Installing CHADO

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Re: Installing CHADO

Hi Mindi,

It is asking for the password of the user you are currently logged in
as.  If entering that password does not work, it means that the user
does not have sudo capability.  Users that have sudo capability can
run things as the superuser (thus the "su" in "sudo") by preceding the
command with "sudo".

Are you the administrator of your machine, or do you have a separate
sys admin staff?  If you have a separate sys admin staff then you may
have to ask them to do part of the install for you (as they may or may
not want to give you sudo ability).

If you are the administrator of the system, what version of Linux/Unix
are you running?

Thanks,

Dave C.

On Tue, Nov 4, 2008 at 1:43 PM, Dippold, Mindi (M) <MDippold <at> dow.com> wrote:
> Hello,
> I've been attempting to install the CHADO default schema from gmod-1.0.
> I have all of the perl modules installed and have been able to make the
> install, but when I try 'sudo make install' I am prompted for a password.  I
> have tried my log in passwords, the postgresql user password, and nothing
> seems to work.  Could you kindly please let me know what the installation is
> asking for here so I can give it the correct password?
>
> Thank you.
> Mindi DIppold
>
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Re: [Gmod-help] RE: Installing CHADO

Hi Mindi,

Please reply to the list as well.  You'll find that list members often
have experience with the problems described.

As far as I can tell, "2" is not an error code in Postgres at all.  It
is the code for

PGRES_TUPLES_OK - Successful completion of a command returning data
(such as a SELECT or SHOW).

Which version of Postgres are you using?  We haven't done a lot of
work with PostgreSQL 8.3 yet.  (Postgres 8.3 tightens up casting of
values in ways that may break our Perl code that relies on loose
casting.)  It may be that 8.3 is returning a 2 status somewhere that
it did not return in 8.2.

If you are running 8.3 then please try 8.2.  If you are running 8.2
(or earlier) then, um, hopefully someone on the list will have an
idea.

Thanks,

Dave C.

On Tue, Nov 4, 2008 at 3:18 PM, Dippold, Mindi (M) <MDippold <at> dow.com> wrote:
> Thanks for the reply Dave.
> I ended up doing a sudo login as root for the sudo make install and it
> went fine....and then comes my next question.
> When I get to the 'make load schema' step I get an error that is not
> descriptive and it dies with 'Error 2'.  I think this comes down to how
> I have my user/password/host/port set up for PostgreSQL.  Any specific
> suggestions that will help me out here?  I set up a PostgreSQL user who
> has total access/rights to create databases, etc, and I have the host
> set as localhost and the port set to the default.
> Thanks again.
> Mindi
>
> -----Original Message-----
> From: Dave Clements, GMOD Help Desk [mailto:gmodhelp <at> googlemail.com]
> Sent: Tuesday, November 04, 2008 5:56 PM
> To: Dippold, Mindi (M)
> Cc: gmod-schema <at> lists.sourceforge.net
> Subject: Re: [Gmod-schema] Installing CHADO
>
> Hi Mindi,
>
> It is asking for the password of the user you are currently logged in
> as.  If entering that password does not work, it means that the user
> does not have sudo capability.  Users that have sudo capability can
> run things as the superuser (thus the "su" in "sudo") by preceding the
> command with "sudo".
>
> Are you the administrator of your machine, or do you have a separate
> sys admin staff?  If you have a separate sys admin staff then you may
> have to ask them to do part of the install for you (as they may or may
> not want to give you sudo ability).
>
> If you are the administrator of the system, what version of Linux/Unix
> are you running?
>
> Thanks,
>
> Dave C.
>
>
> On Tue, Nov 4, 2008 at 1:43 PM, Dippold, Mindi (M) <MDippold <at> dow.com>
> wrote:
>> Hello,
>> I've been attempting to install the CHADO default schema from
> gmod-1.0.
>> I have all of the perl modules installed and have been able to make
> the
>> install, but when I try 'sudo make install' I am prompted for a
> password.  I
>> have tried my log in passwords, the postgresql user password, and
> nothing
>> seems to work.  Could you kindly please let me know what the
> installation is
>> asking for here so I can give it the correct password?
>>
>> Thank you.
>> Mindi DIppold
>>
>>
> ------------------------------------------------------------------------
> -
>> This SF.Net email is sponsored by the Moblin Your Move Developer's
> challenge
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>> prizes
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> world
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>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
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>>
>
>
>
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> Was this helpful?  Let us know at
> http://gmod.org/wiki/Help_Desk_Feedback
>
>

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[ANN] News from the FlyWeb Project

Hi all,

I've been lurking on this list for a few months, and thought you might
be interested in some work we've done in the FlyWeb project. We've
made extensive use of Chado, it's been an invaluable resource.

Thoughts, feedback, suggestions, ideas very welcome.

Cheers,

Alistair.

----- Forwarded message from Alistair Miles <alistair.miles <at> zoo.ox.ac.uk> -----

Date: Wed, 5 Nov 2008 16:44:16 +0000
From: Alistair Miles <alistair.miles <at> zoo.ox.ac.uk>
To: public-semweb-lifesci <at> w3.org
Subject: [ANN] News from the FlyWeb Project

Dear all,

This is a summary of work so far by the FlyWeb Project team. We're
exploring integration of life science data in support of Drosophila
(fruit fly) functional genomics. We'd like to develop credible, robust
and genuinely useful tools for the Drosophila research community; and
to provide data and services of value to bioinformaticians and
Semantic Web / Life Science developers.

This is the first time we've announced our work more widely, and we'd
very much appreciate thoughts, suggestions, feedback, re-use and
testing of the applications, services, software and data described
below. Please note however that this is work in progress, and things
may break, change, move or disappear without notice.

= Search Applications =

http://openflydata.org/search/insitus

This application allows you to search for images of in situ RNA
hybridisation experiments, depicting expression of specific genes in
different organs (testes and embryos). It is a mashup of data from the
Berkeley Drosophila Genome Project (BDGP) and the Drosophila Testis
Gene Expression Database (Fly-TED). It also uses data from FlyBase to
disambiguate gene name synonyms.

It's a pure AJAX application using SPARQL to access data from each of
the three sources on the fly (pardon the pun :).

= RDF Data =

The following RDF data used in the search application above are
available for bulk download:

* http://openflydata.org/dump/flybase (latest)
  http://openflydata.org/dump/flybase_genenames_20081017 (snapshot)

  data on D. melanogaster gene identifiers, symbols and synonyms,
  derived from flybase.org; approx 8 million triples; gzipped
  n-triples

* http://openflydata.org/dump/bdgp (latest)
  http://openflydata.org/dump/bdgp_images_20081030 (snapshot)

  metadata on images of embryo in situ gene expression experiments,
  derived from fruitfly.org; approx 1 million triples; gzipped
  n-triples

* http://openflydata.org/dump/flyted (latest)
  http://openflydata.org/dump/flyted_20080626 (snapshot)

  metadata on images testis in situ gene expression experiments,
  derived from www.fly-ted.org; approx 30,000 triples; gzipped turtle

= Data Services =

The following SPARQL endpoints are available for queries over the
above data. See also limitations below.

* http://openflydata.org/query/flybase (latest)
  http://openflydata.org/query/flybase_genenames_20081017 (snapshot)

* http://openflydata.org/query/bdgp (latest)
  http://openflydata.org/query/bdgp_images_20081030 (snapshot)

* http://openflydata.org/query/flyted (latest)
  http://openflydata.org/query/flyted_20080626 (snapshot)

Limitations: only GET requests are supported; only SELECT and ASK
queries are supported; only JSON results format is supported (request
must specify output=json); SELECT queries are limited to max 500
results; no more than 5 requests per second from any one origin

The endpoints are implemented using our own Java SPARQL protocol
implementation (SPARQLite, see below) backed by Jena TDB 0.6
stores. The endpoints run inside Tomcat 5.5 behind Apache 2.2 via
mod_jk, on a small EC2 instance, with TDB storing data on an attached
EBS volume.

= Software Downloads & Source Code =

* FlyUI
  http://flyui.googlecode.com

This is a library of composable javascript widgets, providing a
user-interface to above data. These widgets are used to build the
search application above. FlyUI is built on YAHOO's javascript user
interface library (YUI).

* SPARQLite
  http://sparqlite.googlecode.com

This is an experimental and incomplete implementation of the SPARQL
protocol, designed to work with Jena TDB or SDB stores. We're using
this as a platform to explore a number of quality of service issues
that SPARQL raises.

= Ontologies/Schemas =

The following OWL schemas are used in the above data:

* CHADO OWL Schema 
  http://purl.org/net/chado/schema/

This is an OWL representation of a subset of the CHADO relational
schema used by FlyBase (see http://gmod.org/wiki/Schema).

* FlyBase OWL Synonym Types
  http://purl.org/net/flybase/synonym-types/

This is a micro-ontology, representing the FlyBase synonym type
vocabulary.

* BDGP OWL Schema
  http://purl.org/net/bdgp/schema/

This is an OWL representation of a subset of the BDGP relational
schema.

* FlyTED OWL Schemas

These are under revision, to be published shortly.

= RDF Data Conversion Utilities =

The following utilities were developed to obtain the RDF data
described above:

* CHADO/FlyBase D2RQ Map
  http://code.google.com/p/openflydata/source/browse/trunk/flybase/genenames/d2r-flybase-genenames.ttl

This provides a mapping from the CHADO/FlyBase relational schema to
the CHADO/FlyBase OWL ontologies, for basic D. melanogaster gene
(feature) data (identifiers, symbols, synonyms, species).

* BDGP D2RQ Map
  http://code.google.com/p/openflydata/source/browse/trunk/bdgp/imagemapping/d2r-bdgp-insituimages.ttl

This maps the BDGP relational schema to OWL/RDF.

See also: http://openflydata.googlecode.com

= Future Developments =

We're currently working on improving the user interface to the BDGP
data (grouping and ordering images by developmental stage) and on
integrated expression level data from FlyAtlas.

Other suggestions for future developments are warmly welcomed.

= Acknowledgments =

Thanks especially to Helen White-Cooper and Andy Seaborne for all
their help.

The FlyWeb Project is funded by the UK Joint Information Systems
Committee (JISC).

= Further Information =

The FlyWeb project website is at:

http://imageweb.zoo.ox.ac.uk/wiki/index.php/FlyWeb_project

Graham will be presenting this work at the UK SWIG meeting next week.

Or send us an email :)

Kind regards,

Alistair Miles
Jun Zhao
Graham Klyne
David Shotton

-- 
Alistair Miles
Senior Computing Officer
Image Bioinformatics Research Group
Department of Zoology
The Tinbergen Building
University of Oxford
South Parks Road
Oxford
OX1 3PS
United Kingdom
Web: http://purl.org/net/aliman
Email: alistair.miles <at> zoo.ox.ac.uk
Tel: +44 (0)1865 281993

----- End forwarded message -----

-- 
Alistair Miles
Senior Computing Officer
Image Bioinformatics Research Group
Department of Zoology
The Tinbergen Building
University of Oxford
South Parks Road
Oxford
OX1 3PS
United Kingdom
Web: http://purl.org/net/aliman
Email: alistair.miles <at> zoo.ox.ac.uk
Tel: +44 (0)1865 281993

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The unique constraint on the analysis table

A row in the analysis table is supposed to represent a single run of  
an algorithm (e.g. BLAST), as I understand it.

If that's right, then why is there a UNIQUE constraint on (program,  
programversion, sourcename)? It's certainly
possible to do more than one BLAST against the same database.

Robin

--

-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 

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Re: The unique constraint on the analysis table

Hi Robin,

I haven't really thought about it, but perhaps the unique constraint
should be on (program, programversion, sourcename, sourceversion) to
allow for blast results on the same database obtained on different
dates.  Also, you could encode information about the blast run in the
sourcename if you were going to do more than one blast against the
same database using different parameters, like "nr_high_sensitivity"
and "nr_low_sensitivity".  I don't know if I really like that though.

Any one else have thoughts (FlyBase, I'm looking at you all 

Scott

On Thu, Nov 13, 2008 at 9:19 AM, Robin Houston <rh11 <at> sanger.ac.uk> wrote:
> A row in the analysis table is supposed to represent a single run of
> an algorithm (e.g. BLAST), as I understand it.
>
> If that's right, then why is there a UNIQUE constraint on (program,
> programversion, sourcename)? It's certainly
> possible to do more than one BLAST against the same database.
>
> Robin
>
>
> --
>  The Wellcome Trust Sanger Institute is operated by Genome Research
>  Limited, a charity registered in England with number 1021457 and a
>  company registered in England with number 2742969, whose registered
>  office is 215 Euston Road, London, NW1 2BE.
>
> -------------------------------------------------------------------------
> This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
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--

-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Re: The unique constraint on the analysis table

Scott-

One possibility--assuming that the BLAST results are loaded into chado
from a file or set of files on disk--is to use the sourcename field to
record the (hopefully unique) location of that file or files.  For
example, we might have a sourcename =
"/path/to/blast_run_4562_processed_results.xml". The practice serves
two purposes: it gets around the unique constraint, and it helps to
track the provenance of the data, providing a reference to the source
file (XML/BSML in our group's case) from which the analysis results
were loaded.  The various BLAST parameters (including the target
database name) can then be stored as analysisprops, as they should be.
 Looking at the wiki it does seem that this practice disagrees with
the documented use of the sourcename field, but as Robin points out
it's difficult to see how to adhere to the documentation without
violating the unique constraint...

Jonathan

On Thu, Nov 13, 2008 at 10:00 AM, Scott Cain <cain.cshl <at> gmail.com> wrote:
> Hi Robin,
>
> I haven't really thought about it, but perhaps the unique constraint
> should be on (program, programversion, sourcename, sourceversion) to
> allow for blast results on the same database obtained on different
> dates.  Also, you could encode information about the blast run in the
> sourcename if you were going to do more than one blast against the
> same database using different parameters, like "nr_high_sensitivity"
> and "nr_low_sensitivity".  I don't know if I really like that though.
>
> Any one else have thoughts (FlyBase, I'm looking at you all 
>
> Scott
>
>
> On Thu, Nov 13, 2008 at 9:19 AM, Robin Houston <rh11 <at> sanger.ac.uk> wrote:
>> A row in the analysis table is supposed to represent a single run of
>> an algorithm (e.g. BLAST), as I understand it.
>>
>> If that's right, then why is there a UNIQUE constraint on (program,
>> programversion, sourcename)? It's certainly
>> possible to do more than one BLAST against the same database.
>>
>> Robin
>>
>>
>> --
>>  The Wellcome Trust Sanger Institute is operated by Genome Research
>>  Limited, a charity registered in England with number 1021457 and a
>>  company registered in England with number 2742969, whose registered
>>  office is 215 Euston Road, London, NW1 2BE.
>>
>> -------------------------------------------------------------------------
>> This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
>> Build the coolest Linux based applications with Moblin SDK & win great prizes
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>> Gmod-schema <at> lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>
> -------------------------------------------------------------------------
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Re: The unique constraint on the analysis table

I don't know how common our situation is, but our database has dozens  
of different organisms and we won't typically run analyses across the  
entire database at once. So we could run an analysis of, say,  
Plasmodium against a particular database, and also an analysis of  
Trypanosoma against the same database.

The current uniqueness constraint only kicks in if the sourcename is  
specified. Because (NULL = NULL) is not true, you can have many rows  
with the same program and programversion, provided that none of them  
has a sourcename. Quite often at the moment we're loading data from  
legacy files in which the source database is not specified, so this is  
our commonest case at present and avoids the uniqueness problem, but  
it's hard to believe this was the intention.

Is there any reason the uniqueness constraint should not simply be  
dropped?

Robin

On 13 Nov 2008, at 15:00, Scott Cain wrote:

> Hi Robin,
>
> I haven't really thought about it, but perhaps the unique constraint
> should be on (program, programversion, sourcename, sourceversion) to
> allow for blast results on the same database obtained on different
> dates.  Also, you could encode information about the blast run in the
> sourcename if you were going to do more than one blast against the
> same database using different parameters, like "nr_high_sensitivity"
> and "nr_low_sensitivity".  I don't know if I really like that though.
>
> Any one else have thoughts (FlyBase, I'm looking at you all 
>
> Scott
>
>
> On Thu, Nov 13, 2008 at 9:19 AM, Robin Houston <rh11 <at> sanger.ac.uk>  
> wrote:
>> A row in the analysis table is supposed to represent a single run of
>> an algorithm (e.g. BLAST), as I understand it.
>>
>> If that's right, then why is there a UNIQUE constraint on (program,
>> programversion, sourcename)? It's certainly
>> possible to do more than one BLAST against the same database.
>>
>> Robin
>>
>>
>> --
>> The Wellcome Trust Sanger Institute is operated by Genome Research
>> Limited, a charity registered in England with number 1021457 and a
>> company registered in England with number 2742969, whose registered
>> office is 215 Euston Road, London, NW1 2BE.
>>
>> -------------------------------------------------------------------------
>> This SF.Net email is sponsored by the Moblin Your Move Developer's  
>> challenge
>> Build the coolest Linux based applications with Moblin SDK & win  
>> great prizes
>> Grand prize is a trip for two to an Open Source event anywhere in  
>> the world
>> http://moblin-contest.org/redirect.php?banner_id=100&url=/
>> _______________________________________________
>> Gmod-schema mailing list
>> Gmod-schema <at> lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>
>
>
>
> -- 
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at  
> scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research

--

-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 

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Re: The unique constraint on the analysis table

I've ended up putting options into the program column.  So I have stuff 
like "orthomcl --pmatch_cutoff=50" and "orthomcl --pmatch_cutoff=40" in 
the program column.

Scott Cain wrote:
> Hi Robin,
>
> I haven't really thought about it, but perhaps the unique constraint
> should be on (program, programversion, sourcename, sourceversion) to
> allow for blast results on the same database obtained on different
> dates.  Also, you could encode information about the blast run in the
> sourcename if you were going to do more than one blast against the
> same database using different parameters, like "nr_high_sensitivity"
> and "nr_low_sensitivity".  I don't know if I really like that though.
>
> Any one else have thoughts (FlyBase, I'm looking at you all 
>
> Scott
>
>
> On Thu, Nov 13, 2008 at 9:19 AM, Robin Houston <rh11 <at> sanger.ac.uk> wrote:
>   
>> A row in the analysis table is supposed to represent a single run of
>> an algorithm (e.g. BLAST), as I understand it.
>>
>> If that's right, then why is there a UNIQUE constraint on (program,
>> programversion, sourcename)? It's certainly
>> possible to do more than one BLAST against the same database.
>>
>> Robin
>>
>>
>> --
>>  The Wellcome Trust Sanger Institute is operated by Genome Research
>>  Limited, a charity registered in England with number 1021457 and a
>>  company registered in England with number 2742969, whose registered
>>  office is 215 Euston Road, London, NW1 2BE.
>>
>> -------------------------------------------------------------------------
>> This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
>> Build the coolest Linux based applications with Moblin SDK & win great prizes
>> Grand prize is a trip for two to an Open Source event anywhere in the world
>> http://moblin-contest.org/redirect.php?banner_id=100&url=/
>> _______________________________________________
>> Gmod-schema mailing list
>> Gmod-schema <at> lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>
>>     
>
>
>
>   

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BLAST data representation in Chado

Hi all,

I was just looking though the wiki files for chado implementations on 
the gmod site (been a while since I visited it) and I noticed some 
inconsistencies between the way the "Load_BLAST_Into_Chado" program 
represents a BLAST result and the way I thought was correct.

On both http://gmod.org/wiki/Load_BLAST_Into_Chado and 
http://gmod.org/wiki/Chado_Best_Practices#Results_from_BLAST it states 
that an Hit to query featureloc will have a rank of 0 and the Hit to 
target featureloc will have a rank of 0.  However, it also says that the 
HSP to query featureloc will have a rank of 1.  I don't understand the 
latter statement.  What is the purpose of increasing the rank of the HSP 
featureloc and if the HSP to query featureloc is rank 1 what is the rank 
of the HSP to target featureloc?

I always assumed (and implemented) for BLAST that all featurelocs to the 
query were rank 0 and all featurelocs to the target were rank 1.

Thanks in advance.

Keith Boroevich

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