECT f.feature_id FROM feature f WHERE (f.uniquename =3D=20
> > 'BLP00001' OR f.name =3D 'BLP00001') AND f.type_id =3D null
> > =20
> > to chado database, and popped up an error message saying the gene=20
> > can't be found.
> > =20
> > In fact, the feature 'BLP00001' has the cv term 'gene' associated=20
> > with
>=20
> > it, and I verified it at the database level with the following SQL=20
> > query
> > =20
> > chado=3D# select f.uniquename, t.name from feature f, cvterm t where =
> > f.type_id =3D t.cvterm_id and f.uniquename =3D 'BLP00001'; =
uniquename |
> > name
> > ------------+------
> > BLP00001 | gene
> > (1 row)
> >=20
> > Besides, column 'type_id' of table 'feature' has 'NOT NULL'
> > constraint, so it doesn't make sense for Apollo to send query with=20
> > type_id =3D null.
> > =20
> > I'm wondering if someone came across the same problem before. How=20
> > should I configure Apollo data adapter so that it can find the=20
> > correct
>=20
> > type_id for a feature?
> > =20
> > Any assistance/advice will be highly appreciated.
> > =20
> > Thanks a million!
> > =20
> > Henry
> > =20
> > PS: My chado-adapter.xml looks like this:
> > =20
> > <?xml version=3D"1.0" encoding=3D"UTF-8"?>
> > <!-- This file is used to config chado database adapter -->=20
> > <chado-adapter>
> > <chadoInstance id=3D"referenceInstance" default=3D"true">
> >=20
> >
> <writebackXmlTemplateFile>transactionXMLTemplate.xml</writebackXmlTemp
> la
> teFile>
> > <featureCV>sequence</featureCV>
> > <polypeptideType>polypeptide</polypeptideType>
> > <relationshipCV>relationship</relationshipCV>
> > <propertyTypeCV>feature_property</propertyTypeCV>
> > <!-- default is part_of -->
> > <partOfCvTerm>part_of</partOfCvTerm>
> > <transProtRelationTerm>derives_from</transProtRelationTerm>
> > <searchHitsHaveFeatLocs>true</searchHitsHaveFeatLocs>
> >=20
> > <clsName>apollo.dataadapter.chado.jdbc.FlybaseChadoInstance</clsName
> > >
> > =20
> > <oneLevelAnnotTypes>
> > <type>promoter</type>
> > <type>insertion site</type>
> > <type>transposable_element</type>
> > <type>transposable_element_insertion_site</type>
> > <type>remark</type>
> > <type>repeat_region</type>=20
> > </oneLevelAnnotTypes>
> > =20
> > <threeLevelAnnotTypes>
> > <type>gene</type>
> > <type>pseudogene</type>
> > <type>tRNA</type>
> > <type>snRNA</type>
> > <type>snoRNA</type>
> > <type>ncRNA</type>
> > <type>rRNA</type>
> > <type>miRNA</type>
> > </threeLevelAnnotTypes> =20
> > =20
> > </chadoInstance>
> > =20
> > <chadoInstance id=3D"riceInstance" default=3D"true">
> > <inheritsInstance>referenceInstance</inheritsInstance>
> > <sequenceTypes>
> > <type>gene</type>
> > <type>
> > <name>chromosome</name>
> > <useStartAndEnd>true</useStartAndEnd>
> > <queryForValueList>true</queryForValueList>
> > <isTopLevel>true</isTopLevel>
> > </type>
> > </sequenceTypes>
> > =20
> >=20
> >
> <writebackXmlTemplateFile>transactionXMLTemplate_rice.xml</writebackXm
> lT
> emplateFile>
> > <featureCV>Sequence Ontology Feature Annotation</featureCV>
> > <relationshipCV>Relationship Ontology</relationshipCV>
> > <propertyTypeCV>autocreated</propertyTypeCV>
> > =20
> > <genePredictionPrograms>
> > <program>FgenesH</program>
> > </genePredictionPrograms>
> > <searchHitPrograms>
> > <program>blat</program>
> > </searchHitPrograms> =20
> > <searchHitsHaveFeatLocs>true</searchHitsHaveFeatLocs>
> >=20
> > <clsName>apollo.dataadapter.chado.jdbc.RiceChadoInstance</clsName>
> > <oneLevelAnnotTypes>
> > <type>promoter</type>
> > <type>transposable_element</type>
> > <type>remark</type>
> > <type>repeat_region</type>=20
> > </oneLevelAnnotTypes>
> > </chadoInstance>
> > =20
> > <!-- Test chado database at rip.usca.nzcorp.net -->
> > <chadodb>
> > <name>Test chado database on rip</name>
> >=20
> >
<adapter>apollo.dataadapter.chado.jdbc.PostgresChadoAdapter</adapter>
> > <url>jdbc:postgresql://rip.usca.nzcorp.net:5432/chado</url>
> > <dbName>chado</dbName>
> > <dbUser>chado</dbUser>
> > <dbInstance>riceInstance</dbInstance>
> > <style>rice.style</style>
> > </chadodb>
> > </chado-adapter>
> > =20
> >=20
> >=20
> > --------------------------------------------------------------------
> > --
> > --- Using Tomcat but need to do more? Need to support web services,=20
> > security?
> > Get stuff done quickly with pre-integrated technology to make your=20
> > job
>=20
> > easier Download IBM WebSphere Application Server v.1.0.1 based on=20
> > Apache Geronimo
> > =
http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D120709&bid=3D263057&dat=3D=
12
> > 16
> > 42 _______________________________________________ Gmod-schema=20
> > mailing
>=20
> > list Gmo...@li...=20
> > https://lists.sourceforge.net/lists/listinfo/gmod-schema
> --
>
------------------------------------------------------------------------
> Scott Cain, Ph. D.
cai...@gm...
> GMOD Coordinator (http://www.gmod.org/)
216-392-3087
> Cold Spring Harbor Laboratory
>=20
--
------------------------------------------------------------------------
Scott Cain, Ph. D. cai...@gm...
GMOD Coordinator (http://www.gmod.org/) 216-392-3087
Cold Spring Harbor Laboratory

Henry - Im so sorry for not replying - I thought I had but clearly I havent (my
email server has been shaky - i think my reply got lost - who knows)
HXI (Henry Xiang) wrote:
> Hi,
> 
> Has someone successfully done Apollo-Chado integration so that Apollo
> can directly talk to Chado database via jdbc? I desperatelly need help
> from Apollo/Chado gurus.
> 
You should set
DEBUG "true'
in apollo.cfg (in conf or ~/.apollo) - this will cause all (or most at least)
your sql to print to stdout - very helpful for debugging.
> I'm testing on a very simple Chado instance. When I searched for a gene
> with unique ID 'BLP00001', Apollo sent the following query
> 
> SELECT f.feature_id FROM feature f WHERE (f.uniquename = 'BLP00001'
> OR f.name = 'BLP00001') AND f.type_id = null
so its not finding "gene" in cvterm.
> 
> to chado database, and popped up an error message saying the gene can't
> be found.
> 
> In fact, the feature 'BLP00001' has the cv term 'gene' associated with
> it, and I verified it at the database level with the following SQL query
> 
> chado=# select f.uniquename, t.name from feature f, cvterm t where
> f.type_id = t.cvterm_id and f.uniquename = 'BLP00001';
> uniquename | name
> ------------+------
> BLP00001 | gene
> (1 row)
I think the problem is in how the ontology name is configured.
> Besides, column 'type_id' of table 'feature' has 'NOT NULL' constraint,
> so it doesn't make sense for Apollo to send query with type_id = null.
thats true - should be better error checking/message here.
> 
> I'm wondering if someone came across the same problem before. How should
> I configure Apollo data adapter so that it can find the correct type_id
> for a feature?
> 
> Any assistance/advice will be highly appreciated.
> 
> Thanks a million!
> 
> Henry
> 
> PS: My chado-adapter.xml looks like this:
> 
> <?xml version="1.0" encoding="UTF-8"?>
> <!-- This file is used to config chado database adapter -->
> <chado-adapter>
> <chadoInstance id="referenceInstance" default="true">
> 
> <writebackXmlTemplateFile>transactionXMLTemplate.xml</writebackXmlTemplateFile>
> <featureCV>sequence</featureCV>
this is overidden below
> <polypeptideType>polypeptide</polypeptideType>
> <relationshipCV>relationship</relationshipCV>
> <propertyTypeCV>feature_property</propertyTypeCV>
> <!-- default is part_of -->
> <partOfCvTerm>part_of</partOfCvTerm>
> <transProtRelationTerm>derives_from</transProtRelationTerm>
> <searchHitsHaveFeatLocs>true</searchHitsHaveFeatLocs>
> <clsName>apollo.dataadapter.chado.jdbc.FlybaseChadoInstance</clsName>
> 
> <oneLevelAnnotTypes>
> <type>promoter</type>
> <type>insertion site</type>
> <type>transposable_element</type>
> <type>transposable_element_insertion_site</type>
> <type>remark</type>
> <type>repeat_region</type> 
> </oneLevelAnnotTypes>
> 
> <threeLevelAnnotTypes>
> <type>gene</type>
> <type>pseudogene</type>
> <type>tRNA</type>
> <type>snRNA</type>
> <type>snoRNA</type>
> <type>ncRNA</type>
> <type>rRNA</type>
> <type>miRNA</type>
> </threeLevelAnnotTypes> 
> 
> </chadoInstance>
> 
> <chadoInstance id="riceInstance" default="true">
> <inheritsInstance>referenceInstance</inheritsInstance>
> <sequenceTypes>
> <type>gene</type>
> <type>
> <name>chromosome</name>
> <useStartAndEnd>true</useStartAndEnd>
> <queryForValueList>true</queryForValueList>
> <isTopLevel>true</isTopLevel>
> </type>
> </sequenceTypes>
> 
> 
> <writebackXmlTemplateFile>transactionXMLTemplate_rice.xml</writebackXmlTemplateFile>
> <featureCV>Sequence Ontology Feature Annotation</featureCV>
I think this is the crucial bit here. This is where you configure what the name
of the ontology is that feature cv terms will come from. Do you have an ontology
named "Sequence Ontology Feature Annotation" in cv? Does that ontology contain
the cvterm "gene"? In your query above what ontology does the cvterm gene came
from - it could come from a very related ontology called SO or sequence - the
heavier sofa basically
> <relationshipCV>Relationship Ontology</relationshipCV>
> <propertyTypeCV>autocreated</propertyTypeCV>
> 
> <genePredictionPrograms>
> <program>FgenesH</program>
> </genePredictionPrograms>
> <searchHitPrograms>
> <program>blat</program>
> </searchHitPrograms> 
> <searchHitsHaveFeatLocs>true</searchHitsHaveFeatLocs>
> <clsName>apollo.dataadapter.chado.jdbc.RiceChadoInstance</clsName>
> <oneLevelAnnotTypes>
> <type>promoter</type>
> <type>transposable_element</type>
> <type>remark</type>
> <type>repeat_region</type> 
> </oneLevelAnnotTypes>
> </chadoInstance> 
> 
> <!-- Test chado database at rip.usca.nzcorp.net -->
> <chadodb>
> <name>Test chado database on rip</name>
> <adapter>apollo.dataadapter.chado.jdbc.PostgresChadoAdapter</adapter>
> <url>jdbc:postgresql://rip.usca.nzcorp.net:5432/chado</url>
> <dbName>chado</dbName>
> <dbUser>chado</dbUser>
> <dbInstance>riceInstance</dbInstance>
> <style>rice.style</style>
> </chadodb>
> </chado-adapter>
> 
> 
> 
> ------------------------------------------------------------------------
> 
> -------------------------------------------------------------------------
> 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

Hi Henry,
I cc'ed this back to the schema mailing list so my answer can be
archived...
Some sample GFF that I load and subsequently can edit with Apollo is a
very good idea. I'll see if I can work something up today. A dump of a
chado database would also be a good idea, so I'll try to do that too.
On thing that occurred to me in reading your email that isn't laid out
anywhere is that Apollo is somewhat (ok, very) finicky about the
structure of gene annotations. It expects there to be a gene feature
with one or more child transcript features with one or more child exon
features, which is why the yeast GFF file won't work with it. I've
occasionally toyed with the idea of modifying the GFF loader to detect
instances of gene structures that Apollo won't like and then fixing them
on the fly, but it is a difficult thing to do right on many levels.
Scott
On Mon, 2006年09月25日 at 09:42 -0700, HXI (Henry Xiang) wrote:
> Hi, Scott,
>=20
> Thank you so much for the reply. I hope you're getting better with your
> jetlag.=20
>=20
> To answer your questions: I'm using the newest version of gmod/chado
> checked out from cvs just two weeks ago, and I'm using Apollo 1.6.5,
> which I think is also the newest version.
>=20
> To be perfectly honest, I read ALL of the human readable docs in the
> source tree. However, it seems that I'm still missing something
> somewhere. :-) As a matter of fact, although I'm successful in loading
> the chado database, I've never been able to make a apollo-chado
> "round-trip" via either XORT or jdbc connector. I tried Saccharomyces
> cerevisiae sample database from SGD and a trivial two-entry database
> like this:
>=20
> ##gff-version 3
> SJ1904 NZCA chromosome 1 4345449 . + .
> ID=3DSJ1904
> SJ1904 NZCA gene 506 1846 . + .
> ID=3DBLP00001
> ###
> ##FASTA
> >SJ1904
> cgaaagcctaatttcatttttcctcaattttagcttaaaagattttttt......
> =20
> Both of them worked for "one-way trip", but none of them worked for
> "round-trip". I sent my questions to both gmod schema and Apollo mailing
> lists a month ago, but so far I only got one reply (which is from you).=20
>=20
> I think what I need most right now is=20
> a) someone who has the hands-on experience of gmod-apollo integration
> and is willing to show me the rope, or
> b) some working instance of gmod-apollo that I can "borrow" and figure
> out things by myself.
>=20
> I'm just wondering if any of those options is possible. I'll appreciate
> your inputs/advice/direction/guidance. :-)
>=20
> Thanks,
>=20
> Henry
> =20
> -----Original Message-----
> From: Scott Cain [mailto:cai...@gm...]=20
> Sent: Thursday, September 21, 2006 10:33 AM
> To: HXI (Henry Xiang)
> Cc: gmo...@li...
> Subject: Re: [Gmod-schema] Apollo-Chado Integration
>=20
> Hi Henry,
>=20
> I am back from England and very nearly awake today :-)
>=20
> So, some questions:
>=20
> What version of gmod/chado are you using? Did you get a reasonably
> recent checkout from cvs?
>=20
> What version of Apollo are you using?
>=20
> I'm not exactly sure where the 'f.type_id =3D null' is coming from, but I
> agree that it doesn't make much sense.
>=20
> Also, you can take a look at the updated doc I wrote on apollo and chado
> at =20
>=20
> http://gmod.cvs.sourceforge.net/*checkout*/gmod/schema/chado/README.Apol
> lo.pod
>=20
> It is still a little skimpy on details, but it is getting better.
>=20
> Scott
>=20
>=20
> On Wed, 2006年09月13日 at 10:10 -0700, HXI (Henry Xiang) wrote:
> > Hi,
> > =20
> > Has someone successfully done Apollo-Chado integration so that Apollo=20
> > can directly talk to Chado database via jdbc? I desperatelly need help
>=20
> > from Apollo/Chado gurus.
> > =20
> > I'm testing on a very simple Chado instance. When I searched for a=20
> > gene with unique ID 'BLP00001', Apollo sent the following query
> > =20
> > SELECT f.feature_id FROM feature f WHERE (f.uniquename =3D=20
> > 'BLP00001' OR f.name =3D 'BLP00001') AND f.type_id =3D null
> > =20
> > to chado database, and popped up an error message saying the gene=20
> > can't be found.
> > =20
> > In fact, the feature 'BLP00001' has the cv term 'gene' associated with
>=20
> > it, and I verified it at the database level with the following SQL=20
> > query
> > =20
> > chado=3D# select f.uniquename, t.name from feature f, cvterm t where=20
> > f.type_id =3D t.cvterm_id and f.uniquename =3D 'BLP00001'; uniquename =
|=20
> > name
> > ------------+------
> > BLP00001 | gene
> > (1 row)
> >=20
> > Besides, column 'type_id' of table 'feature' has 'NOT NULL'
> > constraint, so it doesn't make sense for Apollo to send query with=20
> > type_id =3D null.
> > =20
> > I'm wondering if someone came across the same problem before. How=20
> > should I configure Apollo data adapter so that it can find the correct
>=20
> > type_id for a feature?
> > =20
> > Any assistance/advice will be highly appreciated.
> > =20
> > Thanks a million!
> > =20
> > Henry
> > =20
> > PS: My chado-adapter.xml looks like this:
> > =20
> > <?xml version=3D"1.0" encoding=3D"UTF-8"?>
> > <!-- This file is used to config chado database adapter -->=20
> > <chado-adapter>
> > <chadoInstance id=3D"referenceInstance" default=3D"true">
> >=20
> >
> <writebackXmlTemplateFile>transactionXMLTemplate.xml</writebackXmlTempla
> teFile>
> > <featureCV>sequence</featureCV>
> > <polypeptideType>polypeptide</polypeptideType>
> > <relationshipCV>relationship</relationshipCV>
> > <propertyTypeCV>feature_property</propertyTypeCV>
> > <!-- default is part_of -->
> > <partOfCvTerm>part_of</partOfCvTerm>
> > <transProtRelationTerm>derives_from</transProtRelationTerm>
> > <searchHitsHaveFeatLocs>true</searchHitsHaveFeatLocs>
> >=20
> > <clsName>apollo.dataadapter.chado.jdbc.FlybaseChadoInstance</clsName>
> > =20
> > <oneLevelAnnotTypes>
> > <type>promoter</type>
> > <type>insertion site</type>
> > <type>transposable_element</type>
> > <type>transposable_element_insertion_site</type>
> > <type>remark</type>
> > <type>repeat_region</type>=20
> > </oneLevelAnnotTypes>
> > =20
> > <threeLevelAnnotTypes>
> > <type>gene</type>
> > <type>pseudogene</type>
> > <type>tRNA</type>
> > <type>snRNA</type>
> > <type>snoRNA</type>
> > <type>ncRNA</type>
> > <type>rRNA</type>
> > <type>miRNA</type>
> > </threeLevelAnnotTypes> =20
> > =20
> > </chadoInstance>
> > =20
> > <chadoInstance id=3D"riceInstance" default=3D"true">
> > <inheritsInstance>referenceInstance</inheritsInstance>
> > <sequenceTypes>
> > <type>gene</type>
> > <type>
> > <name>chromosome</name>
> > <useStartAndEnd>true</useStartAndEnd>
> > <queryForValueList>true</queryForValueList>
> > <isTopLevel>true</isTopLevel>
> > </type>
> > </sequenceTypes>
> > =20
> >=20
> >
> <writebackXmlTemplateFile>transactionXMLTemplate_rice.xml</writebackXmlT
> emplateFile>
> > <featureCV>Sequence Ontology Feature Annotation</featureCV>
> > <relationshipCV>Relationship Ontology</relationshipCV>
> > <propertyTypeCV>autocreated</propertyTypeCV>
> > =20
> > <genePredictionPrograms>
> > <program>FgenesH</program>
> > </genePredictionPrograms>
> > <searchHitPrograms>
> > <program>blat</program>
> > </searchHitPrograms> =20
> > <searchHitsHaveFeatLocs>true</searchHitsHaveFeatLocs>
> >=20
> > <clsName>apollo.dataadapter.chado.jdbc.RiceChadoInstance</clsName>
> > <oneLevelAnnotTypes>
> > <type>promoter</type>
> > <type>transposable_element</type>
> > <type>remark</type>
> > <type>repeat_region</type>=20
> > </oneLevelAnnotTypes>
> > </chadoInstance>
> > =20
> > <!-- Test chado database at rip.usca.nzcorp.net -->
> > <chadodb>
> > <name>Test chado database on rip</name>
> >=20
> > <adapter>apollo.dataadapter.chado.jdbc.PostgresChadoAdapter</adapter>
> > <url>jdbc:postgresql://rip.usca.nzcorp.net:5432/chado</url>
> > <dbName>chado</dbName>
> > <dbUser>chado</dbUser>
> > <dbInstance>riceInstance</dbInstance>
> > <style>rice.style</style>
> > </chadodb>
> > </chado-adapter>
> > =20
> >=20
> >=20
> > ----------------------------------------------------------------------
> > --- Using Tomcat but need to do more? Need to support web services,=20
> > security?
> > Get stuff done quickly with pre-integrated technology to make your job
>=20
> > easier Download IBM WebSphere Application Server v.1.0.1 based on=20
> > Apache Geronimo
> > http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D120709&bid=3D263057&dat=
=3D1216
> > 42 _______________________________________________ Gmod-schema mailing
>=20
> > list Gmo...@li...=20
> > https://lists.sourceforge.net/lists/listinfo/gmod-schema
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D. cai...@gm...
> GMOD Coordinator (http://www.gmod.org/) 216-392-3087
> Cold Spring Harbor Laboratory
>=20
--=20
------------------------------------------------------------------------
Scott Cain, Ph. D. cai...@gm...
GMOD Coordinator (http://www.gmod.org/) 216-392-3087
Cold Spring Harbor Laboratory

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Hi Henry,
I am back from England and very nearly awake today :-)
So, some questions:
 What version of gmod/chado are you using? Did you get a reasonably
recent checkout from cvs?
 What version of Apollo are you using?
I'm not exactly sure where the 'f.type_id =3D null' is coming from, but I
agree that it doesn't make much sense.
Also, you can take a look at the updated doc I wrote on apollo and chado
at =20
http://gmod.cvs.sourceforge.net/*checkout*/gmod/schema/chado/README.Apollo.=
pod
It is still a little skimpy on details, but it is getting better.
Scott
On Wed, 2006年09月13日 at 10:10 -0700, HXI (Henry Xiang) wrote:
> Hi,
> =20
> Has someone successfully done Apollo-Chado integration so that Apollo
> can directly talk to Chado database via jdbc? I desperatelly need help
> from Apollo/Chado gurus.
> =20
> I'm testing on a very simple Chado instance. When I searched for a
> gene with unique ID 'BLP00001', Apollo sent the following query
> =20
> SELECT f.feature_id FROM feature f WHERE (f.uniquename =3D
> 'BLP00001' OR f.name =3D 'BLP00001') AND f.type_id =3D null
> =20
> to chado database, and popped up an error message saying the gene
> can't be found.
> =20
> In fact, the feature 'BLP00001' has the cv term 'gene' associated with
> it, and I verified it at the database level with the following SQL
> query
> =20
> chado=3D# select f.uniquename, t.name from feature f, cvterm t where
> f.type_id =3D t.cvterm_id and f.uniquename =3D 'BLP00001';
> uniquename | name
> ------------+------
> BLP00001 | gene
> (1 row)
>=20
> Besides, column 'type_id' of table 'feature' has 'NOT NULL'
> constraint, so it doesn't make sense for Apollo to send query with
> type_id =3D null.=20
> =20
> I'm wondering if someone came across the same problem before. How
> should I configure Apollo data adapter so that it can find the correct
> type_id for a feature?
> =20
> Any assistance/advice will be highly appreciated.
> =20
> Thanks a million!
> =20
> Henry
> =20
> PS: My chado-adapter.xml looks like this:
> =20
> <?xml version=3D"1.0" encoding=3D"UTF-8"?>
> <!-- This file is used to config chado database adapter -->
> <chado-adapter>
> <chadoInstance id=3D"referenceInstance" default=3D"true">
>=20
> <writebackXmlTemplateFile>transactionXMLTemplate.xml</writebackXmlTemplat=
eFile>
> <featureCV>sequence</featureCV>
> <polypeptideType>polypeptide</polypeptideType>
> <relationshipCV>relationship</relationshipCV>
> <propertyTypeCV>feature_property</propertyTypeCV>
> <!-- default is part_of -->
> <partOfCvTerm>part_of</partOfCvTerm>
> <transProtRelationTerm>derives_from</transProtRelationTerm>
> <searchHitsHaveFeatLocs>true</searchHitsHaveFeatLocs>
>=20
> <clsName>apollo.dataadapter.chado.jdbc.FlybaseChadoInstance</clsName>
> =20
> <oneLevelAnnotTypes>
> <type>promoter</type>
> <type>insertion site</type>
> <type>transposable_element</type>
> <type>transposable_element_insertion_site</type>
> <type>remark</type>
> <type>repeat_region</type>=20
> </oneLevelAnnotTypes>
> =20
> <threeLevelAnnotTypes>
> <type>gene</type>
> <type>pseudogene</type>
> <type>tRNA</type>
> <type>snRNA</type>
> <type>snoRNA</type>
> <type>ncRNA</type>
> <type>rRNA</type>
> <type>miRNA</type>
> </threeLevelAnnotTypes> =20
> =20
> </chadoInstance>
> =20
> <chadoInstance id=3D"riceInstance" default=3D"true">
> <inheritsInstance>referenceInstance</inheritsInstance>
> <sequenceTypes>
> <type>gene</type>
> <type>
> <name>chromosome</name>
> <useStartAndEnd>true</useStartAndEnd>
> <queryForValueList>true</queryForValueList>
> <isTopLevel>true</isTopLevel>
> </type>
> </sequenceTypes>
> =20
>=20
> <writebackXmlTemplateFile>transactionXMLTemplate_rice.xml</writebackXmlTe=
mplateFile>
> <featureCV>Sequence Ontology Feature Annotation</featureCV>
> <relationshipCV>Relationship Ontology</relationshipCV>
> <propertyTypeCV>autocreated</propertyTypeCV>
> =20
> <genePredictionPrograms>
> <program>FgenesH</program>
> </genePredictionPrograms>
> <searchHitPrograms>
> <program>blat</program>
> </searchHitPrograms> =20
> <searchHitsHaveFeatLocs>true</searchHitsHaveFeatLocs>
>=20
> <clsName>apollo.dataadapter.chado.jdbc.RiceChadoInstance</clsName>
> <oneLevelAnnotTypes>
> <type>promoter</type>
> <type>transposable_element</type>
> <type>remark</type>
> <type>repeat_region</type>=20
> </oneLevelAnnotTypes>
> </chadoInstance> =20
> =20
> <!-- Test chado database at rip.usca.nzcorp.net -->
> <chadodb>
> <name>Test chado database on rip</name>
>=20
> <adapter>apollo.dataadapter.chado.jdbc.PostgresChadoAdapter</adapter>
> <url>jdbc:postgresql://rip.usca.nzcorp.net:5432/chado</url>
> <dbName>chado</dbName>
> <dbUser>chado</dbUser>
> <dbInstance>riceInstance</dbInstance>
> <style>rice.style</style>
> </chadodb>=20
> </chado-adapter>
> =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/listi=
nfo/gmod-schema
--=20
------------------------------------------------------------------------
Scott Cain, Ph. D. cai...@gm...
GMOD Coordinator (http://www.gmod.org/) 216-392-3087
Cold Spring Harbor Laboratory

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--------------------------------------------------------------------------------
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-----------------------
Putting the cart before the horse. The sun will shine into our yard to. There may be snow on the roof, but there's fire in the belly. Throw pearls before swine. Walking on thin ice. Stone cold sober. A rolling stone gathers no moss. Shit end of the stick. There's no time like the present. Stand your ground. Weed out. Shit happens. Sly as a fox. Were you born in a barn? Tall as a tree. She's a nut. 
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Henry - apologies for not replying sooner. You should post to the
ap...@fr... mailing list in the future.
HXI (Henry Xiang) wrote:
> Hi, Mark,
> 
> My name is Henry Xiang and I work with Novozymes, Inc. at Davis, CA.
> 
> I've been tring to integrate Apollo with Chado so that Apollo can
> read/write data directly from/to database. However, I come across some
> problems doing this.
> 
> Let me lay out the things for you so that you can have some background
> information.
> 
> First, I loaded a very simple two-entry GFF3 into Chado. The file looks
> like this:
> 
> ------------------ Sample GFF3 File -----------------------------------
> ##gff-version 3
> SJ1904 NZCA chromosome 1 4345449 . + . 
> ID=SJ1904
> SJ1904 NZCA gene 506 1846 . + . ID=BLP00001
> ###
> ##FASTA
>>SJ1904
> cgaaagcctaatttcatttttcctcaattttagcttaaaagattttttt......
> ------------------------------------------------------------------------------
> 
> Next, I ran 'cv_inserts,sql', 'apollo.inserts' and
> 'gmod_apollo_triggers.pl' to make Chado more 'Apollo-friendly'.
great
> 
> Then, I used Rich ChadoInstance as a template to configure the
> chado-adapter.xml file. Here's my configuration.
> 
> --------------------- chado-adpapter.xml ------------------------------
> <chado-adapter>
> <chadoInstance id="riceInstance" default="true">
> <inheritsInstance>referenceInstance</inheritsInstance>
> <sequenceTypes>
> <type>gene</type>
> <type>
> <name>chromosome</name>
> <useStartAndEnd>true</useStartAndEnd>
> <queryForValueList>true</queryForValueList>
> <isTopLevel>true</isTopLevel>
> </type>
> </sequenceTypes>
> 
> <writebackXmlTemplateFile>transactionXMLTemplate_rice.xml</writebackXmlTemplateFile>
> <featureCV>Sequence Ontology Feature Annotation</featureCV>
do you have the type chromosome in the cv called "Sequence Ontology Feature
Annotation" - do a select * on cv and see what ontologies are there - chromosome
may be in an ontology "SO"
i think its a similar issue with your gene post (to gmod-schema)
chado=# select f.uniquename, t.name from feature f, cvterm t where f.type_id =
t.cvterm_id and f.uniquename = 'BLP00001';
 uniquename | name
------------+------
 BLP00001 | gene
(1 row)
we need to further figure out cv name cvterm name "gene" is in
also if you arent already doing do put
DEBUG "true"
in conf/apollo.cfg (or ~/.apollo/apollo.cfg)
and all (or at least most) of the SQL will spew to stdout which is very helpful
for debugging.
hope this helps - let me know what you find.
> <relationshipCV>Relationship Ontology</relationshipCV>
> <propertyTypeCV>autocreated</propertyTypeCV>
> <genePredictionPrograms>
> <program>FgenesH</program>
> </genePredictionPrograms>
> <searchHitPrograms>
> <program>blat</program>
> </searchHitPrograms>
> <searchHitsHaveFeatLocs>true</searchHitsHaveFeatLocs>
> <clsName>apollo.dataadapter.chado.jdbc.RiceChadoInstance</clsName>
> <oneLevelAnnotTypes>
> <type>promoter</type>
> <type>transposable_element</type>
> <type>remark</type>
> <type>repeat_region</type>
> </oneLevelAnnotTypes>
> </chadoInstance>
> 
> <!-- Test chado database at rip.usca.nzcorp.net -->
> <chadodb>
> <name>Test chado database on rip</name>
> 
> <adapter>apollo.dataadapter.chado.jdbc.PostgresChadoAdapter</adapter>
> <url>jdbc:postgresql://rip.usca.nzcorp.net:5432/chado</url>
> <dbName>chado</dbName>
> <dbUser>chado</dbUser>
> <dbInstance>riceInstance</dbInstance>
> <style>rice.style</style>
> </chadodb>
> </chado-adapter>
> -------------------------------------------------------------------------------------
> 
> So far so good until I launch the Apollo and try to view the gene and
> chromosome feature. And here're the error messages I caught from the
> console.
> 
> ------------------- Apollo console output ----------------------------------
> APOLLO_ROOT set to /usr/src/gmod/apollo.1.6.5
> Couldn't find JavaPath line in apollo.cfg file, trying to guess path to
> java...
> /usr/bin/apollo: line 196: unalias: java: not found
> Using version of Java in /usr: /usr/bin/java
> Web browser = /usr/bin/mozilla
> Starting apollo (memory = 800M)...
> /usr/bin/java -ms50M -Xmx800M -classpath
> /usr/src/gmod/apollo.1.6.5/jars/apollo.jar:/usr/src/gmod/apollo.1.6.5/jars/biojava.jar:/usr/src/gmod/apollo.1.6.5/jars/crimson.jar:/usr/src/gmod/apollo.1.6.5/jars/ecp1_0beta.jar:/usr/src/gmod/apollo.1.6.5/jars/ensj-compatibility-19.0.jar:/usr/src/gmod/apollo.1.6.5/jars/ensj.jar:/usr/src/gmod/apollo.1.6.5/jars/jakarta-oro-2.0.6.jar:/usr/src/gmod/apollo.1.6.5/jars/jaxp.jar:/usr/src/gmod/apollo.1.6.5/jars/jnlp.jar:/usr/src/gmod/apollo.1.6.5/jars/junit.jar:/usr/src/gmod/apollo.1.6.5/jars/log4j-1.2.6.jar:/usr/src/gmod/apollo.1.6.5/jars/mysql-connector-java-3.1.8-bin.jar:/usr/src/gmod/apollo.1.6.5/jars/org.mortbay.jetty.jar:/usr/src/gmod/apollo.1.6.5/jars/patbinfree153.jar:/usr/src/gmod/apollo.1.6.5/jars/pg74.213.jdbc3.jar:/usr/src/gmod/apollo.1.6.5/jars/psgr2.jar:/usr/src/gmod/apollo.1.6.5/jars/servlet-tomcat.jar:/usr/src/gmod/apollo.1.6.5/jars/te-common.jar:/usr/src/gmod/apollo.1.6.5/jars/xerces.jar:/usr/src/gmod/apollo.1.6.5/data:
> -DAPOLLO_ROOT=/usr/src/gmod/apollo.1.6.5
> -Dorg.xml.sax.driver=org.apache.crimson.parser.XMLReaderImpl
> apollo.main.Apollo
> APOLLO_ROOT: /usr/src/gmod/apollo.1.6.5
> OS name: Linux
> OS arch: i386
> Java version: 1.5.0_07
> Reading config file /usr/src/gmod/apollo.1.6.5/conf/apollo.cfg
> Using history file /root/.apollo/apollo.history
> Using backup file /root/.apollo/apollo.backup
> 
> This is Apollo Genome Annotation and Curation Tool, version 1.6.5, last
> updated Jun 27 2006, 15:20
> Set style to /usr/src/gmod/apollo.1.6.5/conf/rice.style; style file
> source(s): /usr/src/gmod/apollo.1.6.5/conf/rice.style,
> /usr/src/gmod/apollo.1.6.5/conf/game.style
> Using tiers file rice.tiers
> Chado schema version appears to be fmb
> false falseSELECT f.feature_id FROM feature f WHERE (f.uniquename =
> 'BLP00001' OR f.name = 'BLP00001') AND f.type_id = null
> Cannot find sequence of type 'gene' with uniquename 'BLP00001'
> Chado schema version appears to be fmb
> Failed to get cv_term id for type chromosome! This feature type does not
> seem to be presnt in your chado database. Either the database or the
> configuration needs to be ammended
The problem seems to be its not finding the type chromosome
> java.lang.Throwable
> at
> apollo.dataadapter.chado.jdbc.JdbcChadoAdapter.getFeatNamesByType(JdbcChadoAdapter.java:438)
> at
> apollo.dataadapter.chado.SeqType.getLocationTopLevelSeqIds(SeqType.java:40)
> at
> apollo.dataadapter.chado.ChadoDatabase.getLocationTopLevelSeqIds(ChadoDatabase.java:209)
> at
> apollo.dataadapter.chado.ChadoAdapterGUI.setLocationTopLevelSeqIdList(ChadoAdapterGUI.java:897)
> at
> apollo.dataadapter.chado.ChadoAdapterGUI.setChromosomeGUIVisible(ChadoAdapterGUI.java:865)
> at
> apollo.dataadapter.chado.ChadoAdapterGUI.itemStateChanged(ChadoAdapterGUI.java:403)
> at javax.swing.JComboBox.fireItemStateChanged(JComboBox.java:1162)
> at javax.swing.JComboBox.selectedItemChanged(JComboBox.java:1210)
> at javax.swing.JComboBox.contentsChanged(JComboBox.java:1266)
> at
> javax.swing.AbstractListModel.fireContentsChanged(AbstractListModel.java:100)
> at
> javax.swing.DefaultComboBoxModel.setSelectedItem(DefaultComboBoxModel.java:88)
> at javax.swing.JComboBox.setSelectedItem(JComboBox.java:551)
> at javax.swing.JComboBox.setSelectedIndex(JComboBox.java:597)
> at
> javax.swing.plaf.basic.BasicComboPopup$Handler.mouseReleased(BasicComboPopup.java:808)
> at
> java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:232)
> at java.awt.Component.processMouseEvent(Component.java:5488)
> at javax.swing.JComponent.processMouseEvent(JComponent.java:3126)
> at
> javax.swing.plaf.basic.BasicComboPopup1ドル.processMouseEvent(BasicComboPopup.java:476)
> at java.awt.Component.processEvent(Component.java:5253)
> at java.awt.Container.processEvent(Container.java:1966)
> at java.awt.Component.dispatchEventImpl(Component.java:3955)
> at java.awt.Container.dispatchEventImpl(Container.java:2024)
> at java.awt.Component.dispatchEvent(Component.java:3803)
> at
> java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4212)
> at
> java.awt.LightweightDispatcher.processMouseEvent(Container.java:3892) 
> at java.awt.LightweightDispatcher.dispatchEvent(Container.java:3822)
> at java.awt.Container.dispatchEventImpl(Container.java:2010)
> at java.awt.Window.dispatchEventImpl(Window.java:1774)
> at java.awt.Component.dispatchEvent(Component.java:3803)
> at java.awt.EventQueue.dispatchEvent(EventQueue.java:463)
> at
> java.awt.EventDispatchThread.pumpOneEventForHierarchy(EventDispatchThread.java:242)
> at
> java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:163)
> at
> java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:153)
> at java.awt.Dialog1ドル.run(Dialog.java:517)
> at java.awt.Dialog2ドル.run(Dialog.java:545)
> at java.security.AccessController.doPrivileged(Native Method)
> at java.awt.Dialog.show(Dialog.java:543)
> at
> org.bdgp.swing.widget.DataAdapterChooser.show(DataAdapterChooser.java:218)
> at apollo.main.DataLoader$DataChooserThread.run(DataLoader.java:452)
> at apollo.main.DataLoader.getData(DataLoader.java:352)
> at
> apollo.main.DataLoader.getCompositeDataHolder(DataLoader.java:139)
> at apollo.main.Apollo1ドル.run(Apollo.java:124)
> at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209)
> at java.awt.EventQueue.dispatchEvent(EventQueue.java:461)
> at
> java.awt.EventDispatchThread.pumpOneEventForHierarchy(EventDispatchThread.java:242)
> at
> java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:163)
> at
> java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:157) 
> at
> java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:149) 
> at java.awt.EventDispatchThread.run(EventDispatchThread.java:110)
> No features returned for type chromosome either check db for chromosome
> in cvterm and feature tables or ammend your config file 
> (chado-adapter.xml), change seq type or config values.
> is not valid in this field--expecting positive integer value.
> 
> Set style to /usr/src/gmod/apollo.1.6.5/conf/rice.style; style file
> source(s): /usr/src/gmod/apollo.1.6.5/conf/rice.style,
> /usr/src/gmod/apollo.1.6.5/conf/game.style
> Using tiers file rice.tiers
> Chado schema version appears to be fmb
> Exception in thread "Thread-3" java.lang.NullPointerException
> at
> apollo.dataadapter.chado.jdbc.JdbcChadoAdapter.validateConnectionAndSequence(JdbcChadoAdapter.java:226)
> at
> apollo.dataadapter.chado.ChadoAdapter.getCurationSet(ChadoAdapter.java:243)
> at
> apollo.dataadapter.chado.ChadoAdapterGUI.doOperation(ChadoAdapterGUI.java:300)
> at
> org.bdgp.swing.widget.DataAdapterChooser.doCommitWithExceptions(DataAdapterChooser.java:361)
> at
> apollo.main.DataLoader$ApolloAdapterChooser.doCommit(DataLoader.java:739)
> at
> org.bdgp.swing.widget.DataAdapterChooser$CommitRunnable.run(DataAdapterChooser.java:136)
> at java.lang.Thread.run(Thread.java:595)
> ---------------------------------------------------------------------------------------------------------------
> 
> I apologize for this hard to read email, but I deperately need your
> help. Any advice will be appreciated.
> 
> Henry

Hi,
=20
Has someone successfully done Apollo-Chado integration so that Apollo
can directly talk to Chado database via jdbc? I desperatelly need help
from Apollo/Chado gurus.
=20
I'm testing on a very simple Chado instance. When I searched for a gene
with unique ID 'BLP00001', Apollo sent the following query
=20
 SELECT f.feature_id FROM feature f WHERE (f.uniquename =3D =
'BLP00001'
OR f.name =3D 'BLP00001') AND f.type_id =3D null
=20
to chado database, and popped up an error message saying the gene can't
be found.
=20
In fact, the feature 'BLP00001' has the cv term 'gene' associated with
it, and I verified it at the database level with the following SQL query
=20
chado=3D# select f.uniquename, t.name from feature f, cvterm t where
f.type_id =3D t.cvterm_id and f.uniquename =3D 'BLP00001';
 uniquename | name
------------+------
 BLP00001 | gene
(1 row)
Besides, column 'type_id' of table 'feature' has 'NOT NULL' constraint,
so it doesn't make sense for Apollo to send query with type_id =3D null. =
=20
I'm wondering if someone came across the same problem before. How should
I configure Apollo data adapter so that it can find the correct type_id
for a feature?
=20
Any assistance/advice will be highly appreciated.
=20
Thanks a million!
=20
Henry
=20
PS: My chado-adapter.xml looks like this:
=20
<?xml version=3D"1.0" encoding=3D"UTF-8"?>
<!-- This file is used to config chado database adapter -->
<chado-adapter>
 <chadoInstance id=3D"referenceInstance" default=3D"true">
=20
<writebackXmlTemplateFile>transactionXMLTemplate.xml</writebackXmlTempla
teFile>
 <featureCV>sequence</featureCV>
 <polypeptideType>polypeptide</polypeptideType>
 <relationshipCV>relationship</relationshipCV>
 <propertyTypeCV>feature_property</propertyTypeCV>
 <!-- default is part_of -->
 <partOfCvTerm>part_of</partOfCvTerm>
 <transProtRelationTerm>derives_from</transProtRelationTerm>
 <searchHitsHaveFeatLocs>true</searchHitsHaveFeatLocs>
=20
<clsName>apollo.dataadapter.chado.jdbc.FlybaseChadoInstance</clsName>
 =20
 <oneLevelAnnotTypes>
 <type>promoter</type>
 <type>insertion site</type>
 <type>transposable_element</type>
 <type>transposable_element_insertion_site</type>
 <type>remark</type>
 <type>repeat_region</type>=20
 </oneLevelAnnotTypes>
 =20
 <threeLevelAnnotTypes>
 <type>gene</type>
 <type>pseudogene</type>
 <type>tRNA</type>
 <type>snRNA</type>
 <type>snoRNA</type>
 <type>ncRNA</type>
 <type>rRNA</type>
 <type>miRNA</type>
 </threeLevelAnnotTypes> =20
=20
 </chadoInstance>
=20
 <chadoInstance id=3D"riceInstance" default=3D"true">
 <inheritsInstance>referenceInstance</inheritsInstance>
 <sequenceTypes>
 <type>gene</type>
 <type>
 <name>chromosome</name>
 <useStartAndEnd>true</useStartAndEnd>
 <queryForValueList>true</queryForValueList>
 <isTopLevel>true</isTopLevel>
 </type>
 </sequenceTypes>
=20
=20
<writebackXmlTemplateFile>transactionXMLTemplate_rice.xml</writebackXmlT
emplateFile>
 <featureCV>Sequence Ontology Feature Annotation</featureCV>
 <relationshipCV>Relationship Ontology</relationshipCV>
 <propertyTypeCV>autocreated</propertyTypeCV>
=20
 <genePredictionPrograms>
 <program>FgenesH</program>
 </genePredictionPrograms>
 <searchHitPrograms>
 <program>blat</program>
 </searchHitPrograms> =20
 <searchHitsHaveFeatLocs>true</searchHitsHaveFeatLocs>
 <clsName>apollo.dataadapter.chado.jdbc.RiceChadoInstance</clsName>
 <oneLevelAnnotTypes>
 <type>promoter</type>
 <type>transposable_element</type>
 <type>remark</type>
 <type>repeat_region</type>=20
 </oneLevelAnnotTypes>
 </chadoInstance> =20
=20
 <!-- Test chado database at rip.usca.nzcorp.net -->
 <chadodb>
 <name>Test chado database on rip</name>
=20
<adapter>apollo.dataadapter.chado.jdbc.PostgresChadoAdapter</adapter>
 <url>jdbc:postgresql://rip.usca.nzcorp.net:5432/chado</url>
 <dbName>chado</dbName>
 <dbUser>chado</dbUser>
 <dbInstance>riceInstance</dbInstance>
 <style>rice.style</style>
 </chadodb>=20
</chado-adapter>
=20