From midori at ebi.ac.uk  Tue Apr  1 06:32:38 2008
From: midori at ebi.ac.uk (Midori Harris)
Date: Tue, 1 Apr 2008 14:32:38 +0100 (BST)
Subject: [Go] Ontology development - March highlights
Message-ID: <Pine.LNX.4.64.0803311349570.24397@pigeon.ebi.ac.uk>

Dear GO,

The most recent monthly report on ontology content, for March 2008, is now 
available at:

   http://gocwiki.geneontology.org/index.php/Mar2008_report

Ontology development highlights from March:

  * The 'regulates' relationships have gone live! They are now used in the 
gene_ontology*.obo files and will be visible in AmiGO very soon (if they 
aren't already). Many thanks to all who helped with this work, especially 
David, Tanya and Chris.

  * We're down to one live 'sensu' term, and it will be changed before the 
GOC meeting (main wiki page: 
http://gocwiki.geneontology.org/index.php/Sensu_Main_Page; outstanding 
items: http://gocwiki.geneontology.org/index.php/Meeting_Notes_3).

  * Reorganization of electron transport terms has been implemented 
(http://wiki.geneontology.org/index.php/Electron_transport).

  * Two pilot projects are under way, one on electron transport and the 
other on glycolysis and the TCA cycle, to document links between function 
terms and process terms. Function-process main page: 
http://wiki.geneontology.org/index.php/Function-Process_Links.

  * An overhaul of signal transduction process terms has begun 
(http://wiki.geneontology.org/index.php/Signaling).

In April, the function-process pilot projects will continue, as will the 
signaling overhaul and quality control work connected with the regulation 
terms. We also hope to implement changes stemming from the lung 
development content meeting 
(http://wiki.geneontology.org/index.php/Lung_Development).

There are several content-related items proposed for the GOC meeting 
agenda 
(http://wiki.geneontology.org/index.php/SLC_GO_Consortium_Meeting#Agenda_Items).

As usual, details of small- and medium-scale changes are available in the 
SourceForge Curator Requests tracker. Please contact us if you want to help out 
with ontology work in a particular area, or if you have any comments or 
questions about what's going on.

Ontology Development wiki:
http://wiki.geneontology.org/index.php/Ontology_Development

SourceForge Curator Requests tracker:
https://sourceforge.net/tracker/?group_id=36855&atid=440764

Midori & David
on behalf of GO's ontology developers

From pgaudet at northwestern.edu  Tue Apr  1 06:38:23 2008
From: pgaudet at northwestern.edu (Pascale Gaudet)
Date: Tue, 01 Apr 2008 09:38:23 -0400
Subject: [Go] March 26 managers call - minutes available
Message-ID: <47F23ACF.9020102@northwestern.edu>

Hello,

The minutes from last week's GO Managers conference call are now on the wiki:

   http://wiki.geneontology.org/index.php/Managers_26March

If you would like a particular issue to be discussed at the next managers' 
call, please contact the relevant manager(s):

Reference Genomes: Pascale
User Advocacy and Outreach: Jennifer and Jane
Content Development: Midori and David
Software: Chris

For general management and budget issues, contact the GO PIs 
<go-top at genome.stanford.edu>.


Pascale 




From midori at ebi.ac.uk  Tue Apr  1 09:00:16 2008
From: midori at ebi.ac.uk (midori at ebi.ac.uk)
Date: Tue, 1 Apr 2008 16:00:16 UT
Subject: [Go] SourceForge Update
Message-ID: <200804011600.m31G0GR1529750@mozart.ebi.ac.uk>

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From ma11 at gen.cam.ac.uk  Tue Apr  1 08:43:33 2008
From: ma11 at gen.cam.ac.uk (Michael Ashburner)
Date: Tue, 1 Apr 2008 08:43:33 -0700
Subject: [Go] Ontology development - March highlights
In-Reply-To: <Pine.LNX.4.64.0803311349570.24397@pigeon.ebi.ac.uk>
References: <Pine.LNX.4.64.0803311349570.24397@pigeon.ebi.ac.uk>
Message-ID: <5D8DEDC4-3E21-4172-975E-15089B5C3B1E@gen.cam.ac.uk>

Thankyou Midori.

Michael

On 1 Apr 2008, at 06:32, Midori Harris wrote:

> Dear GO,
>
> The most recent monthly report on ontology content, for March 2008,  
> is now
> available at:
>
>    http://gocwiki.geneontology.org/index.php/Mar2008_report
>
> Ontology development highlights from March:
>
>   * The 'regulates' relationships have gone live! They are now used  
> in the
> gene_ontology*.obo files and will be visible in AmiGO very soon (if  
> they
> aren't already). Many thanks to all who helped with this work,  
> especially
> David, Tanya and Chris.
>
>   * We're down to one live 'sensu' term, and it will be changed  
> before the
> GOC meeting (main wiki page:
> http://gocwiki.geneontology.org/index.php/Sensu_Main_Page; outstanding
> items: http://gocwiki.geneontology.org/index.php/Meeting_Notes_3).
>
>   * Reorganization of electron transport terms has been implemented
> (http://wiki.geneontology.org/index.php/Electron_transport).
>
>   * Two pilot projects are under way, one on electron transport and  
> the
> other on glycolysis and the TCA cycle, to document links between  
> function
> terms and process terms. Function-process main page:
> http://wiki.geneontology.org/index.php/Function-Process_Links.
>
>   * An overhaul of signal transduction process terms has begun
> (http://wiki.geneontology.org/index.php/Signaling).
>
> In April, the function-process pilot projects will continue, as  
> will the
> signaling overhaul and quality control work connected with the  
> regulation
> terms. We also hope to implement changes stemming from the lung
> development content meeting
> (http://wiki.geneontology.org/index.php/Lung_Development).
>
> There are several content-related items proposed for the GOC meeting
> agenda
> (http://wiki.geneontology.org/index.php/ 
> SLC_GO_Consortium_Meeting#Agenda_Items).
>
> As usual, details of small- and medium-scale changes are available  
> in the
> SourceForge Curator Requests tracker. Please contact us if you want  
> to help out
> with ontology work in a particular area, or if you have any  
> comments or
> questions about what's going on.
>
> Ontology Development wiki:
> http://wiki.geneontology.org/index.php/Ontology_Development
>
> SourceForge Curator Requests tracker:
> https://sourceforge.net/tracker/?group_id=36855&atid=440764
>
> Midori & David
> on behalf of GO's ontology developers
> _______________________________________________
> Go mailing list
> Go at geneontology.org
> http://fafner.stanford.edu/mailman/listinfo/go


From cherry at stanford.edu  Tue Apr  1 15:38:59 2008
From: cherry at stanford.edu (Mike Cherry)
Date: Tue, 1 Apr 2008 15:38:59 -0700
Subject: [Go] [Evidence] ISS new documentation is up
In-Reply-To: <592A6460-FE36-40FB-B91C-E2ED2116C3D6@genome.stanford.edu>
References: <47F288F4.80206@informatics.jax.org>
	<592A6460-FE36-40FB-B91C-E2ED2116C3D6@genome.stanford.edu>
Message-ID: <9BFF1B26-91D7-49F8-9353-CE2EDEE20AF4@stanford.edu>

The filtering script has been updated in CVS.  So for alll newly  
committed files the new standard applies.  This includes the  
reprocessing of all gene association files on Saturday evenings.

With the now current version of the filtering script.  The WITH column  
for ISS and ISM has cardinality = 0.  For ISO and ISA the WITH column  
has cardinality = 1.

That means the requirement for something in the WITH column for ISS  
annotations has now been removed.

Please let me know if you find any problems with the new filtering  
script.

-Mike


On Apr 1, 2008, at 1:47 PM, Rama Balakrishnan wrote:
> The new documentation is LIVE now.
> http://www.geneontology.org/GO.evidence.shtml#iss
>
> Please note that formatting is not perfect and is not consistent with
> the rest of the page (I wanted to get this up as quickly as possible
> and did not have time to format the PMIDs etc etc).
>
> Rama
>
>
> On Apr 1, 2008, at 12:11 PM, Harold Drabkin wrote:
>
>> Hi All
>>
>> I was under the impression that the new E-codes would go "live" at  
>> the
>> GO on April 1; However, I notice that the older docs are there (ie,no
>> mention of ISO,ISM, ISA). Has this time schedule changed?
>>
>> Harold
>>
>> _______________________________________________
>> Evidence mailing list
>> Evidence at geneontology.org
>> http://fafner.stanford.edu/mailman/listinfo/evidence
>
> _______________________________________________
> Evidence mailing list
> Evidence at geneontology.org
> http://fafner.stanford.edu/mailman/listinfo/evidence


From cjm at fruitfly.org  Tue Apr  1 18:16:22 2008
From: cjm at fruitfly.org (Chris Mungall)
Date: Tue, 1 Apr 2008 18:16:22 -0700
Subject: [Go] AmiGO 1.5 is live
Message-ID: <96B2CD3C-0F2C-4CDD-8A1A-9B7B4AD22BC1@fruitfly.org>

http://amigo.geneontology.org

gasp in awe at the new regulates icons..

let us know what you think of the new front page - we can easily  
revert to the older more google-like one

well done the production team, the web presence working group, Amelia  
and Seth

We'll be sending a proper note out to gofriends shortly; stay tuned


From erika at cribi.unipd.it  Wed Apr  2 00:31:55 2008
From: erika at cribi.unipd.it (Erika Feltrin)
Date: Wed, 02 Apr 2008 09:31:55 +0200
Subject: [Go] AmiGO 1.5 is live
In-Reply-To: <96B2CD3C-0F2C-4CDD-8A1A-9B7B4AD22BC1@fruitfly.org>
References: <96B2CD3C-0F2C-4CDD-8A1A-9B7B4AD22BC1@fruitfly.org>
Message-ID: <1207121515.4195.40.camel@sophie.cribi.unipd.it>

Thank you for all this BIG job with AmiGO.

It is very nice and the regulates icons look great.


Il giorno mar, 01/04/2008 alle 18.16 -0700, Chris Mungall ha scritto:
> http://amigo.geneontology.org
> 
> gasp in awe at the new regulates icons..
> 
> let us know what you think of the new front page - we can easily  
> revert to the older more google-like one
> 
> well done the production team, the web presence working group, Amelia  
> and Seth
> 
> We'll be sending a proper note out to gofriends shortly; stay tuned
> 
> _______________________________________________
> Go mailing list
> Go at geneontology.org
> http://fafner.stanford.edu/mailman/listinfo/go


From erika at cribi.unipd.it  Wed Apr  2 00:47:17 2008
From: erika at cribi.unipd.it (Erika Feltrin)
Date: Wed, 02 Apr 2008 09:47:17 +0200
Subject: [Go] AmiGO 1.5 is live
In-Reply-To: <96B2CD3C-0F2C-4CDD-8A1A-9B7B4AD22BC1@fruitfly.org>
References: <96B2CD3C-0F2C-4CDD-8A1A-9B7B4AD22BC1@fruitfly.org>
Message-ID: <1207122437.4195.53.camel@sophie.cribi.unipd.it>

sorry! I sent an incomplete email!

Thank you for all this BIG job with AmiGO.
It is very nice and the regulates icons look great.
GOOSE and GO Slimmer are very useful tools and I am sure users will like
them a lot.

About the new front page. The new interface is very nice and I think it
is more informative since the AmiGO functions with a brief description
are all listed in the home page.  But I would prefer the older one with
the big central search window and the menu bar on the top. If a user do
not know what a function item does, he could just hovers the cursor over
it, and a tool tip with supplementary information regarding the item
being hovered over. In this case user has the necessary information in
one single web page instead of scroll down the page.
This is my thoughts.

Cheers
Erika




Il giorno mar, 01/04/2008 alle 18.16 -0700, Chris Mungall ha scritto:
> http://amigo.geneontology.org
> 
> gasp in awe at the new regulates icons..
> 
> let us know what you think of the new front page - we can easily  
> revert to the older more google-like one
> 
> well done the production team, the web presence working group, Amelia  
> and Seth
> 
> We'll be sending a proper note out to gofriends shortly; stay tuned
> 
> _______________________________________________
> Go mailing list
> Go at geneontology.org
> http://fafner.stanford.edu/mailman/listinfo/go


From jdeegan at ebi.ac.uk  Wed Apr  2 07:23:01 2008
From: jdeegan at ebi.ac.uk (Jennifer Deegan (nee Clark))
Date: Wed, 02 Apr 2008 15:23:01 +0100
Subject: [Go] Gene Symbols as GO synonyms
Message-ID: <47F396C5.4080708@ebi.ac.uk>

Hi,

A couple of GO terms currently contain a problematically large number of 
  gene symbols
as related synonyms.
The synonyms were imported into the OBO file during updates from Enzyme
Commission data.

The synonyms are a problem because they mess up the display in GO
browsers. For example:

http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?term=GO:0004714&session_id=6392amigo1207145654

They are also confusing for users as they resemble annotations, but are
only related synonyms.

To resolve this problem, on 16th April we are going to remove the list
of gene products as related synonyms from the following terms:

GO:0004714 (transmembrane receptor protein tyrosine kinase activity)
(201 gene symbols included as synonyms)

GO:0004715 (non-membrane spanning protein tyrosine kinase activity) (84
gene symbols included as synonyms)

If you have any objection to this removal please reply to Jennifer
Deegan and Emily Dimmer.

Thanks,

Jennifer and Emily.


-- 
Jennifer Deegan (nee Clark)
EMBL-European Bioinformatics Institute
Gene Ontology Consortium

From ma11 at gen.cam.ac.uk  Wed Apr  2 08:23:35 2008
From: ma11 at gen.cam.ac.uk (Michael Ashburner)
Date: Wed, 2 Apr 2008 08:23:35 -0700
Subject: [Go] AmiGO 1.5 is live
In-Reply-To: <96B2CD3C-0F2C-4CDD-8A1A-9B7B4AD22BC1@fruitfly.org>
References: <96B2CD3C-0F2C-4CDD-8A1A-9B7B4AD22BC1@fruitfly.org>
Message-ID: <C87F7C1B-F2E4-4373-9B82-FFF538297327@gen.cam.ac.uk>

Awsome !

But I find the new front page a bit big and clunky, I think I  
prerered the earlier version.

Michael
On 1 Apr 2008, at 18:16, Chris Mungall wrote:

> http://amigo.geneontology.org
>
> gasp in awe at the new regulates icons..
>
> let us know what you think of the new front page - we can easily
> revert to the older more google-like one
>
> well done the production team, the web presence working group, Amelia
> and Seth
>
> We'll be sending a proper note out to gofriends shortly; stay tuned
>
> _______________________________________________
> Go mailing list
> Go at geneontology.org
> http://fafner.stanford.edu/mailman/listinfo/go


From stacia at genome.stanford.edu  Wed Apr  2 08:45:54 2008
From: stacia at genome.stanford.edu (Stacia Engel)
Date: Wed, 2 Apr 2008 08:45:54 -0700
Subject: [Go] AmiGO 1.5 is live
In-Reply-To: <C87F7C1B-F2E4-4373-9B82-FFF538297327@gen.cam.ac.uk>
References: <96B2CD3C-0F2C-4CDD-8A1A-9B7B4AD22BC1@fruitfly.org>
	<C87F7C1B-F2E4-4373-9B82-FFF538297327@gen.cam.ac.uk>
Message-ID: <3305353D-44EF-40DF-B394-AC8F42569EDD@genome.stanford.edu>

i like the new homepage!

stacia

On Apr 2, 2008, at 8:23 AM, Michael Ashburner wrote:

> Awsome !
>
> But I find the new front page a bit big and clunky, I think I
> prerered the earlier version.
>
> Michael
> On 1 Apr 2008, at 18:16, Chris Mungall wrote:
>
>> http://amigo.geneontology.org
>>
>> gasp in awe at the new regulates icons..
>>
>> let us know what you think of the new front page - we can easily
>> revert to the older more google-like one
>>
>> well done the production team, the web presence working group, Amelia
>> and Seth
>>
>> We'll be sending a proper note out to gofriends shortly; stay tuned
>>
>> _______________________________________________
>> Go mailing list
>> Go at geneontology.org
>> http://fafner.stanford.edu/mailman/listinfo/go
>
> _______________________________________________
> Go mailing list
> Go at geneontology.org
> http://fafner.stanford.edu/mailman/listinfo/go


From keilbeck at genetics.utah.edu  Wed Apr  2 08:56:10 2008
From: keilbeck at genetics.utah.edu (Karen Eilbeck)
Date: Wed, 2 Apr 2008 09:56:10 -0600
Subject: [Go] AmiGO 1.5 is live
In-Reply-To: <96B2CD3C-0F2C-4CDD-8A1A-9B7B4AD22BC1@fruitfly.org>
Message-ID: <C41908BA.6482%keilbeck@genetics.utah.edu>

Thank you all so much.
The reloading of the page when I click on a node is much improved. The new icons are OK too.
:o)
--Karen


On 4/1/08 7:16 PM, "Chris Mungall" <cjm at fruitfly.org> wrote:

http://amigo.geneontology.org

gasp in awe at the new regulates icons..

let us know what you think of the new front page - we can easily
revert to the older more google-like one

well done the production team, the web presence working group, Amelia
and Seth

We'll be sending a proper note out to gofriends shortly; stay tuned

_______________________________________________
Go mailing list
Go at geneontology.org
http://fafner.stanford.edu/mailman/listinfo/go


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From kchris at genome.stanford.edu  Wed Apr  2 14:16:37 2008
From: kchris at genome.stanford.edu (Karen Christie)
Date: Wed, 2 Apr 2008 14:16:37 -0700 (PDT)
Subject: [Go] AmiGO 1.5 is live
In-Reply-To: <C87F7C1B-F2E4-4373-9B82-FFF538297327@gen.cam.ac.uk>
References: <96B2CD3C-0F2C-4CDD-8A1A-9B7B4AD22BC1@fruitfly.org>
	<C87F7C1B-F2E4-4373-9B82-FFF538297327@gen.cam.ac.uk>
Message-ID: <Pine.GSO.4.64.0804021407470.9811@fafner.Stanford.EDU>

my sentiments as well.

The regulates icons stuff was all discussed in advance and that's great, 
and thanks for all the work to make that work :)

... but the changes to the AmiGO front page, was this discussed and agreed 
upon? I know we're trying to not have so many people involved in each 
project, and I think that's fine. But if we're rolling out major changes 
in the look & functionality of our website pages without getting an OK 
from the consortium as a whole, maybe we've gone a bit too far the other 
way. Although you say that we could always roll it back to the previous 
version, it makes us look a bit as if we don't know what we're doing if we 
roll out a big change in our look and then switch it back a few days 
later.

my 2p,

-Karen

On Wed, 2 Apr 2008, Michael Ashburner wrote:

> Awsome !
>
> But I find the new front page a bit big and clunky, I think I
> prerered the earlier version.
>
> Michael
> On 1 Apr 2008, at 18:16, Chris Mungall wrote:
>
>> http://amigo.geneontology.org
>>
>> gasp in awe at the new regulates icons..
>>
>> let us know what you think of the new front page - we can easily
>> revert to the older more google-like one
>>
>> well done the production team, the web presence working group, Amelia
>> and Seth
>>
>> We'll be sending a proper note out to gofriends shortly; stay tuned
>>
>> _______________________________________________
>> Go mailing list
>> Go at geneontology.org
>> http://fafner.stanford.edu/mailman/listinfo/go
>
> _______________________________________________
> Go mailing list
> Go at geneontology.org
> http://fafner.stanford.edu/mailman/listinfo/go
>

From dbarrell at ebi.ac.uk  Wed Apr  2 09:03:23 2008
From: dbarrell at ebi.ac.uk (Daniel Barrell)
Date: Wed, 02 Apr 2008 17:03:23 +0100
Subject: [Go] [Gofriends] April 2008 GOA release
In-Reply-To: <42690FC8.8010409@ebi.ac.uk>
References: <42690FC8.8010409@ebi.ac.uk>
Message-ID: <47F3AE4B.5080204@ebi.ac.uk>

GOA releases: April 2008
============================

GOA (GO Annotation at EBI) is a project run by the European Bioinformatics
Institute that aims to provide assignments of gene products to the Gene
Ontology (GO) resource.

The data can be obtained via:

            EBI FTP: ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/

            EBI SRS: http://srs.ebi.ac.uk. Search GOA data library

            GO FTP: ftp://ftp.geneontology.org/pub/go/gene-associations/

            GO CVS: http://www.geneontology.org/GO.CVS.help.html

		(the last two will be updated overnight)

For further information read: http://www.ebi.ac.uk/GOA or contact
goa at ebi.ac.uk.

The GOA group has started to produce, in collaboration with the British 
Heart Foundation-funded Cardiovascular Gene Ontology Annotation 
Initiative, a BHF-UCL gene association file, which contains all GO 
annotations for 4,027 human proteins implicated in cardiovascular 
development or disease.  The BHF-UCL file is a sub-set of the UniProt 
gene association file, and will provide the cardiovascular community 
with a discrete set of relevant GO annotations. This file will be 
updated by GOA monthly and can be downloaded from:
ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/bhf-ucl/gene_association.goa_bhf-ucl.gz

The University College London based Gene Ontology Annotation Initiative 
aims to prioritise the manual annotation of genes associated with the 
cardiovascular system, for further information on this project, please see:
http://www.ucl.ac.uk/medicine/cardiovascular-genetics/geneontology.html
http://wiki.geneontology.org/index.php/Cardiovascular_Gene_Page

Regards

The UniProt GOA Team









_______________________________________________
Gofriends mailing list
Gofriends at geneontology.org
http://fafner.stanford.edu/mailman/listinfo/gofriends

From jblake at informatics.jax.org  Wed Apr  2 16:06:51 2008
From: jblake at informatics.jax.org (Judith Blake)
Date: Wed, 02 Apr 2008 19:06:51 -0400
Subject: [Go] Gene Symbols as GO synonyms
In-Reply-To: <47F396C5.4080708@ebi.ac.uk>
References: <47F396C5.4080708@ebi.ac.uk>
Message-ID: <47F4118B.5080607@informatics.jax.org>

I agree with your proposal.

Would you not remove gene symbols as synonyms from all terms?

Judy

Jennifer Deegan (nee Clark) wrote:
> Hi,
>
> A couple of GO terms currently contain a problematically large number of 
>   gene symbols
> as related synonyms.
> The synonyms were imported into the OBO file during updates from Enzyme
> Commission data.
>
> The synonyms are a problem because they mess up the display in GO
> browsers. For example:
>
> http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?term=GO:0004714&session_id=6392amigo1207145654
>
> They are also confusing for users as they resemble annotations, but are
> only related synonyms.
>
> To resolve this problem, on 16th April we are going to remove the list
> of gene products as related synonyms from the following terms:
>
> GO:0004714 (transmembrane receptor protein tyrosine kinase activity)
> (201 gene symbols included as synonyms)
>
> GO:0004715 (non-membrane spanning protein tyrosine kinase activity) (84
> gene symbols included as synonyms)
>
> If you have any objection to this removal please reply to Jennifer
> Deegan and Emily Dimmer.
>
> Thanks,
>
> Jennifer and Emily.
>
>
>   



From jimhu at tamu.edu  Wed Apr  2 16:11:24 2008
From: jimhu at tamu.edu (Jim Hu)
Date: Wed, 2 Apr 2008 18:11:24 -0500
Subject: [Go] Gene Symbols as GO synonyms
In-Reply-To: <47F4118B.5080607@informatics.jax.org>
References: <47F396C5.4080708@ebi.ac.uk> <47F4118B.5080607@informatics.jax.org>
Message-ID: <9352A705-0DBE-41BD-B5D4-1FB0942D7854@tamu.edu>

I agree with Judy that removing them from all terms is a good idea.   
If us microbiologists ever get our act together and start getting all  
the genes from metagenomics, you'll be glad you did! ;)

Jim


On Apr 2, 2008, at 6:06 PM, Judith Blake wrote:

> I agree with your proposal.
>
> Would you not remove gene symbols as synonyms from all terms?
>
> Judy
>
> Jennifer Deegan (nee Clark) wrote:
>> Hi,
>>
>> A couple of GO terms currently contain a problematically large  
>> number of
>>  gene symbols
>> as related synonyms.
>> The synonyms were imported into the OBO file during updates from  
>> Enzyme
>> Commission data.
>>
>> The synonyms are a problem because they mess up the display in GO
>> browsers. For example:
>>
>> http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?term=GO:0004714&session_id=6392amigo1207145654
>>
>> They are also confusing for users as they resemble annotations, but  
>> are
>> only related synonyms.
>>
>> To resolve this problem, on 16th April we are going to remove the  
>> list
>> of gene products as related synonyms from the following terms:
>>
>> GO:0004714 (transmembrane receptor protein tyrosine kinase activity)
>> (201 gene symbols included as synonyms)
>>
>> GO:0004715 (non-membrane spanning protein tyrosine kinase activity)  
>> (84
>> gene symbols included as synonyms)
>>
>> If you have any objection to this removal please reply to Jennifer
>> Deegan and Emily Dimmer.
>>
>> Thanks,
>>
>> Jennifer and Emily.
>>
>>
>>
>
>
> _______________________________________________
> Go mailing list
> Go at geneontology.org
> http://fafner.stanford.edu/mailman/listinfo/go

=====================================
Jim Hu
Associate Professor
Dept. of Biochemistry and Biophysics
2128 TAMU
Texas A&M Univ.
College Station, TX 77843-2128
979-862-4054


-------------- next part --------------
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From jblake at informatics.jax.org  Wed Apr  2 16:27:32 2008
From: jblake at informatics.jax.org (Judith Blake)
Date: Wed, 02 Apr 2008 19:27:32 -0400
Subject: [Go] Gene Symbols as GO synonyms
In-Reply-To: <9352A705-0DBE-41BD-B5D4-1FB0942D7854@tamu.edu>
References: <47F396C5.4080708@ebi.ac.uk> <47F4118B.5080607@informatics.jax.org>
	<9352A705-0DBE-41BD-B5D4-1FB0942D7854@tamu.edu>
Message-ID: <47F41664.1090405@informatics.jax.org>

not the least because they aren't synonyms....

judy

Jim Hu wrote:
> I agree with Judy that removing them from all terms is a good idea. 
>  If us microbiologists ever get our act together and start getting all 
> the genes from metagenomics, you'll be glad you did! ;)
>
> Jim
>
>
> On Apr 2, 2008, at 6:06 PM, Judith Blake wrote:
>> I agree with your proposal.
>>
>> Would you not remove gene symbols as synonyms from all terms?
>>
>> Judy
>>
>> Jennifer Deegan (nee Clark) wrote:
>>> Hi,
>>>
>>> A couple of GO terms currently contain a problematically large 
>>> number of
>>>  gene symbols
>>> as related synonyms.
>>> The synonyms were imported into the OBO file during updates from Enzyme
>>> Commission data.
>>>
>>> The synonyms are a problem because they mess up the display in GO
>>> browsers. For example:
>>>
>>> http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?term=GO:0004714&session_id=6392amigo1207145654 
>>> <http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?term=GO:0004714&session_id=6392amigo1207145654>
>>>
>>> They are also confusing for users as they resemble annotations, but are
>>> only related synonyms.
>>>
>>> To resolve this problem, on 16th April we are going to remove the list
>>> of gene products as related synonyms from the following terms:
>>>
>>> GO:0004714 (transmembrane receptor protein tyrosine kinase activity)
>>> (201 gene symbols included as synonyms)
>>>
>>> GO:0004715 (non-membrane spanning protein tyrosine kinase activity) (84
>>> gene symbols included as synonyms)
>>>
>>> If you have any objection to this removal please reply to Jennifer
>>> Deegan and Emily Dimmer.
>>>
>>> Thanks,
>>>
>>> Jennifer and Emily.
>>>
>>>
>>>
>>
>>
>> _______________________________________________
>> Go mailing list
>> Go at geneontology.org <mailto:Go at geneontology.org>
>> http://fafner.stanford.edu/mailman/listinfo/go
>
> =====================================
>
> Jim Hu
>
> Associate Professor
>
> Dept. of Biochemistry and Biophysics
>
> 2128 TAMU
>
> Texas A&M Univ.
>
> College Station, TX 77843-2128
>
> 979-862-4054
>
>
>



From cjm at fruitfly.org  Wed Apr  2 16:35:01 2008
From: cjm at fruitfly.org (Chris Mungall)
Date: Wed, 2 Apr 2008 16:35:01 -0700
Subject: [Go] AmiGO 1.5 is live
In-Reply-To: <Pine.GSO.4.64.0804021407470.9811@fafner.Stanford.EDU>
References: <96B2CD3C-0F2C-4CDD-8A1A-9B7B4AD22BC1@fruitfly.org>
	<C87F7C1B-F2E4-4373-9B82-FFF538297327@gen.cam.ac.uk>
	<Pine.GSO.4.64.0804021407470.9811@fafner.Stanford.EDU>
Message-ID: <048F3E6E-4968-4896-84AA-B4FC83BC1596@fruitfly.org>


Hi Karen

I agree, the new front page going live was a mistake due to me  
hurrying the release out. It shouldn't have happened.

On Apr 2, 2008, at 2:16 PM, Karen Christie wrote:

> my sentiments as well.
>
> The regulates icons stuff was all discussed in advance and that's  
> great, and thanks for all the work to make that work :)
>
> ... but the changes to the AmiGO front page, was this discussed and  
> agreed upon? I know we're trying to not have so many people  
> involved in each project, and I think that's fine. But if we're  
> rolling out major changes in the look & functionality of our  
> website pages without getting an OK from the consortium as a whole,  
> maybe we've gone a bit too far the other way. Although you say that  
> we could always roll it back to the previous version, it makes us  
> look a bit as if we don't know what we're doing if we roll out a  
> big change in our look and then switch it back a few days later.
>
> my 2p,
>
> -Karen
>
> On Wed, 2 Apr 2008, Michael Ashburner wrote:
>
>> Awsome !
>>
>> But I find the new front page a bit big and clunky, I think I
>> prerered the earlier version.
>>
>> Michael
>> On 1 Apr 2008, at 18:16, Chris Mungall wrote:
>>
>>> http://amigo.geneontology.org
>>>
>>> gasp in awe at the new regulates icons..
>>>
>>> let us know what you think of the new front page - we can easily
>>> revert to the older more google-like one
>>>
>>> well done the production team, the web presence working group,  
>>> Amelia
>>> and Seth
>>>
>>> We'll be sending a proper note out to gofriends shortly; stay tuned
>>>
>>> _______________________________________________
>>> Go mailing list
>>> Go at geneontology.org
>>> http://fafner.stanford.edu/mailman/listinfo/go
>>
>> _______________________________________________
>> Go mailing list
>> Go at geneontology.org
>> http://fafner.stanford.edu/mailman/listinfo/go
>>
>


From jdeegan at ebi.ac.uk  Thu Apr  3 02:41:25 2008
From: jdeegan at ebi.ac.uk (Jennifer Deegan (nee Clark))
Date: Thu, 03 Apr 2008 10:41:25 +0100
Subject: [Go] Gene Symbols as GO synonyms
In-Reply-To: <47F41664.1090405@informatics.jax.org>
References: <47F396C5.4080708@ebi.ac.uk> <47F4118B.5080607@informatics.jax.org>
	<9352A705-0DBE-41BD-B5D4-1FB0942D7854@tamu.edu>
	<47F41664.1090405@informatics.jax.org>
Message-ID: <47F4A645.4000207@ebi.ac.uk>

Hi Judy,

We did think about this, but I remember that the group who work on p53 
were very keen that a term covering an activity of this gene product 
should carry a synonym 'p53' to help them find the term. I am reluctant 
to remove all gene symbols as synonyms because of that, but thought I 
would just tidy up these two problematic terms. We could certainly 
consider removing all gene symbol synonyms in the long term, but it 
seems to me that the effort required to track them all down and discuss 
individually whether they are required might not be worthwhile, since we 
have other time-consuming projects that are a higher priority. Would you 
agree?

Thanks for thinking about it.

Jen


Judith Blake wrote:

> not the least because they aren't synonyms....
> 
> judy
> 
> Jim Hu wrote:
> 
>> I agree with Judy that removing them from all terms is a good idea. 
>>  If us microbiologists ever get our act together and start getting all 
>> the genes from metagenomics, you'll be glad you did! ;)
>>
>> Jim
>>
>>
>> On Apr 2, 2008, at 6:06 PM, Judith Blake wrote:
>>
>>> I agree with your proposal.
>>>
>>> Would you not remove gene symbols as synonyms from all terms?
>>>
>>> Judy
>>>
>>> Jennifer Deegan (nee Clark) wrote:
>>>
>>>> Hi,
>>>>
>>>> A couple of GO terms currently contain a problematically large 
>>>> number of
>>>>  gene symbols
>>>> as related synonyms.
>>>> The synonyms were imported into the OBO file during updates from Enzyme
>>>> Commission data.
>>>>
>>>> The synonyms are a problem because they mess up the display in GO
>>>> browsers. For example:
>>>>
>>>> http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?term=GO:0004714&session_id=6392amigo1207145654 
>>>> <http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?term=GO:0004714&session_id=6392amigo1207145654> 
>>>>
>>>>
>>>> They are also confusing for users as they resemble annotations, but are
>>>> only related synonyms.
>>>>
>>>> To resolve this problem, on 16th April we are going to remove the list
>>>> of gene products as related synonyms from the following terms:
>>>>
>>>> GO:0004714 (transmembrane receptor protein tyrosine kinase activity)
>>>> (201 gene symbols included as synonyms)
>>>>
>>>> GO:0004715 (non-membrane spanning protein tyrosine kinase activity) (84
>>>> gene symbols included as synonyms)
>>>>
>>>> If you have any objection to this removal please reply to Jennifer
>>>> Deegan and Emily Dimmer.
>>>>
>>>> Thanks,
>>>>
>>>> Jennifer and Emily.
>>>>
>>>>
>>>>
>>>
>>>
>>> _______________________________________________
>>> Go mailing list
>>> Go at geneontology.org <mailto:Go at geneontology.org>
>>> http://fafner.stanford.edu/mailman/listinfo/go
>>
>>
>> =====================================
>>
>> Jim Hu
>>
>> Associate Professor
>>
>> Dept. of Biochemistry and Biophysics
>>
>> 2128 TAMU
>>
>> Texas A&M Univ.
>>
>> College Station, TX 77843-2128
>>
>> 979-862-4054
>>
>>
>>
> 

-- 
Jennifer Deegan (nee Clark)
EMBL-European Bioinformatics Institute
Gene Ontology Consortium

From jblake at informatics.jax.org  Thu Apr  3 03:46:50 2008
From: jblake at informatics.jax.org (Judith Blake)
Date: Thu, 03 Apr 2008 06:46:50 -0400
Subject: [Go] Gene Symbols as GO synonyms
In-Reply-To: <47F4A645.4000207@ebi.ac.uk>
References: <47F396C5.4080708@ebi.ac.uk> <47F4118B.5080607@informatics.jax.org>
	<9352A705-0DBE-41BD-B5D4-1FB0942D7854@tamu.edu>
	<47F41664.1090405@informatics.jax.org> <47F4A645.4000207@ebi.ac.uk>
Message-ID: <47F4B59A.9080308@informatics.jax.org>

Hi Jen,

When I search GO terms for 'p53', this does not come back as a synonym, 
although synonyms with the string 'p53' as part of the long series of 
strings as a synonym do come back.  So I don't think that argument holds 
anymore.  I agree that grinding through looking for synonyms that are 
gene symbols is not a productive use of time, but such synonyms, I 
think, should be removed as a matter of course while working on the 
ontology in general as they are found.  I do not see, if 'p53' is not an 
issue, where anything else would be an issue.

Does anyone object to having gene symbols routinely removed as found as 
synonyms?  Certainly the ontology editors can bring such synonyms 
forward if they think there might be an issue. what do you think Jen?

Judy


Jennifer Deegan (nee Clark) wrote:
> Hi Judy,
>
> We did think about this, but I remember that the group who work on p53 
> were very keen that a term covering an activity of this gene product 
> should carry a synonym 'p53' to help them find the term. I am 
> reluctant to remove all gene symbols as synonyms because of that, but 
> thought I would just tidy up these two problematic terms. We could 
> certainly consider removing all gene symbol synonyms in the long term, 
> but it seems to me that the effort required to track them all down and 
> discuss individually whether they are required might not be 
> worthwhile, since we have other time-consuming projects that are a 
> higher priority. Would you agree?
>
> Thanks for thinking about it.
>
> Jen
>
>
> Judith Blake wrote:
>
>> not the least because they aren't synonyms....
>>
>> judy
>>
>> Jim Hu wrote:
>>
>>> I agree with Judy that removing them from all terms is a good idea. 
>>>  If us microbiologists ever get our act together and start getting 
>>> all the genes from metagenomics, you'll be glad you did! ;)
>>>
>>> Jim
>>>
>>>
>>> On Apr 2, 2008, at 6:06 PM, Judith Blake wrote:
>>>
>>>> I agree with your proposal.
>>>>
>>>> Would you not remove gene symbols as synonyms from all terms?
>>>>
>>>> Judy
>>>>
>>>> Jennifer Deegan (nee Clark) wrote:
>>>>
>>>>> Hi,
>>>>>
>>>>> A couple of GO terms currently contain a problematically large 
>>>>> number of
>>>>>  gene symbols
>>>>> as related synonyms.
>>>>> The synonyms were imported into the OBO file during updates from 
>>>>> Enzyme
>>>>> Commission data.
>>>>>
>>>>> The synonyms are a problem because they mess up the display in GO
>>>>> browsers. For example:
>>>>>
>>>>> http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?term=GO:0004714&session_id=6392amigo1207145654 
>>>>> <http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?term=GO:0004714&session_id=6392amigo1207145654> 
>>>>>
>>>>>
>>>>> They are also confusing for users as they resemble annotations, 
>>>>> but are
>>>>> only related synonyms.
>>>>>
>>>>> To resolve this problem, on 16th April we are going to remove the 
>>>>> list
>>>>> of gene products as related synonyms from the following terms:
>>>>>
>>>>> GO:0004714 (transmembrane receptor protein tyrosine kinase activity)
>>>>> (201 gene symbols included as synonyms)
>>>>>
>>>>> GO:0004715 (non-membrane spanning protein tyrosine kinase 
>>>>> activity) (84
>>>>> gene symbols included as synonyms)
>>>>>
>>>>> If you have any objection to this removal please reply to Jennifer
>>>>> Deegan and Emily Dimmer.
>>>>>
>>>>> Thanks,
>>>>>
>>>>> Jennifer and Emily.
>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> Go mailing list
>>>> Go at geneontology.org <mailto:Go at geneontology.org>
>>>> http://fafner.stanford.edu/mailman/listinfo/go
>>>
>>>
>>> =====================================
>>>
>>> Jim Hu
>>>
>>> Associate Professor
>>>
>>> Dept. of Biochemistry and Biophysics
>>>
>>> 2128 TAMU
>>>
>>> Texas A&M Univ.
>>>
>>> College Station, TX 77843-2128
>>>
>>> 979-862-4054
>>>
>>>
>>>
>>
>



From jdeegan at ebi.ac.uk  Thu Apr  3 03:52:41 2008
From: jdeegan at ebi.ac.uk (Jennifer Deegan (nee Clark))
Date: Thu, 03 Apr 2008 11:52:41 +0100
Subject: [Go] Gene Symbols as GO synonyms
In-Reply-To: <47F4B59A.9080308@informatics.jax.org>
References: <47F396C5.4080708@ebi.ac.uk> <47F4118B.5080607@informatics.jax.org>
	<9352A705-0DBE-41BD-B5D4-1FB0942D7854@tamu.edu>
	<47F41664.1090405@informatics.jax.org> <47F4A645.4000207@ebi.ac.uk>
	<47F4B59A.9080308@informatics.jax.org>
Message-ID: <47F4B6F9.4010308@ebi.ac.uk>

Hi Judy,

It sounds fine to me, but I'd be interested to wait for a little while 
and hear if there are others who feel that these synonyms are useful.

Thanks,

Jen



Judith Blake wrote:

> Hi Jen,
> 
> When I search GO terms for 'p53', this does not come back as a synonym, 
> although synonyms with the string 'p53' as part of the long series of 
> strings as a synonym do come back.  So I don't think that argument holds 
> anymore.  I agree that grinding through looking for synonyms that are 
> gene symbols is not a productive use of time, but such synonyms, I 
> think, should be removed as a matter of course while working on the 
> ontology in general as they are found.  I do not see, if 'p53' is not an 
> issue, where anything else would be an issue.
> 
> Does anyone object to having gene symbols routinely removed as found as 
> synonyms?  Certainly the ontology editors can bring such synonyms 
> forward if they think there might be an issue. what do you think Jen?
> 
> Judy
> 
> 
> Jennifer Deegan (nee Clark) wrote:
> 
>> Hi Judy,
>>
>> We did think about this, but I remember that the group who work on p53 
>> were very keen that a term covering an activity of this gene product 
>> should carry a synonym 'p53' to help them find the term. I am 
>> reluctant to remove all gene symbols as synonyms because of that, but 
>> thought I would just tidy up these two problematic terms. We could 
>> certainly consider removing all gene symbol synonyms in the long term, 
>> but it seems to me that the effort required to track them all down and 
>> discuss individually whether they are required might not be 
>> worthwhile, since we have other time-consuming projects that are a 
>> higher priority. Would you agree?
>>
>> Thanks for thinking about it.
>>
>> Jen
>>
>>
>> Judith Blake wrote:
>>
>>> not the least because they aren't synonyms....
>>>
>>> judy
>>>
>>> Jim Hu wrote:
>>>
>>>> I agree with Judy that removing them from all terms is a good idea. 
>>>>  If us microbiologists ever get our act together and start getting 
>>>> all the genes from metagenomics, you'll be glad you did! ;)
>>>>
>>>> Jim
>>>>
>>>>
>>>> On Apr 2, 2008, at 6:06 PM, Judith Blake wrote:
>>>>
>>>>> I agree with your proposal.
>>>>>
>>>>> Would you not remove gene symbols as synonyms from all terms?
>>>>>
>>>>> Judy
>>>>>
>>>>> Jennifer Deegan (nee Clark) wrote:
>>>>>
>>>>>> Hi,
>>>>>>
>>>>>> A couple of GO terms currently contain a problematically large 
>>>>>> number of
>>>>>>  gene symbols
>>>>>> as related synonyms.
>>>>>> The synonyms were imported into the OBO file during updates from 
>>>>>> Enzyme
>>>>>> Commission data.
>>>>>>
>>>>>> The synonyms are a problem because they mess up the display in GO
>>>>>> browsers. For example:
>>>>>>
>>>>>> http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?term=GO:0004714&session_id=6392amigo1207145654 
>>>>>> <http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?term=GO:0004714&session_id=6392amigo1207145654> 
>>>>>>
>>>>>>
>>>>>> They are also confusing for users as they resemble annotations, 
>>>>>> but are
>>>>>> only related synonyms.
>>>>>>
>>>>>> To resolve this problem, on 16th April we are going to remove the 
>>>>>> list
>>>>>> of gene products as related synonyms from the following terms:
>>>>>>
>>>>>> GO:0004714 (transmembrane receptor protein tyrosine kinase activity)
>>>>>> (201 gene symbols included as synonyms)
>>>>>>
>>>>>> GO:0004715 (non-membrane spanning protein tyrosine kinase 
>>>>>> activity) (84
>>>>>> gene symbols included as synonyms)
>>>>>>
>>>>>> If you have any objection to this removal please reply to Jennifer
>>>>>> Deegan and Emily Dimmer.
>>>>>>
>>>>>> Thanks,
>>>>>>
>>>>>> Jennifer and Emily.
>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Go mailing list
>>>>> Go at geneontology.org <mailto:Go at geneontology.org>
>>>>> http://fafner.stanford.edu/mailman/listinfo/go
>>>>
>>>>
>>>>
>>>> =====================================
>>>>
>>>> Jim Hu
>>>>
>>>> Associate Professor
>>>>
>>>> Dept. of Biochemistry and Biophysics
>>>>
>>>> 2128 TAMU
>>>>
>>>> Texas A&M Univ.
>>>>
>>>> College Station, TX 77843-2128
>>>>
>>>> 979-862-4054
>>>>
>>>>
>>>>
>>>
>>
> 

-- 
Jennifer Deegan (nee Clark)
EMBL-European Bioinformatics Institute
Gene Ontology Consortium

From r.lovering at ucl.ac.uk  Thu Apr  3 04:29:01 2008
From: r.lovering at ucl.ac.uk (Ruth Lovering)
Date: Thu, 3 Apr 2008 12:29:01 +0100
Subject: [Go] Gene Symbols as GO synonyms
In-Reply-To: <47F4B59A.9080308@informatics.jax.org>
References: <47F396C5.4080708@ebi.ac.uk> <47F4118B.5080607@informatics.jax.org>
	<9352A705-0DBE-41BD-B5D4-1FB0942D7854@tamu.edu>
	<47F41664.1090405@informatics.jax.org> <47F4A645.4000207@ebi.ac.uk>
	<47F4B59A.9080308@informatics.jax.org>
Message-ID: <A96E7BCC-3110-4114-AF98-0B5D006416BC@ucl.ac.uk>

Hi Jen

when I first looked at GO I found it rather disconcerting to see gene  
symbols listed as synonyms for the GO term, because I didn't  
appreciate the [related] and [exact] concepts.

As the annotation of genes improves I do think that the use of  
synonyms becomes redundant, as the option of looking at what genes are  
associated with the term and provides the same information as the  
synonym.

I guess that the ideal approach would be to make sure that any deleted  
gene symbol synonyms are annotated with that GO term (if only - sorry  
to say this - with a TAS statement). And that in future editors,  
rather than add the gene symbol as a synonym, make this annotation  
directly to the gene itself.  (sorry bit radical)

If this was achieved then people could find terms they are interested  
in by looking at the annotation of p53, and would see other  
potentially relevant terms too.

Ruth


From jane at ebi.ac.uk  Thu Apr  3 06:07:54 2008
From: jane at ebi.ac.uk (Jane Lomax)
Date: Thu, 3 Apr 2008 14:07:54 +0100 (BST)
Subject: [Go] Gene Symbols as GO synonyms
In-Reply-To: <47F4B59A.9080308@informatics.jax.org>
References: <47F396C5.4080708@ebi.ac.uk> <47F4118B.5080607@informatics.jax.org>
	<9352A705-0DBE-41BD-B5D4-1FB0942D7854@tamu.edu>
	<47F41664.1090405@informatics.jax.org>
	<47F4A645.4000207@ebi.ac.uk> <47F4B59A.9080308@informatics.jax.org>
Message-ID: <Pine.LNX.4.62.0804031406270.31293@puffin.ebi.ac.uk>

Hi Judy - the gene symbol synonyms can sometimes be very useful for the 
purposes of mappings, especially for things like enzymes where some groups 
use the gene symbol in their vocabulary term name (this has been the case 
for the IMG and FIGS mappings recently). So I'd rather not see them 
removed completely.

However I do agree that seeing them can be very confusing for users - I 
wonder whether we could agree to suppress RELATED synonyms in the GO interfaces? 
Maybe only show them when they match a search?

jane

  On Thu, 3 Apr 2008, Judith Blake wrote:

> Hi Jen,
>
> When I search GO terms for 'p53', this does not come back as a synonym,
> although synonyms with the string 'p53' as part of the long series of
> strings as a synonym do come back.  So I don't think that argument holds
> anymore.  I agree that grinding through looking for synonyms that are
> gene symbols is not a productive use of time, but such synonyms, I
> think, should be removed as a matter of course while working on the
> ontology in general as they are found.  I do not see, if 'p53' is not an
> issue, where anything else would be an issue.
>
> Does anyone object to having gene symbols routinely removed as found as
> synonyms?  Certainly the ontology editors can bring such synonyms
> forward if they think there might be an issue. what do you think Jen?
>
> Judy
>
>
> Jennifer Deegan (nee Clark) wrote:
>> Hi Judy,
>>
>> We did think about this, but I remember that the group who work on p53
>> were very keen that a term covering an activity of this gene product
>> should carry a synonym 'p53' to help them find the term. I am
>> reluctant to remove all gene symbols as synonyms because of that, but
>> thought I would just tidy up these two problematic terms. We could
>> certainly consider removing all gene symbol synonyms in the long term,
>> but it seems to me that the effort required to track them all down and
>> discuss individually whether they are required might not be
>> worthwhile, since we have other time-consuming projects that are a
>> higher priority. Would you agree?
>>
>> Thanks for thinking about it.
>>
>> Jen
>>
>>
>> Judith Blake wrote:
>>
>>> not the least because they aren't synonyms....
>>>
>>> judy
>>>
>>> Jim Hu wrote:
>>>
>>>> I agree with Judy that removing them from all terms is a good idea.
>>>>  If us microbiologists ever get our act together and start getting
>>>> all the genes from metagenomics, you'll be glad you did! ;)
>>>>
>>>> Jim
>>>>
>>>>
>>>> On Apr 2, 2008, at 6:06 PM, Judith Blake wrote:
>>>>
>>>>> I agree with your proposal.
>>>>>
>>>>> Would you not remove gene symbols as synonyms from all terms?
>>>>>
>>>>> Judy
>>>>>
>>>>> Jennifer Deegan (nee Clark) wrote:
>>>>>
>>>>>> Hi,
>>>>>>
>>>>>> A couple of GO terms currently contain a problematically large
>>>>>> number of
>>>>>>  gene symbols
>>>>>> as related synonyms.
>>>>>> The synonyms were imported into the OBO file during updates from
>>>>>> Enzyme
>>>>>> Commission data.
>>>>>>
>>>>>> The synonyms are a problem because they mess up the display in GO
>>>>>> browsers. For example:
>>>>>>
>>>>>> http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?term=GO:0004714&session_id=6392amigo1207145654
>>>>>> <http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?term=GO:0004714&session_id=6392amigo1207145654>
>>>>>>
>>>>>>
>>>>>> They are also confusing for users as they resemble annotations,
>>>>>> but are
>>>>>> only related synonyms.
>>>>>>
>>>>>> To resolve this problem, on 16th April we are going to remove the
>>>>>> list
>>>>>> of gene products as related synonyms from the following terms:
>>>>>>
>>>>>> GO:0004714 (transmembrane receptor protein tyrosine kinase activity)
>>>>>> (201 gene symbols included as synonyms)
>>>>>>
>>>>>> GO:0004715 (non-membrane spanning protein tyrosine kinase
>>>>>> activity) (84
>>>>>> gene symbols included as synonyms)
>>>>>>
>>>>>> If you have any objection to this removal please reply to Jennifer
>>>>>> Deegan and Emily Dimmer.
>>>>>>
>>>>>> Thanks,
>>>>>>
>>>>>> Jennifer and Emily.
>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Go mailing list
>>>>> Go at geneontology.org <mailto:Go at geneontology.org>
>>>>> http://fafner.stanford.edu/mailman/listinfo/go
>>>>
>>>>
>>>> =====================================
>>>>
>>>> Jim Hu
>>>>
>>>> Associate Professor
>>>>
>>>> Dept. of Biochemistry and Biophysics
>>>>
>>>> 2128 TAMU
>>>>
>>>> Texas A&M Univ.
>>>>
>>>> College Station, TX 77843-2128
>>>>
>>>> 979-862-4054
>>>>
>>>>
>>>>
>>>
>>
>
>
> _______________________________________________
> Go mailing list
> Go at geneontology.org
> http://fafner.stanford.edu/mailman/listinfo/go
>

Dr Jane Lomax
GO Editorial Office
EMBL-EBI
Wellcome Trust Genome Campus
Hinxton
Cambridgeshire, UK
CB10 1SD

p: +44 1223 492516
f: +44 1223 494468

From midori at ebi.ac.uk  Thu Apr  3 07:28:03 2008
From: midori at ebi.ac.uk (Midori Harris)
Date: Thu, 3 Apr 2008 15:28:03 +0100 (BST)
Subject: [Go] secretory pathway (SF 1912842)
In-Reply-To: <Pine.LNX.4.64.0803251203210.17076@pigeon.ebi.ac.uk>
References: <Pine.LNX.4.64.0803251203210.17076@pigeon.ebi.ac.uk>
Message-ID: <Pine.LNX.4.64.0804031526490.2077@pigeon.ebi.ac.uk>

A few responses have come in via email and in the SF item. Most favor, or 
at least accept, making GO:0045045 obsolete. Official alert email on the 
way as soon as I get annotation counts.

m

On Tue, 25 Mar 2008, Midori Harris wrote:

> Dear GO,
>
> Questions have arisen about the process term 'secretory pathway'
> (GO:0045045). At first the aim was to improve the definition, but
> upon further discussion we're now leaningtowards making the term obsolete.
> Could people take a look at the SourceForge item and let us know if
> there's a case for keeping the term? If no arguments in its favor emerge,
> I'll send the formal obsoletion warning email in a few days.
>
> https://sourceforge.net/tracker/index.php?func=detail&aid=1912842&group_id=36855&atid=440764
>
> Thanks,
> Midori
> _______________________________________________
> Go mailing list
> Go at geneontology.org
> http://fafner.stanford.edu/mailman/listinfo/go
>

From ma11 at gen.cam.ac.uk  Thu Apr  3 07:38:16 2008
From: ma11 at gen.cam.ac.uk (Michael Ashburner)
Date: Thu, 3 Apr 2008 07:38:16 -0700
Subject: [Go] Gene Symbols as GO synonyms
In-Reply-To: <Pine.LNX.4.62.0804031406270.31293@puffin.ebi.ac.uk>
References: <47F396C5.4080708@ebi.ac.uk> <47F4118B.5080607@informatics.jax.org>
	<9352A705-0DBE-41BD-B5D4-1FB0942D7854@tamu.edu>
	<47F41664.1090405@informatics.jax.org> <47F4A645.4000207@ebi.ac.uk>
	<47F4B59A.9080308@informatics.jax.org>
	<Pine.LNX.4.62.0804031406270.31293@puffin.ebi.ac.uk>
Message-ID: <6E7F3A24-F79C-497F-B0FD-02ECA3BC997B@gen.cam.ac.uk>

That sounds a good medium solution Jane.

Michael

On 3 Apr 2008, at 06:07, Jane Lomax wrote:

> Hi Judy - the gene symbol synonyms can sometimes be very useful for  
> the
> purposes of mappings, especially for things like enzymes where some  
> groups
> use the gene symbol in their vocabulary term name (this has been  
> the case
> for the IMG and FIGS mappings recently). So I'd rather not see them
> removed completely.
>
> However I do agree that seeing them can be very confusing for users  
> - I
> wonder whether we could agree to suppress RELATED synonyms in the  
> GO interfaces?
> Maybe only show them when they match a search?
>
> jane
>
>   On Thu, 3 Apr 2008, Judith Blake wrote:
>
>> Hi Jen,
>>
>> When I search GO terms for 'p53', this does not come back as a  
>> synonym,
>> although synonyms with the string 'p53' as part of the long series of
>> strings as a synonym do come back.  So I don't think that argument  
>> holds
>> anymore.  I agree that grinding through looking for synonyms that are
>> gene symbols is not a productive use of time, but such synonyms, I
>> think, should be removed as a matter of course while working on the
>> ontology in general as they are found.  I do not see, if 'p53' is  
>> not an
>> issue, where anything else would be an issue.
>>
>> Does anyone object to having gene symbols routinely removed as  
>> found as
>> synonyms?  Certainly the ontology editors can bring such synonyms
>> forward if they think there might be an issue. what do you think Jen?
>>
>> Judy
>>
>>
>> Jennifer Deegan (nee Clark) wrote:
>>> Hi Judy,
>>>
>>> We did think about this, but I remember that the group who work  
>>> on p53
>>> were very keen that a term covering an activity of this gene product
>>> should carry a synonym 'p53' to help them find the term. I am
>>> reluctant to remove all gene symbols as synonyms because of that,  
>>> but
>>> thought I would just tidy up these two problematic terms. We could
>>> certainly consider removing all gene symbol synonyms in the long  
>>> term,
>>> but it seems to me that the effort required to track them all  
>>> down and
>>> discuss individually whether they are required might not be
>>> worthwhile, since we have other time-consuming projects that are a
>>> higher priority. Would you agree?
>>>
>>> Thanks for thinking about it.
>>>
>>> Jen
>>>
>>>
>>> Judith Blake wrote:
>>>
>>>> not the least because they aren't synonyms....
>>>>
>>>> judy
>>>>
>>>> Jim Hu wrote:
>>>>
>>>>> I agree with Judy that removing them from all terms is a good  
>>>>> idea.
>>>>>  If us microbiologists ever get our act together and start getting
>>>>> all the genes from metagenomics, you'll be glad you did! ;)
>>>>>
>>>>> Jim
>>>>>
>>>>>
>>>>> On Apr 2, 2008, at 6:06 PM, Judith Blake wrote:
>>>>>
>>>>>> I agree with your proposal.
>>>>>>
>>>>>> Would you not remove gene symbols as synonyms from all terms?
>>>>>>
>>>>>> Judy
>>>>>>
>>>>>> Jennifer Deegan (nee Clark) wrote:
>>>>>>
>>>>>>> Hi,
>>>>>>>
>>>>>>> A couple of GO terms currently contain a problematically large
>>>>>>> number of
>>>>>>>  gene symbols
>>>>>>> as related synonyms.
>>>>>>> The synonyms were imported into the OBO file during updates from
>>>>>>> Enzyme
>>>>>>> Commission data.
>>>>>>>
>>>>>>> The synonyms are a problem because they mess up the display  
>>>>>>> in GO
>>>>>>> browsers. For example:
>>>>>>>
>>>>>>> http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi? 
>>>>>>> term=GO:0004714&session_id=6392amigo1207145654
>>>>>>> <http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi? 
>>>>>>> term=GO:0004714&session_id=6392amigo1207145654>
>>>>>>>
>>>>>>>
>>>>>>> They are also confusing for users as they resemble annotations,
>>>>>>> but are
>>>>>>> only related synonyms.
>>>>>>>
>>>>>>> To resolve this problem, on 16th April we are going to remove  
>>>>>>> the
>>>>>>> list
>>>>>>> of gene products as related synonyms from the following terms:
>>>>>>>
>>>>>>> GO:0004714 (transmembrane receptor protein tyrosine kinase  
>>>>>>> activity)
>>>>>>> (201 gene symbols included as synonyms)
>>>>>>>
>>>>>>> GO:0004715 (non-membrane spanning protein tyrosine kinase
>>>>>>> activity) (84
>>>>>>> gene symbols included as synonyms)
>>>>>>>
>>>>>>> If you have any objection to this removal please reply to  
>>>>>>> Jennifer
>>>>>>> Deegan and Emily Dimmer.
>>>>>>>
>>>>>>> Thanks,
>>>>>>>
>>>>>>> Jennifer and Emily.
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Go mailing list
>>>>>> Go at geneontology.org <mailto:Go at geneontology.org>
>>>>>> http://fafner.stanford.edu/mailman/listinfo/go
>>>>>
>>>>>
>>>>> =====================================
>>>>>
>>>>> Jim Hu
>>>>>
>>>>> Associate Professor
>>>>>
>>>>> Dept. of Biochemistry and Biophysics
>>>>>
>>>>> 2128 TAMU
>>>>>
>>>>> Texas A&M Univ.
>>>>>
>>>>> College Station, TX 77843-2128
>>>>>
>>>>> 979-862-4054
>>>>>
>>>>>
>>>>>
>>>>
>>>
>>
>>
>> _______________________________________________
>> Go mailing list
>> Go at geneontology.org
>> http://fafner.stanford.edu/mailman/listinfo/go
>>
>
> Dr Jane Lomax
> GO Editorial Office
> EMBL-EBI
> Wellcome Trust Genome Campus
> Hinxton
> Cambridgeshire, UK
> CB10 1SD
>
> p: +44 1223 492516
> f: +44 1223 494468
> _______________________________________________
> Go mailing list
> Go at geneontology.org
> http://fafner.stanford.edu/mailman/listinfo/go


From jimhu at tamu.edu  Thu Apr  3 07:55:50 2008
From: jimhu at tamu.edu (Jim Hu)
Date: Thu, 3 Apr 2008 09:55:50 -0500
Subject: [Go] Gene Symbols as GO synonyms
In-Reply-To: <47F4B59A.9080308@informatics.jax.org>
References: <47F396C5.4080708@ebi.ac.uk> <47F4118B.5080607@informatics.jax.org>
	<9352A705-0DBE-41BD-B5D4-1FB0942D7854@tamu.edu>
	<47F41664.1090405@informatics.jax.org> <47F4A645.4000207@ebi.ac.uk>
	<47F4B59A.9080308@informatics.jax.org>
Message-ID: <1F34A5FF-23F4-4992-BCEC-DED7E0310E6A@tamu.edu>

Hi,

I agree with Judy that gene symbols are not synonyms for GO terms.   
After all, the whole point of GO is that each gene should have three  
or more GO terms, and each GO term is associated with many genes  
across lots of organisms.  That's just not what "synonym" means to me.

On the other hand, I understand and sympathize with Jen's explanation  
for why the group wanted p53 in the term record.  Now that the  
associations are there, you can just look for the gene name in the  
gene associations, but while since the annotation process is not  
complete, there are other situations where finding terms is helped by  
having some gene names "associated" with a term at a level that would  
not be accepted as a completed annotation - i.e. no evidence code or  
reference.  I think the gene names here are still potentially useful  
in that way; not as true synonyms, but as listings of examples to  
guide curation.  I'm wondering if something like that would still be  
useful to have in the term record.

Not sure what to call it or how to implement, though.  Example is too  
broad.  I'm thinking that you don't just want examples, you want the  
cases where something is a paradigm for that GO term.  For example,  
for GO:0030983:mismatched DNA binding, mutS would be a paradigm  
example, along with the MSH _family_ of proteins.  But listing every  
MSH gene from every organism would be overkill.  For broader things  
like ATPase activity, you wouldn't want to pick a particular example  
as a paradigm, as that molecular function is connected to too many  
disparate things.

I don't think RELATED captures this notion.  I'd almost prefer to see  
just freetext comments, as I suspect that the kind of knowledge from  
fuzzy examples I'm talking about hre is not a good ontological idea.

Jim


On Apr 3, 2008, at 5:46 AM, Judith Blake wrote:

> Hi Jen,
>
> When I search GO terms for 'p53', this does not come back as a  
> synonym, although synonyms with the string 'p53' as part of the long  
> series of strings as a synonym do come back.  So I don't think that  
> argument holds anymore.  I agree that grinding through looking for  
> synonyms that are gene symbols is not a productive use of time, but  
> such synonyms, I think, should be removed as a matter of course  
> while working on the ontology in general as they are found.  I do  
> not see, if 'p53' is not an issue, where anything else would be an  
> issue.
>
> Does anyone object to having gene symbols routinely removed as found  
> as synonyms?  Certainly the ontology editors can bring such synonyms  
> forward if they think there might be an issue. what do you think Jen?
>
> Judy
>
>
> Jennifer Deegan (nee Clark) wrote:
>> Hi Judy,
>>
>> We did think about this, but I remember that the group who work on  
>> p53 were very keen that a term covering an activity of this gene  
>> product should carry a synonym 'p53' to help them find the term. I  
>> am reluctant to remove all gene symbols as synonyms because of  
>> that, but thought I would just tidy up these two problematic terms.  
>> We could certainly consider removing all gene symbol synonyms in  
>> the long term, but it seems to me that the effort required to track  
>> them all down and discuss individually whether they are required  
>> might not be worthwhile, since we have other time-consuming  
>> projects that are a higher priority. Would you agree?
>>
>> Thanks for thinking about it.
>>
>> Jen
>>
>>
>> Judith Blake wrote:
>>
>>> not the least because they aren't synonyms....
>>>
>>> judy
>>>
>>> Jim Hu wrote:
>>>
>>>> I agree with Judy that removing them from all terms is a good  
>>>> idea.  If us microbiologists ever get our act together and start  
>>>> getting all the genes from metagenomics, you'll be glad you did! ;)
>>>>
>>>> Jim
>>>>
>>>>
>>>> On Apr 2, 2008, at 6:06 PM, Judith Blake wrote:
>>>>
>>>>> I agree with your proposal.
>>>>>
>>>>> Would you not remove gene symbols as synonyms from all terms?
>>>>>
>>>>> Judy
>>>>>
>>>>> Jennifer Deegan (nee Clark) wrote:
>>>>>
>>>>>> Hi,
>>>>>>
>>>>>> A couple of GO terms currently contain a problematically large  
>>>>>> number of
>>>>>> gene symbols
>>>>>> as related synonyms.
>>>>>> The synonyms were imported into the OBO file during updates  
>>>>>> from Enzyme
>>>>>> Commission data.
>>>>>>
>>>>>> The synonyms are a problem because they mess up the display in GO
>>>>>> browsers. For example:
>>>>>>
>>>>>> http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?term=GO:0004714&session_id=6392amigo1207145654 
>>>>>>  <http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?term=GO:0004714&session_id=6392amigo1207145654 
>>>>>> >
>>>>>>
>>>>>> They are also confusing for users as they resemble annotations,  
>>>>>> but are
>>>>>> only related synonyms.
>>>>>>
>>>>>> To resolve this problem, on 16th April we are going to remove  
>>>>>> the list
>>>>>> of gene products as related synonyms from the following terms:
>>>>>>
>>>>>> GO:0004714 (transmembrane receptor protein tyrosine kinase  
>>>>>> activity)
>>>>>> (201 gene symbols included as synonyms)
>>>>>>
>>>>>> GO:0004715 (non-membrane spanning protein tyrosine kinase  
>>>>>> activity) (84
>>>>>> gene symbols included as synonyms)
>>>>>>
>>>>>> If you have any objection to this removal please reply to  
>>>>>> Jennifer
>>>>>> Deegan and Emily Dimmer.
>>>>>>
>>>>>> Thanks,
>>>>>>
>>>>>> Jennifer and Emily.
>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Go mailing list
>>>>> Go at geneontology.org <mailto:Go at geneontology.org>
>>>>> http://fafner.stanford.edu/mailman/listinfo/go
>>>>
>>>>
>>>> =====================================
>>>>
>>>> Jim Hu
>>>>
>>>> Associate Professor
>>>>
>>>> Dept. of Biochemistry and Biophysics
>>>>
>>>> 2128 TAMU
>>>>
>>>> Texas A&M Univ.
>>>>
>>>> College Station, TX 77843-2128
>>>>
>>>> 979-862-4054
>>>>
>>>>
>>>>
>>>
>>
>
>

=====================================
Jim Hu
Associate Professor
Dept. of Biochemistry and Biophysics
2128 TAMU
Texas A&M Univ.
College Station, TX 77843-2128
979-862-4054


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From editorial at biomedcentral.com  Thu Apr  3 06:05:55 2008
From: editorial at biomedcentral.com (BioMed Central Editorial)
Date: 3 Apr 2008 14:05:55 +0100
Subject: [Go] 4357463361924841 Muscle Research and Gene Ontology: New
 standards for improved data integration.
Message-ID: <590808.1207227955213.JavaMail.lscswebadmin@LSCBA03P1>

Article title: Muscle Research and Gene Ontology: New standards
for improved data integration.
MS ID        : 4357463361924841 
Authors      : Erika Feltrin, Giorgio Valle, Muscle Meeting Working Group and Jennifer Deegan n?e Clark
Journal      : BMC Medical Genomics

Dear Dr Feltrin

Thank you for submitting your article. This acknowledgement and any queries below are for the contact author. This e-mail has also been copied to each author on the paper, as well as the person submitting. Please bear in mind that all queries regarding the paper should be made through the contact author.

A pdf file has been generated from your submitted manuscript and figures. We would be most grateful if you could check this file and let us know if any aspect is missing or incorrect.

http://www.biomedcentral.com/imedia/4357463361924841_article.pdf  (181K)

For your records, please find below link(s) to the correspondence you uploaded with this submission. Please note there may be a short delay in creating this file.

http://www.biomedcentral.com/imedia/7576047501924870_comment.pdf 
 

If the PDF does not contain the comments which you uploaded, please upload the cover letter again, click "Continue" at the bottom of the page, and then proceed with the manuscript submission again. If the letter will not upload, please send a copy to editorial at biomedcentral.com. 

We will assign peer reviewers as soon as possible, and will aim to contact you with an initial decision on the manuscript shortly. The submitting author can check on the status of your manuscript in peer review at any time by logging into 'My BioMed Central' (http://www.biomedcentral.com/my).

In the meantime, if you have any queries about the manuscript you may contact us on editorial at biomedcentral.com. We would also welcome feedback about the online submission process.

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Regards

The BioMed Central Editorial Team

Tel: +44 (0)20 7631 9921
Facsimile: +44 (0)20 7631 9923
e-mail: editorial at biomedcentral.com
Web: http://www.biomedcentral.com/





From midori at ebi.ac.uk  Thu Apr  3 08:49:52 2008
From: midori at ebi.ac.uk (Midori Harris)
Date: Thu, 3 Apr 2008 16:49:52 +0100 (BST)
Subject: [Go] Alert: Proposal to obsolete GO:0045045 (biological process)
 that impacts existing annotations
Message-ID: <Pine.LNX.4.64.0804031530150.2077@pigeon.ebi.ac.uk>

Dear GO,

The proposal has been made to obsolete

   secertory pathway ; GO:0045045

Annotations to this term exist at present as follows:

 	DB		total
 	GeneDB_Spombe	14 (no IEA)
 	CGD	1 (ISS)
 	FB	2 (IMP)
 	goa_cow	1 (IEA)
 	goa_human	5 (no IEA)
 	goa_uniprot	3 (1 IEA)
 	Gramene	5 (IC)
 	MGI	3 (no IEA)
 	RGD	9 (1 IEA)
 	SGD	21 (no IEA)
 	TAIR	12 (no IEA)
 	WB	1 (ISS)
 	ZFIN	10 (no IEA)

Annotations can be transferred to 'secretion by cell ; GO:0032940' or one 
or more of its children.

This term is not used in any external2go mappings; it is in the PIR GO 
slim and the prokaryote GO subset maintained within the OBO flat file.

The reasons for making this term obsolete is that it artificially groups a 
numbre of other terms, leading to path problems; its definition is unclear 
(and lacks genus-differentia features); and annotators suspect it has been 
used incorrectly.

SourceForge link:
https://sourceforge.net/tracker/index.php?func=detail&aid=1912842&group_id=36855&atid=440764

The comment period ends on Friday, April 18, 2008.

*** Unless objections are received by April 18,
     we will assume that you agree to this change. ***

Midori

From midori at ebi.ac.uk  Thu Apr  3 09:00:25 2008
From: midori at ebi.ac.uk (midori at ebi.ac.uk)
Date: Thu, 3 Apr 2008 16:00:25 UT
Subject: [Go] SourceForge Update
Message-ID: <200804031600.m33G0Px1567236@mozart.ebi.ac.uk>

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From suzi at fruitfly.org  Thu Apr  3 11:34:50 2008
From: suzi at fruitfly.org (Suzanna Lewis)
Date: Thu, 3 Apr 2008 11:34:50 -0700
Subject: [Go] Gene Symbols as GO synonyms
In-Reply-To: <6E7F3A24-F79C-497F-B0FD-02ECA3BC997B@gen.cam.ac.uk>
References: <47F396C5.4080708@ebi.ac.uk> <47F4118B.5080607@informatics.jax.org>
	<9352A705-0DBE-41BD-B5D4-1FB0942D7854@tamu.edu>
	<47F41664.1090405@informatics.jax.org> <47F4A645.4000207@ebi.ac.uk>
	<47F4B59A.9080308@informatics.jax.org>
	<Pine.LNX.4.62.0804031406270.31293@puffin.ebi.ac.uk>
	<6E7F3A24-F79C-497F-B0FD-02ECA3BC997B@gen.cam.ac.uk>
Message-ID: <C0945A19-B30A-467D-9258-B9CB9CF8DBB9@fruitfly.org>

I agree with a flexible solution.

While we 'know' that the string (for example) "p53" is used as a gene  
symbol to specifically indicate a particular protein/gene, we also  
must realize that the same string "p53" is also used colloquially to  
denote types of proteins/genes of that ilk.

So I think in these cases we must allow the use of these strings as  
related synonyms. Not be dogmatic and recognized that people use the  
same string is slightly different ways (and we'll support the  
colloquial usage of classifying a type by example).

-S

On Apr 3, 2008, at 7:38 AM, Michael Ashburner wrote:

> That sounds a good medium solution Jane.
>
> Michael
>
> On 3 Apr 2008, at 06:07, Jane Lomax wrote:
>
>> Hi Judy - the gene symbol synonyms can sometimes be very useful for
>> the
>> purposes of mappings, especially for things like enzymes where some
>> groups
>> use the gene symbol in their vocabulary term name (this has been
>> the case
>> for the IMG and FIGS mappings recently). So I'd rather not see them
>> removed completely.
>>
>> However I do agree that seeing them can be very confusing for users
>> - I
>> wonder whether we could agree to suppress RELATED synonyms in the
>> GO interfaces?
>> Maybe only show them when they match a search?
>>
>> jane
>>
>>  On Thu, 3 Apr 2008, Judith Blake wrote:
>>
>>> Hi Jen,
>>>
>>> When I search GO terms for 'p53', this does not come back as a
>>> synonym,
>>> although synonyms with the string 'p53' as part of the long series  
>>> of
>>> strings as a synonym do come back.  So I don't think that argument
>>> holds
>>> anymore.  I agree that grinding through looking for synonyms that  
>>> are
>>> gene symbols is not a productive use of time, but such synonyms, I
>>> think, should be removed as a matter of course while working on the
>>> ontology in general as they are found.  I do not see, if 'p53' is
>>> not an
>>> issue, where anything else would be an issue.
>>>
>>> Does anyone object to having gene symbols routinely removed as
>>> found as
>>> synonyms?  Certainly the ontology editors can bring such synonyms
>>> forward if they think there might be an issue. what do you think  
>>> Jen?
>>>
>>> Judy
>>>
>>>
>>> Jennifer Deegan (nee Clark) wrote:
>>>> Hi Judy,
>>>>
>>>> We did think about this, but I remember that the group who work
>>>> on p53
>>>> were very keen that a term covering an activity of this gene  
>>>> product
>>>> should carry a synonym 'p53' to help them find the term. I am
>>>> reluctant to remove all gene symbols as synonyms because of that,
>>>> but
>>>> thought I would just tidy up these two problematic terms. We could
>>>> certainly consider removing all gene symbol synonyms in the long
>>>> term,
>>>> but it seems to me that the effort required to track them all
>>>> down and
>>>> discuss individually whether they are required might not be
>>>> worthwhile, since we have other time-consuming projects that are a
>>>> higher priority. Would you agree?
>>>>
>>>> Thanks for thinking about it.
>>>>
>>>> Jen
>>>>
>>>>
>>>> Judith Blake wrote:
>>>>
>>>>> not the least because they aren't synonyms....
>>>>>
>>>>> judy
>>>>>
>>>>> Jim Hu wrote:
>>>>>
>>>>>> I agree with Judy that removing them from all terms is a good
>>>>>> idea.
>>>>>> If us microbiologists ever get our act together and start getting
>>>>>> all the genes from metagenomics, you'll be glad you did! ;)
>>>>>>
>>>>>> Jim
>>>>>>
>>>>>>
>>>>>> On Apr 2, 2008, at 6:06 PM, Judith Blake wrote:
>>>>>>
>>>>>>> I agree with your proposal.
>>>>>>>
>>>>>>> Would you not remove gene symbols as synonyms from all terms?
>>>>>>>
>>>>>>> Judy
>>>>>>>
>>>>>>> Jennifer Deegan (nee Clark) wrote:
>>>>>>>
>>>>>>>> Hi,
>>>>>>>>
>>>>>>>> A couple of GO terms currently contain a problematically large
>>>>>>>> number of
>>>>>>>> gene symbols
>>>>>>>> as related synonyms.
>>>>>>>> The synonyms were imported into the OBO file during updates  
>>>>>>>> from
>>>>>>>> Enzyme
>>>>>>>> Commission data.
>>>>>>>>
>>>>>>>> The synonyms are a problem because they mess up the display
>>>>>>>> in GO
>>>>>>>> browsers. For example:
>>>>>>>>
>>>>>>>> http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?
>>>>>>>> term=GO:0004714&session_id=6392amigo1207145654
>>>>>>>> <http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?
>>>>>>>> term=GO:0004714&session_id=6392amigo1207145654>
>>>>>>>>
>>>>>>>>
>>>>>>>> They are also confusing for users as they resemble annotations,
>>>>>>>> but are
>>>>>>>> only related synonyms.
>>>>>>>>
>>>>>>>> To resolve this problem, on 16th April we are going to remove
>>>>>>>> the
>>>>>>>> list
>>>>>>>> of gene products as related synonyms from the following terms:
>>>>>>>>
>>>>>>>> GO:0004714 (transmembrane receptor protein tyrosine kinase
>>>>>>>> activity)
>>>>>>>> (201 gene symbols included as synonyms)
>>>>>>>>
>>>>>>>> GO:0004715 (non-membrane spanning protein tyrosine kinase
>>>>>>>> activity) (84
>>>>>>>> gene symbols included as synonyms)
>>>>>>>>
>>>>>>>> If you have any objection to this removal please reply to
>>>>>>>> Jennifer
>>>>>>>> Deegan and Emily Dimmer.
>>>>>>>>
>>>>>>>> Thanks,
>>>>>>>>
>>>>>>>> Jennifer and Emily.
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Go mailing list
>>>>>>> Go at geneontology.org <mailto:Go at geneontology.org>
>>>>>>> http://fafner.stanford.edu/mailman/listinfo/go
>>>>>>
>>>>>>
>>>>>> =====================================
>>>>>>
>>>>>> Jim Hu
>>>>>>
>>>>>> Associate Professor
>>>>>>
>>>>>> Dept. of Biochemistry and Biophysics
>>>>>>
>>>>>> 2128 TAMU
>>>>>>
>>>>>> Texas A&M Univ.
>>>>>>
>>>>>> College Station, TX 77843-2128
>>>>>>
>>>>>> 979-862-4054
>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>>
>>> _______________________________________________
>>> Go mailing list
>>> Go at geneontology.org
>>> http://fafner.stanford.edu/mailman/listinfo/go
>>>
>>
>> Dr Jane Lomax
>> GO Editorial Office
>> EMBL-EBI
>> Wellcome Trust Genome Campus
>> Hinxton
>> Cambridgeshire, UK
>> CB10 1SD
>>
>> p: +44 1223 492516
>> f: +44 1223 494468
>> _______________________________________________
>> Go mailing list
>> Go at geneontology.org
>> http://fafner.stanford.edu/mailman/listinfo/go
>
> _______________________________________________
> Go mailing list
> Go at geneontology.org
> http://fafner.stanford.edu/mailman/listinfo/go
>



From cjm at fruitfly.org  Thu Apr  3 17:17:57 2008
From: cjm at fruitfly.org (Chris Mungall)
Date: Thu, 3 Apr 2008 17:17:57 -0700
Subject: [Go] Gene Symbols as GO synonyms
In-Reply-To: <Pine.LNX.4.62.0804031406270.31293@puffin.ebi.ac.uk>
References: <47F396C5.4080708@ebi.ac.uk> <47F4118B.5080607@informatics.jax.org>
	<9352A705-0DBE-41BD-B5D4-1FB0942D7854@tamu.edu>
	<47F41664.1090405@informatics.jax.org> <47F4A645.4000207@ebi.ac.uk>
	<47F4B59A.9080308@informatics.jax.org>
	<Pine.LNX.4.62.0804031406270.31293@puffin.ebi.ac.uk>
Message-ID: <E38ED239-F948-4A77-B2F6-C29728E8F3D9@fruitfly.org>


On Apr 3, 2008, at 6:07 AM, Jane Lomax wrote:

> Hi Judy - the gene symbol synonyms can sometimes be very useful for  
> the
> purposes of mappings, especially for things like enzymes where some  
> groups
> use the gene symbol in their vocabulary term name (this has been  
> the case
> for the IMG and FIGS mappings recently). So I'd rather not see them
> removed completely.
>
> However I do agree that seeing them can be very confusing for users  
> - I
> wonder whether we could agree to suppress RELATED synonyms in the  
> GO interfaces?
> Maybe only show them when they match a search?

This seems slightly awkward - we'd have to coordinate this with every  
GO browser out there. And what about the RELATED synonyms that are  
not gene products?

How about introducing a new synonym category (called "gene" for  
example)? Note that these synonyms would still be RELATED, there  
would just be additional metadata indicating the context for the  
synonym.

I still don't think this is perfect. We shouldn't go overloading  
existing tags just because it happens to help with searching in a few  
cases.

> jane
>
>   On Thu, 3 Apr 2008, Judith Blake wrote:
>
>> Hi Jen,
>>
>> When I search GO terms for 'p53', this does not come back as a  
>> synonym,
>> although synonyms with the string 'p53' as part of the long series of
>> strings as a synonym do come back.  So I don't think that argument  
>> holds
>> anymore.  I agree that grinding through looking for synonyms that are
>> gene symbols is not a productive use of time, but such synonyms, I
>> think, should be removed as a matter of course while working on the
>> ontology in general as they are found.  I do not see, if 'p53' is  
>> not an
>> issue, where anything else would be an issue.
>>
>> Does anyone object to having gene symbols routinely removed as  
>> found as
>> synonyms?  Certainly the ontology editors can bring such synonyms
>> forward if they think there might be an issue. what do you think Jen?
>>
>> Judy
>>
>>
>> Jennifer Deegan (nee Clark) wrote:
>>> Hi Judy,
>>>
>>> We did think about this, but I remember that the group who work  
>>> on p53
>>> were very keen that a term covering an activity of this gene product
>>> should carry a synonym 'p53' to help them find the term. I am
>>> reluctant to remove all gene symbols as synonyms because of that,  
>>> but
>>> thought I would just tidy up these two problematic terms. We could
>>> certainly consider removing all gene symbol synonyms in the long  
>>> term,
>>> but it seems to me that the effort required to track them all  
>>> down and
>>> discuss individually whether they are required might not be
>>> worthwhile, since we have other time-consuming projects that are a
>>> higher priority. Would you agree?
>>>
>>> Thanks for thinking about it.
>>>
>>> Jen
>>>
>>>
>>> Judith Blake wrote:
>>>
>>>> not the least because they aren't synonyms....
>>>>
>>>> judy
>>>>
>>>> Jim Hu wrote:
>>>>
>>>>> I agree with Judy that removing them from all terms is a good  
>>>>> idea.
>>>>>  If us microbiologists ever get our act together and start getting
>>>>> all the genes from metagenomics, you'll be glad you did! ;)
>>>>>
>>>>> Jim
>>>>>
>>>>>
>>>>> On Apr 2, 2008, at 6:06 PM, Judith Blake wrote:
>>>>>
>>>>>> I agree with your proposal.
>>>>>>
>>>>>> Would you not remove gene symbols as synonyms from all terms?
>>>>>>
>>>>>> Judy
>>>>>>
>>>>>> Jennifer Deegan (nee Clark) wrote:
>>>>>>
>>>>>>> Hi,
>>>>>>>
>>>>>>> A couple of GO terms currently contain a problematically large
>>>>>>> number of
>>>>>>>  gene symbols
>>>>>>> as related synonyms.
>>>>>>> The synonyms were imported into the OBO file during updates from
>>>>>>> Enzyme
>>>>>>> Commission data.
>>>>>>>
>>>>>>> The synonyms are a problem because they mess up the display  
>>>>>>> in GO
>>>>>>> browsers. For example:
>>>>>>>
>>>>>>> http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi? 
>>>>>>> term=GO:0004714&session_id=6392amigo1207145654
>>>>>>> <http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi? 
>>>>>>> term=GO:0004714&session_id=6392amigo1207145654>
>>>>>>>
>>>>>>>
>>>>>>> They are also confusing for users as they resemble annotations,
>>>>>>> but are
>>>>>>> only related synonyms.
>>>>>>>
>>>>>>> To resolve this problem, on 16th April we are going to remove  
>>>>>>> the
>>>>>>> list
>>>>>>> of gene products as related synonyms from the following terms:
>>>>>>>
>>>>>>> GO:0004714 (transmembrane receptor protein tyrosine kinase  
>>>>>>> activity)
>>>>>>> (201 gene symbols included as synonyms)
>>>>>>>
>>>>>>> GO:0004715 (non-membrane spanning protein tyrosine kinase
>>>>>>> activity) (84
>>>>>>> gene symbols included as synonyms)
>>>>>>>
>>>>>>> If you have any objection to this removal please reply to  
>>>>>>> Jennifer
>>>>>>> Deegan and Emily Dimmer.
>>>>>>>
>>>>>>> Thanks,
>>>>>>>
>>>>>>> Jennifer and Emily.
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Go mailing list
>>>>>> Go at geneontology.org <mailto:Go at geneontology.org>
>>>>>> http://fafner.stanford.edu/mailman/listinfo/go
>>>>>
>>>>>
>>>>> =====================================
>>>>>
>>>>> Jim Hu
>>>>>
>>>>> Associate Professor
>>>>>
>>>>> Dept. of Biochemistry and Biophysics
>>>>>
>>>>> 2128 TAMU
>>>>>
>>>>> Texas A&M Univ.
>>>>>
>>>>> College Station, TX 77843-2128
>>>>>
>>>>> 979-862-4054
>>>>>
>>>>>
>>>>>
>>>>
>>>
>>
>>
>> _______________________________________________
>> Go mailing list
>> Go at geneontology.org
>> http://fafner.stanford.edu/mailman/listinfo/go
>>
>
> Dr Jane Lomax
> GO Editorial Office
> EMBL-EBI
> Wellcome Trust Genome Campus
> Hinxton
> Cambridgeshire, UK
> CB10 1SD
>
> p: +44 1223 492516
> f: +44 1223 494468
> _______________________________________________
> Go mailing list
> Go at geneontology.org
> http://fafner.stanford.edu/mailman/listinfo/go
>


From val at sanger.ac.uk  Thu Apr  3 23:42:36 2008
From: val at sanger.ac.uk (Valerie Wood)
Date: Fri, 4 Apr 2008 06:42:36 UT
Subject: [Go] Gene Symbols as GO synonyms
Message-ID: <E1JhfdE-0000Lm-89@web-2-05.internal.sanger.ac.uk>

An embedded and charset-unspecified text was scrubbed...
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Url: http://fafner.stanford.edu/pipermail/go/attachments/20080404/174169ff/attachment-0001.pl 

From adiehl at informatics.jax.org  Fri Apr  4 01:20:01 2008
From: adiehl at informatics.jax.org (Alexander Diehl)
Date: Fri, 04 Apr 2008 08:20:01 +0000
Subject: [Go] Gene Symbols as GO synonyms
In-Reply-To: <E1JhfdE-0000Lm-89@web-2-05.internal.sanger.ac.uk>
References: <E1JhfdE-0000Lm-89@web-2-05.internal.sanger.ac.uk>
Message-ID: <47F5E4B1.4030309@informatics.jax.org>

I agree with Chris, Val, and Judy that these gene symbols used as 
synonyms ought to be removed as they can easily be confused for 
annotation, and furthermore, why grant them to some terms but not all.  
I also agree that gene symbols used as part of a synonym phrase, such as 
'p53 class' are different from the bare symbols, and ought to remain.

While I admit I have not idea what the IMG and FIGS mappings are, I 
would suggest that at this point in the history of the GO we have a 
sufficient corpus of annotations built up to allow easy mapping, not to 
mention the EC-to-GO, Interpro-to-GO, and SwissProt-to-GO mappings 
(among others).  If the existing information is so valuable, perhaps we 
can mine it from the GO obo file and create a Gene Symbol-to-GO mapping 
file.  Of course, we already have something similar; it's called the 
Gene Association File.  And it's huge.

-- Alex


Valerie Wood wrote:
> I'm still not sure why we have include them at all. 
>
> In the long term it will confuse users because it might stop tem being able to make the distinction between the ontology and the annotations. Also, it is inconsistent, why do this for a few gene names but not all, and also for some terms which a gene product would be annotated to but not all, this can also lead to confusion, because users might think that a gene name search will always work.
>
> Jen, was the p53 case correct? (as Judy pointed out there are no p53 synonyms), but 'p53 class' is included in the term name of some terms, which is differrent.
>
> Val
>
>
> Chris Mungall <cjm at fruitfly.org> wrote: 
>   
>> On Apr 3, 2008, at 6:07 AM, Jane Lomax wrote:
>>
>>     
>>> Hi Judy - the gene symbol synonyms can sometimes be very useful for  
>>> the
>>> purposes of mappings, especially for things like enzymes where some  
>>> groups
>>> use the gene symbol in their vocabulary term name (this has been  
>>> the case
>>> for the IMG and FIGS mappings recently). So I'd rather not see them
>>> removed completely.
>>>
>>> However I do agree that seeing them can be very confusing for users  
>>> - I
>>> wonder whether we could agree to suppress RELATED synonyms in the  
>>> GO interfaces?
>>> Maybe only show them when they match a search?
>>>       
>> This seems slightly awkward - we'd have to coordinate this with every  
>> GO browser out there. And what about the RELATED synonyms that are  
>> not gene products?
>>
>> How about introducing a new synonym category (called "gene" for  
>> example)? Note that these synonyms would still be RELATED, there  
>> would just be additional metadata indicating the context for the  
>> synonym.
>>
>> I still don't think this is perfect. We shouldn't go overloading  
>> existing tags just because it happens to help with searching in a few  
>> cases.
>>
>>     
>>> jane
>>>
>>>   On Thu, 3 Apr 2008, Judith Blake wrote:
>>>
>>>       
>>>> Hi Jen,
>>>>
>>>> When I search GO terms for 'p53', this does not come back as a  
>>>> synonym,
>>>> although synonyms with the string 'p53' as part of the long series of
>>>> strings as a synonym do come back.  So I don't think that argument  
>>>> holds
>>>> anymore.  I agree that grinding through looking for synonyms that are
>>>> gene symbols is not a productive use of time, but such synonyms, I
>>>> think, should be removed as a matter of course while working on the
>>>> ontology in general as they are found.  I do not see, if 'p53' is  
>>>> not an
>>>> issue, where anything else would be an issue.
>>>>
>>>> Does anyone object to having gene symbols routinely removed as  
>>>> found as
>>>> synonyms?  Certainly the ontology editors can bring such synonyms
>>>> forward if they think there might be an issue. what do you think Jen?
>>>>
>>>> Judy
>>>>
>>>>
>>>> Jennifer Deegan (nee Clark) wrote:
>>>>         
>>>>> Hi Judy,
>>>>>
>>>>> We did think about this, but I remember that the group who work  
>>>>> on p53
>>>>> were very keen that a term covering an activity of this gene product
>>>>> should carry a synonym 'p53' to help them find the term. I am
>>>>> reluctant to remove all gene symbols as synonyms because of that,  
>>>>> but
>>>>> thought I would just tidy up these two problematic terms. We could
>>>>> certainly consider removing all gene symbol synonyms in the long  
>>>>> term,
>>>>> but it seems to me that the effort required to track them all  
>>>>> down and
>>>>> discuss individually whether they are required might not be
>>>>> worthwhile, since we have other time-consuming projects that are a
>>>>> higher priority. Would you agree?
>>>>>
>>>>> Thanks for thinking about it.
>>>>>
>>>>> Jen
>>>>>
>>>>>
>>>>> Judith Blake wrote:
>>>>>
>>>>>           
>>>>>> not the least because they aren't synonyms....
>>>>>>
>>>>>> judy
>>>>>>
>>>>>> Jim Hu wrote:
>>>>>>
>>>>>>             
>>>>>>> I agree with Judy that removing them from all terms is a good  
>>>>>>> idea.
>>>>>>>  If us microbiologists ever get our act together and start getting
>>>>>>> all the genes from metagenomics, you'll be glad you did! ;)
>>>>>>>
>>>>>>> Jim
>>>>>>>
>>>>>>>
>>>>>>> On Apr 2, 2008, at 6:06 PM, Judith Blake wrote:
>>>>>>>
>>>>>>>               
>>>>>>>> I agree with your proposal.
>>>>>>>>
>>>>>>>> Would you not remove gene symbols as synonyms from all terms?
>>>>>>>>
>>>>>>>> Judy
>>>>>>>>
>>>>>>>> Jennifer Deegan (nee Clark) wrote:
>>>>>>>>
>>>>>>>>                 
>>>>>>>>> Hi,
>>>>>>>>>
>>>>>>>>> A couple of GO terms currently contain a problematically large
>>>>>>>>> number of
>>>>>>>>>  gene symbols
>>>>>>>>> as related synonyms.
>>>>>>>>> The synonyms were imported into the OBO file during updates from
>>>>>>>>> Enzyme
>>>>>>>>> Commission data.
>>>>>>>>>
>>>>>>>>> The synonyms are a problem because they mess up the display  
>>>>>>>>> in GO
>>>>>>>>> browsers. For example:
>>>>>>>>>
>>>>>>>>> http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi? 
>>>>>>>>> term=GO:0004714&session_id=6392amigo1207145654
>>>>>>>>> <http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi? 
>>>>>>>>> term=GO:0004714&session_id=6392amigo1207145654>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> They are also confusing for users as they resemble annotations,
>>>>>>>>> but are
>>>>>>>>> only related synonyms.
>>>>>>>>>
>>>>>>>>> To resolve this problem, on 16th April we are going to remove  
>>>>>>>>> the
>>>>>>>>> list
>>>>>>>>> of gene products as related synonyms from the following terms:
>>>>>>>>>
>>>>>>>>> GO:0004714 (transmembrane receptor protein tyrosine kinase  
>>>>>>>>> activity)
>>>>>>>>> (201 gene symbols included as synonyms)
>>>>>>>>>
>>>>>>>>> GO:0004715 (non-membrane spanning protein tyrosine kinase
>>>>>>>>> activity) (84
>>>>>>>>> gene symbols included as synonyms)
>>>>>>>>>
>>>>>>>>> If you have any objection to this removal please reply to  
>>>>>>>>> Jennifer
>>>>>>>>> Deegan and Emily Dimmer.
>>>>>>>>>
>>>>>>>>> Thanks,
>>>>>>>>>
>>>>>>>>> Jennifer and Emily.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>                   
>>>>>>>> _______________________________________________
>>>>>>>> Go mailing list
>>>>>>>> Go at geneontology.org <mailto:Go at geneontology.org>
>>>>>>>> http://fafner.stanford.edu/mailman/listinfo/go
>>>>>>>>                 
>>>>>>> =====================================
>>>>>>>
>>>>>>> Jim Hu
>>>>>>>
>>>>>>> Associate Professor
>>>>>>>
>>>>>>> Dept. of Biochemistry and Biophysics
>>>>>>>
>>>>>>> 2128 TAMU
>>>>>>>
>>>>>>> Texas A&M Univ.
>>>>>>>
>>>>>>> College Station, TX 77843-2128
>>>>>>>
>>>>>>> 979-862-4054
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>               
>>>> _______________________________________________
>>>> Go mailing list
>>>> Go at geneontology.org
>>>> http://fafner.stanford.edu/mailman/listinfo/go
>>>>
>>>>         
>>> Dr Jane Lomax
>>> GO Editorial Office
>>> EMBL-EBI
>>> Wellcome Trust Genome Campus
>>> Hinxton
>>> Cambridgeshire, UK
>>> CB10 1SD
>>>
>>> p: +44 1223 492516
>>> f: +44 1223 494468
>>> _______________________________________________
>>> Go mailing list
>>> Go at geneontology.org
>>> http://fafner.stanford.edu/mailman/listinfo/go
>>>
>>>       
>> _______________________________________________
>> Go mailing list
>> Go at geneontology.org
>> http://fafner.stanford.edu/mailman/listinfo/go
>>
>>
>>     
>
>   
> ------------------------------------------------------------------------
>
> _______________________________________________
> Go mailing list
> Go at geneontology.org
> http://fafner.stanford.edu/mailman/listinfo/go
>   


-- 
Alexander Diehl, Ph.D.
Senior Scientific Curator
Mouse Genome Informatics
The Jackson Laboratory
600 Main Street
Bar Harbor, ME  04609

email:  adiehl at informatics.jax.org
work:  +1 (207) 288-6427
fax:  +1 (207) 288-6131


From jblake at informatics.jax.org  Fri Apr  4 05:34:05 2008
From: jblake at informatics.jax.org (Judith Blake)
Date: Fri, 04 Apr 2008 08:34:05 -0400
Subject: [Go] Gene Symbols as GO synonyms
In-Reply-To: <E1JhfdE-0000Lm-89@web-2-05.internal.sanger.ac.uk>
References: <E1JhfdE-0000Lm-89@web-2-05.internal.sanger.ac.uk>
Message-ID: <47F6203D.4080302@informatics.jax.org>

Jane,

I am fine with Jen's comment that it's not a priority to spend extensive 
time removing gene names as synonyms, and that some inclusion of 
geneproduct-like synoyms is useful for seaching...for example, when we 
were in the attitude of removing all functions that sounded like product 
names, the product names were in fact what the community used as an 
alias for the activity name.  WE have stopped that for the most part.  
But I think the point here is that gene names should not, I think we are 
agreeing, be 'nakedly' posted as synonyms, but rather could be posted 
as, say,  "Bmp4-activity' .

Jane, could you give an example where the gene symbol, nakedly, you 
think should be included as a synonym?  or are you just pulling these 
over....maybe for the enzymes, like before, we could add 'activity'?  or 
is that too simiplistic or are you doing this bulk ?

judy


Valerie Wood wrote:
> I'm still not sure why we have include them at all. 
>
> In the long term it will confuse users because it might stop tem being able to make the distinction between the ontology and the annotations. Also, it is inconsistent, why do this for a few gene names but not all, and also for some terms which a gene product would be annotated to but not all, this can also lead to confusion, because users might think that a gene name search will always work.
>
> Jen, was the p53 case correct? (as Judy pointed out there are no p53 synonyms), but 'p53 class' is included in the term name of some terms, which is differrent.
>
> Val
>
>
> Chris Mungall <cjm at fruitfly.org> wrote: 
>   
>> On Apr 3, 2008, at 6:07 AM, Jane Lomax wrote:
>>
>>     
>>> Hi Judy - the gene symbol synonyms can sometimes be very useful for  
>>> the
>>> purposes of mappings, especially for things like enzymes where some  
>>> groups
>>> use the gene symbol in their vocabulary term name (this has been  
>>> the case
>>> for the IMG and FIGS mappings recently). So I'd rather not see them
>>> removed completely.
>>>
>>> However I do agree that seeing them can be very confusing for users  
>>> - I
>>> wonder whether we could agree to suppress RELATED synonyms in the  
>>> GO interfaces?
>>> Maybe only show them when they match a search?
>>>       
>> This seems slightly awkward - we'd have to coordinate this with every  
>> GO browser out there. And what about the RELATED synonyms that are  
>> not gene products?
>>
>> How about introducing a new synonym category (called "gene" for  
>> example)? Note that these synonyms would still be RELATED, there  
>> would just be additional metadata indicating the context for the  
>> synonym.
>>
>> I still don't think this is perfect. We shouldn't go overloading  
>> existing tags just because it happens to help with searching in a few  
>> cases.
>>
>>     
>>> jane
>>>
>>>   On Thu, 3 Apr 2008, Judith Blake wrote:
>>>
>>>       
>>>> Hi Jen,
>>>>
>>>> When I search GO terms for 'p53', this does not come back as a  
>>>> synonym,
>>>> although synonyms with the string 'p53' as part of the long series of
>>>> strings as a synonym do come back.  So I don't think that argument  
>>>> holds
>>>> anymore.  I agree that grinding through looking for synonyms that are
>>>> gene symbols is not a productive use of time, but such synonyms, I
>>>> think, should be removed as a matter of course while working on the
>>>> ontology in general as they are found.  I do not see, if 'p53' is  
>>>> not an
>>>> issue, where anything else would be an issue.
>>>>
>>>> Does anyone object to having gene symbols routinely removed as  
>>>> found as
>>>> synonyms?  Certainly the ontology editors can bring such synonyms
>>>> forward if they think there might be an issue. what do you think Jen?
>>>>
>>>> Judy
>>>>
>>>>
>>>> Jennifer Deegan (nee Clark) wrote:
>>>>         
>>>>> Hi Judy,
>>>>>
>>>>> We did think about this, but I remember that the group who work  
>>>>> on p53
>>>>> were very keen that a term covering an activity of this gene product
>>>>> should carry a synonym 'p53' to help them find the term. I am
>>>>> reluctant to remove all gene symbols as synonyms because of that,  
>>>>> but
>>>>> thought I would just tidy up these two problematic terms. We could
>>>>> certainly consider removing all gene symbol synonyms in the long  
>>>>> term,
>>>>> but it seems to me that the effort required to track them all  
>>>>> down and
>>>>> discuss individually whether they are required might not be
>>>>> worthwhile, since we have other time-consuming projects that are a
>>>>> higher priority. Would you agree?
>>>>>
>>>>> Thanks for thinking about it.
>>>>>
>>>>> Jen
>>>>>
>>>>>
>>>>> Judith Blake wrote:
>>>>>
>>>>>           
>>>>>> not the least because they aren't synonyms....
>>>>>>
>>>>>> judy
>>>>>>
>>>>>> Jim Hu wrote:
>>>>>>
>>>>>>             
>>>>>>> I agree with Judy that removing them from all terms is a good  
>>>>>>> idea.
>>>>>>>  If us microbiologists ever get our act together and start getting
>>>>>>> all the genes from metagenomics, you'll be glad you did! ;)
>>>>>>>
>>>>>>> Jim
>>>>>>>
>>>>>>>
>>>>>>> On Apr 2, 2008, at 6:06 PM, Judith Blake wrote:
>>>>>>>
>>>>>>>               
>>>>>>>> I agree with your proposal.
>>>>>>>>
>>>>>>>> Would you not remove gene symbols as synonyms from all terms?
>>>>>>>>
>>>>>>>> Judy
>>>>>>>>
>>>>>>>> Jennifer Deegan (nee Clark) wrote:
>>>>>>>>
>>>>>>>>                 
>>>>>>>>> Hi,
>>>>>>>>>
>>>>>>>>> A couple of GO terms currently contain a problematically large
>>>>>>>>> number of
>>>>>>>>>  gene symbols
>>>>>>>>> as related synonyms.
>>>>>>>>> The synonyms were imported into the OBO file during updates from
>>>>>>>>> Enzyme
>>>>>>>>> Commission data.
>>>>>>>>>
>>>>>>>>> The synonyms are a problem because they mess up the display  
>>>>>>>>> in GO
>>>>>>>>> browsers. For example:
>>>>>>>>>
>>>>>>>>> http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi? 
>>>>>>>>> term=GO:0004714&session_id=6392amigo1207145654
>>>>>>>>> <http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi? 
>>>>>>>>> term=GO:0004714&session_id=6392amigo1207145654>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> They are also confusing for users as they resemble annotations,
>>>>>>>>> but are
>>>>>>>>> only related synonyms.
>>>>>>>>>
>>>>>>>>> To resolve this problem, on 16th April we are going to remove  
>>>>>>>>> the
>>>>>>>>> list
>>>>>>>>> of gene products as related synonyms from the following terms:
>>>>>>>>>
>>>>>>>>> GO:0004714 (transmembrane receptor protein tyrosine kinase  
>>>>>>>>> activity)
>>>>>>>>> (201 gene symbols included as synonyms)
>>>>>>>>>
>>>>>>>>> GO:0004715 (non-membrane spanning protein tyrosine kinase
>>>>>>>>> activity) (84
>>>>>>>>> gene symbols included as synonyms)
>>>>>>>>>
>>>>>>>>> If you have any objection to this removal please reply to  
>>>>>>>>> Jennifer
>>>>>>>>> Deegan and Emily Dimmer.
>>>>>>>>>
>>>>>>>>> Thanks,
>>>>>>>>>
>>>>>>>>> Jennifer and Emily.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>                   
>>>>>>>> _______________________________________________
>>>>>>>> Go mailing list
>>>>>>>> Go at geneontology.org <mailto:Go at geneontology.org>
>>>>>>>> http://fafner.stanford.edu/mailman/listinfo/go
>>>>>>>>                 
>>>>>>> =====================================
>>>>>>>
>>>>>>> Jim Hu
>>>>>>>
>>>>>>> Associate Professor
>>>>>>>
>>>>>>> Dept. of Biochemistry and Biophysics
>>>>>>>
>>>>>>> 2128 TAMU
>>>>>>>
>>>>>>> Texas A&M Univ.
>>>>>>>
>>>>>>> College Station, TX 77843-2128
>>>>>>>
>>>>>>> 979-862-4054
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>               
>>>> _______________________________________________
>>>> Go mailing list
>>>> Go at geneontology.org
>>>> http://fafner.stanford.edu/mailman/listinfo/go
>>>>
>>>>         
>>> Dr Jane Lomax
>>> GO Editorial Office
>>> EMBL-EBI
>>> Wellcome Trust Genome Campus
>>> Hinxton
>>> Cambridgeshire, UK
>>> CB10 1SD
>>>
>>> p: +44 1223 492516
>>> f: +44 1223 494468
>>> _______________________________________________
>>> Go mailing list
>>> Go at geneontology.org
>>> http://fafner.stanford.edu/mailman/listinfo/go
>>>
>>>       
>> _______________________________________________
>> Go mailing list
>> Go at geneontology.org
>> http://fafner.stanford.edu/mailman/listinfo/go
>>
>>
>>     
>
>   
> ------------------------------------------------------------------------
>
> _______________________________________________
> Go mailing list
> Go at geneontology.org
> http://fafner.stanford.edu/mailman/listinfo/go
>   



From midori at ebi.ac.uk  Fri Apr  4 09:00:18 2008
From: midori at ebi.ac.uk (midori at ebi.ac.uk)
Date: Fri, 4 Apr 2008 16:00:18 UT
Subject: [Go] SourceForge Update
Message-ID: <200804041600.m34G0Ic1530072@mozart.ebi.ac.uk>

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From hitz at genome.stanford.edu  Fri Apr  4 09:02:24 2008
From: hitz at genome.stanford.edu (Ben Hitz)
Date: Fri, 4 Apr 2008 09:02:24 -0700
Subject: [Go] Gene Symbols as GO synonyms
In-Reply-To: <47F6203D.4080302@informatics.jax.org>
References: <E1JhfdE-0000Lm-89@web-2-05.internal.sanger.ac.uk>
	<47F6203D.4080302@informatics.jax.org>
Message-ID: <248D9524-3B92-4038-88EF-7E21D6AE602B@genome.stanford.edu>

Clearly they should not be synonyms of terms.   The issue (with amigo)  
is that the term and gene product searches are run separately (for  
performance reasons).   What would "solve" the problem is to combine  
the basic search, so that if you type in "p53" you get a list of  
gene_products, and it should be relatively obvious how to get to the  
correct terms from there.

Ben
--
Ben Hitz
Senior Scientific Programmer ** Saccharomyces Genome Database ** GO  
Consortium
Stanford University ** hitz at genome.stanford.edu




From jblake at informatics.jax.org  Fri Apr  4 09:18:30 2008
From: jblake at informatics.jax.org (Judith Blake)
Date: Fri, 04 Apr 2008 12:18:30 -0400
Subject: [Go] Gene Symbols as GO synonyms
In-Reply-To: <248D9524-3B92-4038-88EF-7E21D6AE602B@genome.stanford.edu>
References: <E1JhfdE-0000Lm-89@web-2-05.internal.sanger.ac.uk>
	<47F6203D.4080302@informatics.jax.org>
	<248D9524-3B92-4038-88EF-7E21D6AE602B@genome.stanford.edu>
Message-ID: <47F654D6.1040308@informatics.jax.org>

Great idea Ben,

so in the quick search, the default might be selecting 'all' rather than 
GO term or Gene Product buttons.

then the results would be sorted first by GO term and then by Gene 
Product terms

and synonyms would be searched.

Judy

Ben Hitz wrote:
> Clearly they should not be synonyms of terms.   The issue (with amigo) 
> is that the term and gene product searches are run separately (for 
> performance reasons).   What would "solve" the problem is to combine 
> the basic search, so that if you type in "p53" you get a list of 
> gene_products, and it should be relatively obvious how to get to the 
> correct terms from there.
>
> Ben
> -- 
> Ben Hitz
> Senior Scientific Programmer ** Saccharomyces Genome Database ** GO 
> Consortium
> Stanford University ** hitz at genome.stanford.edu
>
>
>

From Sophie.DERET at galderma.com  Fri Apr  4 00:23:04 2008
From: Sophie.DERET at galderma.com (DERET Sophie)
Date: Fri, 4 Apr 2008 09:23:04 +0200
Subject: [Go] [Gofriends] GO tools
Message-ID: <9C2081B5FF465A4BB637BE293A8A00C208041276@frncemsx01.sd.galderma.com>

Dear all,

Do you know of any GO tool that allows you to visualise simultaneously
the GO

annotations of several gene lists (on the same DAG view) ?

Thanks a lot.

Sophie

 

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Gofriends mailing list
Gofriends at geneontology.org
http://fafner.stanford.edu/mailman/listinfo/gofriends

From jblake at informatics.jax.org  Sat Apr  5 07:15:57 2008
From: jblake at informatics.jax.org (Judith Blake)
Date: Sat, 05 Apr 2008 10:15:57 -0400
Subject: [Go] Ontology development - March highlights
In-Reply-To: <Pine.LNX.4.64.0803311349570.24397@pigeon.ebi.ac.uk>
References: <Pine.LNX.4.64.0803311349570.24397@pigeon.ebi.ac.uk>
Message-ID: <47F7899D.8060505@informatics.jax.org>


Midori, David, and ontology developers.

Congratulations on getting the 'regulates' changes done and for all the 
other work going on.

Thanks for the report.

Judy


Midori Harris wrote:
> Dear GO,
>
> The most recent monthly report on ontology content, for March 2008, is now 
> available at:
>
>    http://gocwiki.geneontology.org/index.php/Mar2008_report
>
> Ontology development highlights from March:
>
>   * The 'regulates' relationships have gone live! They are now used in the 
> gene_ontology*.obo files and will be visible in AmiGO very soon (if they 
> aren't already). Many thanks to all who helped with this work, especially 
> David, Tanya and Chris.
>
>   * We're down to one live 'sensu' term, and it will be changed before the 
> GOC meeting (main wiki page: 
> http://gocwiki.geneontology.org/index.php/Sensu_Main_Page; outstanding 
> items: http://gocwiki.geneontology.org/index.php/Meeting_Notes_3).
>
>   * Reorganization of electron transport terms has been implemented 
> (http://wiki.geneontology.org/index.php/Electron_transport).
>
>   * Two pilot projects are under way, one on electron transport and the 
> other on glycolysis and the TCA cycle, to document links between function 
> terms and process terms. Function-process main page: 
> http://wiki.geneontology.org/index.php/Function-Process_Links.
>
>   * An overhaul of signal transduction process terms has begun 
> (http://wiki.geneontology.org/index.php/Signaling).
>
> In April, the function-process pilot projects will continue, as will the 
> signaling overhaul and quality control work connected with the regulation 
> terms. We also hope to implement changes stemming from the lung 
> development content meeting 
> (http://wiki.geneontology.org/index.php/Lung_Development).
>
> There are several content-related items proposed for the GOC meeting 
> agenda 
> (http://wiki.geneontology.org/index.php/SLC_GO_Consortium_Meeting#Agenda_Items).
>
> As usual, details of small- and medium-scale changes are available in the 
> SourceForge Curator Requests tracker. Please contact us if you want to help out 
> with ontology work in a particular area, or if you have any comments or 
> questions about what's going on.
>
> Ontology Development wiki:
> http://wiki.geneontology.org/index.php/Ontology_Development
>
> SourceForge Curator Requests tracker:
> https://sourceforge.net/tracker/?group_id=36855&atid=440764
>
> Midori & David
> on behalf of GO's ontology developers
> _______________________________________________
> Go mailing list
> Go at geneontology.org
> http://fafner.stanford.edu/mailman/listinfo/go
>   



From midori at ebi.ac.uk  Sat Apr  5 09:00:24 2008
From: midori at ebi.ac.uk (midori at ebi.ac.uk)
Date: Sat, 5 Apr 2008 16:00:24 UT
Subject: [Go] SourceForge Update
Message-ID: <200804051600.m35G0OS1252839@mozart.ebi.ac.uk>

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From goetz_stefan at gmx.de  Sat Apr  5 06:51:41 2008
From: goetz_stefan at gmx.de (Stefan Goetz)
Date: Sat, 05 Apr 2008 15:51:41 +0200
Subject: [Go] [Gofriends] GO tools
In-Reply-To: <9C2081B5FF465A4BB637BE293A8A00C208041276@frncemsx01.sd.galderma.com>
References: <9C2081B5FF465A4BB637BE293A8A00C208041276@frncemsx01.sd.galderma.com>
Message-ID: <47F783ED.3080406@gmx.de>

Dear Sopie,
please have a look at the GO-Graph-Viewer from the Babelomics suite at 
www.babelomics.org.

"The DAG viewer tool generates joined gene ontology graphs (DAGs) to 
create overviews of the functional context of groups of sequences. 
Interactive graph visualization allows the navigation of large and 
unwieldy graphs often generated when trying to biologically explore 
large sets of sequence annotations. Zoom and graph navigation is 
provided through the DAG viewer Java Web Start tool."

You can find a tutorial here:
http://bioinfo.cipf.es/babelomicswiki/doku.php?id=tool:gographviz

If your need any further support or help just contact us again!
Best regards,
Stefan Goetz

--------------------------------------------
Stefan G?tz
Bioinformatics Department
Centro de Investigaci?n Pr?ncipe Felipe (CIPF)
C/E.P. Avda. Autopista del Saler, 16-3 (junto Oceanogr?fico)
46013 Valencia, Spain
Tel: +34 963289680 Ext. 1011
Fax: +34 963289574
E-Mail: sgoetz at cipf.es
http://bioinfo.cipf.es
--------------------------------------------


DERET Sophie wrote:
>
> Dear all,
>
> Do you know** ****of*** *any GO tool that allows you to visualise 
> _simultaneously_ the GO
>
> annotations of _several_ gene lists (on the same DAG view) ?
>
> Thanks a lot.
>
> Sophie
>
>  
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> Gofriends mailing list
> Gofriends at geneontology.org
> http://fafner.stanford.edu/mailman/listinfo/gofriends
>   

_______________________________________________
Gofriends mailing list
Gofriends at geneontology.org
http://fafner.stanford.edu/mailman/listinfo/gofriends


From midori at ebi.ac.uk  Mon Apr  7 09:00:20 2008
From: midori at ebi.ac.uk (midori at ebi.ac.uk)
Date: Mon, 7 Apr 2008 16:00:20 UT
Subject: [Go] SourceForge Update
Message-ID: <200804071600.m37G0Kr1357890@mozart.ebi.ac.uk>

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From suzi at berkeleybop.org  Mon Apr  7 12:09:53 2008
From: suzi at berkeleybop.org (Suzanna Lewis)
Date: Mon, 7 Apr 2008 12:09:53 -0700
Subject: [Go] Ontology development - March highlights
In-Reply-To: <Pine.LNX.4.64.0803311349570.24397@pigeon.ebi.ac.uk>
References: <Pine.LNX.4.64.0803311349570.24397@pigeon.ebi.ac.uk>
Message-ID: <FC1F7B9F-5C29-4478-8AE2-2D4680331123@berkeleybop.org>

Thanks for the report Midori and David.

Nice choices for the pilot project with the process-to-function links.  
We'll be discussing the required relation(s) at the upcoming RO  
meeting in Denver and David, Chris and Tanya will be there to make  
sure it's right in the RO.

-S

On Apr 1, 2008, at 6:32 AM, Midori Harris wrote:

> Dear GO,
>
> The most recent monthly report on ontology content, for March 2008,  
> is now
> available at:
>
>   http://gocwiki.geneontology.org/index.php/Mar2008_report
>
> Ontology development highlights from March:
>
>  * The 'regulates' relationships have gone live! They are now used  
> in the
> gene_ontology*.obo files and will be visible in AmiGO very soon (if  
> they
> aren't already). Many thanks to all who helped with this work,  
> especially
> David, Tanya and Chris.
>
>  * We're down to one live 'sensu' term, and it will be changed  
> before the
> GOC meeting (main wiki page:
> http://gocwiki.geneontology.org/index.php/Sensu_Main_Page; outstanding
> items: http://gocwiki.geneontology.org/index.php/Meeting_Notes_3).
>
>  * Reorganization of electron transport terms has been implemented
> (http://wiki.geneontology.org/index.php/Electron_transport).
>
>  * Two pilot projects are under way, one on electron transport and the
> other on glycolysis and the TCA cycle, to document links between  
> function
> terms and process terms. Function-process main page:
> http://wiki.geneontology.org/index.php/Function-Process_Links.
>
>  * An overhaul of signal transduction process terms has begun
> (http://wiki.geneontology.org/index.php/Signaling).
>
> In April, the function-process pilot projects will continue, as will  
> the
> signaling overhaul and quality control work connected with the  
> regulation
> terms. We also hope to implement changes stemming from the lung
> development content meeting
> (http://wiki.geneontology.org/index.php/Lung_Development).
>
> There are several content-related items proposed for the GOC meeting
> agenda
> (http://wiki.geneontology.org/index.php/SLC_GO_Consortium_Meeting#Agenda_Items 
> ).
>
> As usual, details of small- and medium-scale changes are available  
> in the
> SourceForge Curator Requests tracker. Please contact us if you want  
> to help out
> with ontology work in a particular area, or if you have any comments  
> or
> questions about what's going on.
>
> Ontology Development wiki:
> http://wiki.geneontology.org/index.php/Ontology_Development
>
> SourceForge Curator Requests tracker:
> https://sourceforge.net/tracker/?group_id=36855&atid=440764
>
> Midori & David
> on behalf of GO's ontology developers
> _______________________________________________
> Go mailing list
> Go at geneontology.org
> http://fafner.stanford.edu/mailman/listinfo/go
>


From jane at ebi.ac.uk  Tue Apr  8 05:48:12 2008
From: jane at ebi.ac.uk (Jane Lomax)
Date: Tue, 8 Apr 2008 13:48:12 +0100 (BST)
Subject: [Go] Gene Symbols as GO synonyms
In-Reply-To: <47F6203D.4080302@informatics.jax.org>
References: <E1JhfdE-0000Lm-89@web-2-05.internal.sanger.ac.uk>
	<47F6203D.4080302@informatics.jax.org>
Message-ID: <Pine.LNX.4.62.0804081343310.6770@puffin.ebi.ac.uk>

Hi Judy - I'd be fine adding '-activity' to the gene symbol synonyms if 
people think it would help - for mapping purposes I don't think it would 
make any difference.

Alex - these are prokaryotic mappings, and most of the genes are 
prok-specific and therefore have no manual annotation (or often any 
annotation) so not sure using ga files would work.

Jane


On Fri, 4 Apr 2008, Judith Blake wrote:

> Jane,
>
> I am fine with Jen's comment that it's not a priority to spend extensive
> time removing gene names as synonyms, and that some inclusion of
> geneproduct-like synoyms is useful for seaching...for example, when we
> were in the attitude of removing all functions that sounded like product
> names, the product names were in fact what the community used as an
> alias for the activity name.  WE have stopped that for the most part.
> But I think the point here is that gene names should not, I think we are
> agreeing, be 'nakedly' posted as synonyms, but rather could be posted
> as, say,  "Bmp4-activity' .
>
> Jane, could you give an example where the gene symbol, nakedly, you
> think should be included as a synonym?  or are you just pulling these
> over....maybe for the enzymes, like before, we could add 'activity'?  or
> is that too simiplistic or are you doing this bulk ?
>
> judy
>
>
> Valerie Wood wrote:
>> I'm still not sure why we have include them at all.
>>
>> In the long term it will confuse users because it might stop tem being able to make the distinction between the ontology and the annotations. Also, it is inconsistent, why do this for a few gene names but not all, and also for some terms which a gene product would be annotated to but not all, this can also lead to confusion, because users might think that a gene name search will always work.
>>
>> Jen, was the p53 case correct? (as Judy pointed out there are no p53 synonyms), but 'p53 class' is included in the term name of some terms, which is differrent.
>>
>> Val
>>
>>
>> Chris Mungall <cjm at fruitfly.org> wrote:
>>
>>> On Apr 3, 2008, at 6:07 AM, Jane Lomax wrote:
>>>
>>>
>>>> Hi Judy - the gene symbol synonyms can sometimes be very useful for
>>>> the
>>>> purposes of mappings, especially for things like enzymes where some
>>>> groups
>>>> use the gene symbol in their vocabulary term name (this has been
>>>> the case
>>>> for the IMG and FIGS mappings recently). So I'd rather not see them
>>>> removed completely.
>>>>
>>>> However I do agree that seeing them can be very confusing for users
>>>> - I
>>>> wonder whether we could agree to suppress RELATED synonyms in the
>>>> GO interfaces?
>>>> Maybe only show them when they match a search?
>>>>
>>> This seems slightly awkward - we'd have to coordinate this with every
>>> GO browser out there. And what about the RELATED synonyms that are
>>> not gene products?
>>>
>>> How about introducing a new synonym category (called "gene" for
>>> example)? Note that these synonyms would still be RELATED, there
>>> would just be additional metadata indicating the context for the
>>> synonym.
>>>
>>> I still don't think this is perfect. We shouldn't go overloading
>>> existing tags just because it happens to help with searching in a few
>>> cases.
>>>
>>>
>>>> jane
>>>>
>>>>   On Thu, 3 Apr 2008, Judith Blake wrote:
>>>>
>>>>
>>>>> Hi Jen,
>>>>>
>>>>> When I search GO terms for 'p53', this does not come back as a
>>>>> synonym,
>>>>> although synonyms with the string 'p53' as part of the long series of
>>>>> strings as a synonym do come back.  So I don't think that argument
>>>>> holds
>>>>> anymore.  I agree that grinding through looking for synonyms that are
>>>>> gene symbols is not a productive use of time, but such synonyms, I
>>>>> think, should be removed as a matter of course while working on the
>>>>> ontology in general as they are found.  I do not see, if 'p53' is
>>>>> not an
>>>>> issue, where anything else would be an issue.
>>>>>
>>>>> Does anyone object to having gene symbols routinely removed as
>>>>> found as
>>>>> synonyms?  Certainly the ontology editors can bring such synonyms
>>>>> forward if they think there might be an issue. what do you think Jen?
>>>>>
>>>>> Judy
>>>>>
>>>>>
>>>>> Jennifer Deegan (nee Clark) wrote:
>>>>>
>>>>>> Hi Judy,
>>>>>>
>>>>>> We did think about this, but I remember that the group who work
>>>>>> on p53
>>>>>> were very keen that a term covering an activity of this gene product
>>>>>> should carry a synonym 'p53' to help them find the term. I am
>>>>>> reluctant to remove all gene symbols as synonyms because of that,
>>>>>> but
>>>>>> thought I would just tidy up these two problematic terms. We could
>>>>>> certainly consider removing all gene symbol synonyms in the long
>>>>>> term,
>>>>>> but it seems to me that the effort required to track them all
>>>>>> down and
>>>>>> discuss individually whether they are required might not be
>>>>>> worthwhile, since we have other time-consuming projects that are a
>>>>>> higher priority. Would you agree?
>>>>>>
>>>>>> Thanks for thinking about it.
>>>>>>
>>>>>> Jen
>>>>>>
>>>>>>
>>>>>> Judith Blake wrote:
>>>>>>
>>>>>>
>>>>>>> not the least because they aren't synonyms....
>>>>>>>
>>>>>>> judy
>>>>>>>
>>>>>>> Jim Hu wrote:
>>>>>>>
>>>>>>>
>>>>>>>> I agree with Judy that removing them from all terms is a good
>>>>>>>> idea.
>>>>>>>>  If us microbiologists ever get our act together and start getting
>>>>>>>> all the genes from metagenomics, you'll be glad you did! ;)
>>>>>>>>
>>>>>>>> Jim
>>>>>>>>
>>>>>>>>
>>>>>>>> On Apr 2, 2008, at 6:06 PM, Judith Blake wrote:
>>>>>>>>
>>>>>>>>
>>>>>>>>> I agree with your proposal.
>>>>>>>>>
>>>>>>>>> Would you not remove gene symbols as synonyms from all terms?
>>>>>>>>>
>>>>>>>>> Judy
>>>>>>>>>
>>>>>>>>> Jennifer Deegan (nee Clark) wrote:
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>> Hi,
>>>>>>>>>>
>>>>>>>>>> A couple of GO terms currently contain a problematically large
>>>>>>>>>> number of
>>>>>>>>>>  gene symbols
>>>>>>>>>> as related synonyms.
>>>>>>>>>> The synonyms were imported into the OBO file during updates from
>>>>>>>>>> Enzyme
>>>>>>>>>> Commission data.
>>>>>>>>>>
>>>>>>>>>> The synonyms are a problem because they mess up the display
>>>>>>>>>> in GO
>>>>>>>>>> browsers. For example:
>>>>>>>>>>
>>>>>>>>>> http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?
>>>>>>>>>> term=GO:0004714&session_id=6392amigo1207145654
>>>>>>>>>> <http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?
>>>>>>>>>> term=GO:0004714&session_id=6392amigo1207145654>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> They are also confusing for users as they resemble annotations,
>>>>>>>>>> but are
>>>>>>>>>> only related synonyms.
>>>>>>>>>>
>>>>>>>>>> To resolve this problem, on 16th April we are going to remove
>>>>>>>>>> the
>>>>>>>>>> list
>>>>>>>>>> of gene products as related synonyms from the following terms:
>>>>>>>>>>
>>>>>>>>>> GO:0004714 (transmembrane receptor protein tyrosine kinase
>>>>>>>>>> activity)
>>>>>>>>>> (201 gene symbols included as synonyms)
>>>>>>>>>>
>>>>>>>>>> GO:0004715 (non-membrane spanning protein tyrosine kinase
>>>>>>>>>> activity) (84
>>>>>>>>>> gene symbols included as synonyms)
>>>>>>>>>>
>>>>>>>>>> If you have any objection to this removal please reply to
>>>>>>>>>> Jennifer
>>>>>>>>>> Deegan and Emily Dimmer.
>>>>>>>>>>
>>>>>>>>>> Thanks,
>>>>>>>>>>
>>>>>>>>>> Jennifer and Emily.
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> Go mailing list
>>>>>>>>> Go at geneontology.org <mailto:Go at geneontology.org>
>>>>>>>>> http://fafner.stanford.edu/mailman/listinfo/go
>>>>>>>>>
>>>>>>>> =====================================
>>>>>>>>
>>>>>>>> Jim Hu
>>>>>>>>
>>>>>>>> Associate Professor
>>>>>>>>
>>>>>>>> Dept. of Biochemistry and Biophysics
>>>>>>>>
>>>>>>>> 2128 TAMU
>>>>>>>>
>>>>>>>> Texas A&M Univ.
>>>>>>>>
>>>>>>>> College Station, TX 77843-2128
>>>>>>>>
>>>>>>>> 979-862-4054
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>> _______________________________________________
>>>>> Go mailing list
>>>>> Go at geneontology.org
>>>>> http://fafner.stanford.edu/mailman/listinfo/go
>>>>>
>>>>>
>>>> Dr Jane Lomax
>>>> GO Editorial Office
>>>> EMBL-EBI
>>>> Wellcome Trust Genome Campus
>>>> Hinxton
>>>> Cambridgeshire, UK
>>>> CB10 1SD
>>>>
>>>> p: +44 1223 492516
>>>> f: +44 1223 494468
>>>> _______________________________________________
>>>> Go mailing list
>>>> Go at geneontology.org
>>>> http://fafner.stanford.edu/mailman/listinfo/go
>>>>
>>>>
>>> _______________________________________________
>>> Go mailing list
>>> Go at geneontology.org
>>> http://fafner.stanford.edu/mailman/listinfo/go
>>>
>>>
>>>
>>
>>
>> ------------------------------------------------------------------------
>>
>> _______________________________________________
>> Go mailing list
>> Go at geneontology.org
>> http://fafner.stanford.edu/mailman/listinfo/go
>>
>
>
> _______________________________________________
> Go mailing list
> Go at geneontology.org
> http://fafner.stanford.edu/mailman/listinfo/go
>

Dr Jane Lomax
GO Editorial Office
EMBL-EBI
Wellcome Trust Genome Campus
Hinxton
Cambridgeshire, UK
CB10 1SD

p: +44 1223 492516
f: +44 1223 494468

From jblake at informatics.jax.org  Tue Apr  8 08:34:44 2008
From: jblake at informatics.jax.org (Judith Blake)
Date: Tue, 08 Apr 2008 11:34:44 -0400
Subject: [Go] Gene Symbols as GO synonyms
In-Reply-To: <Pine.LNX.4.62.0804081343310.6770@puffin.ebi.ac.uk>
References: <E1JhfdE-0000Lm-89@web-2-05.internal.sanger.ac.uk>
	<47F6203D.4080302@informatics.jax.org>
	<Pine.LNX.4.62.0804081343310.6770@puffin.ebi.ac.uk>
Message-ID: <47FB9094.9030405@informatics.jax.org>

this would work for me

judy

Jane Lomax wrote:
> Hi Judy - I'd be fine adding '-activity' to the gene symbol synonyms 
> if people think it would help - for mapping purposes I don't think it 
> would make any difference.
>
> Alex - these are prokaryotic mappings, and most of the genes are 
> prok-specific and therefore have no manual annotation (or often any 
> annotation) so not sure using ga files would work.
>
> Jane
>
>
> On Fri, 4 Apr 2008, Judith Blake wrote:
>
>> Jane,
>>
>> I am fine with Jen's comment that it's not a priority to spend extensive
>> time removing gene names as synonyms, and that some inclusion of
>> geneproduct-like synoyms is useful for seaching...for example, when we
>> were in the attitude of removing all functions that sounded like product
>> names, the product names were in fact what the community used as an
>> alias for the activity name.  WE have stopped that for the most part.
>> But I think the point here is that gene names should not, I think we are
>> agreeing, be 'nakedly' posted as synonyms, but rather could be posted
>> as, say,  "Bmp4-activity' .
>>
>> Jane, could you give an example where the gene symbol, nakedly, you
>> think should be included as a synonym?  or are you just pulling these
>> over....maybe for the enzymes, like before, we could add 'activity'?  or
>> is that too simiplistic or are you doing this bulk ?
>>
>> judy
>>
>>
>> Valerie Wood wrote:
>>> I'm still not sure why we have include them at all.
>>>
>>> In the long term it will confuse users because it might stop tem 
>>> being able to make the distinction between the ontology and the 
>>> annotations. Also, it is inconsistent, why do this for a few gene 
>>> names but not all, and also for some terms which a gene product 
>>> would be annotated to but not all, this can also lead to confusion, 
>>> because users might think that a gene name search will always work.
>>>
>>> Jen, was the p53 case correct? (as Judy pointed out there are no p53 
>>> synonyms), but 'p53 class' is included in the term name of some 
>>> terms, which is differrent.
>>>
>>> Val
>>>
>>>
>>> Chris Mungall <cjm at fruitfly.org> wrote:
>>>
>>>> On Apr 3, 2008, at 6:07 AM, Jane Lomax wrote:
>>>>
>>>>
>>>>> Hi Judy - the gene symbol synonyms can sometimes be very useful for
>>>>> the
>>>>> purposes of mappings, especially for things like enzymes where some
>>>>> groups
>>>>> use the gene symbol in their vocabulary term name (this has been
>>>>> the case
>>>>> for the IMG and FIGS mappings recently). So I'd rather not see them
>>>>> removed completely.
>>>>>
>>>>> However I do agree that seeing them can be very confusing for users
>>>>> - I
>>>>> wonder whether we could agree to suppress RELATED synonyms in the
>>>>> GO interfaces?
>>>>> Maybe only show them when they match a search?
>>>>>
>>>> This seems slightly awkward - we'd have to coordinate this with every
>>>> GO browser out there. And what about the RELATED synonyms that are
>>>> not gene products?
>>>>
>>>> How about introducing a new synonym category (called "gene" for
>>>> example)? Note that these synonyms would still be RELATED, there
>>>> would just be additional metadata indicating the context for the
>>>> synonym.
>>>>
>>>> I still don't think this is perfect. We shouldn't go overloading
>>>> existing tags just because it happens to help with searching in a few
>>>> cases.
>>>>
>>>>
>>>>> jane
>>>>>
>>>>>   On Thu, 3 Apr 2008, Judith Blake wrote:
>>>>>
>>>>>
>>>>>> Hi Jen,
>>>>>>
>>>>>> When I search GO terms for 'p53', this does not come back as a
>>>>>> synonym,
>>>>>> although synonyms with the string 'p53' as part of the long 
>>>>>> series of
>>>>>> strings as a synonym do come back.  So I don't think that argument
>>>>>> holds
>>>>>> anymore.  I agree that grinding through looking for synonyms that 
>>>>>> are
>>>>>> gene symbols is not a productive use of time, but such synonyms, I
>>>>>> think, should be removed as a matter of course while working on the
>>>>>> ontology in general as they are found.  I do not see, if 'p53' is
>>>>>> not an
>>>>>> issue, where anything else would be an issue.
>>>>>>
>>>>>> Does anyone object to having gene symbols routinely removed as
>>>>>> found as
>>>>>> synonyms?  Certainly the ontology editors can bring such synonyms
>>>>>> forward if they think there might be an issue. what do you think 
>>>>>> Jen?
>>>>>>
>>>>>> Judy
>>>>>>
>>>>>>
>>>>>> Jennifer Deegan (nee Clark) wrote:
>>>>>>
>>>>>>> Hi Judy,
>>>>>>>
>>>>>>> We did think about this, but I remember that the group who work
>>>>>>> on p53
>>>>>>> were very keen that a term covering an activity of this gene 
>>>>>>> product
>>>>>>> should carry a synonym 'p53' to help them find the term. I am
>>>>>>> reluctant to remove all gene symbols as synonyms because of that,
>>>>>>> but
>>>>>>> thought I would just tidy up these two problematic terms. We could
>>>>>>> certainly consider removing all gene symbol synonyms in the long
>>>>>>> term,
>>>>>>> but it seems to me that the effort required to track them all
>>>>>>> down and
>>>>>>> discuss individually whether they are required might not be
>>>>>>> worthwhile, since we have other time-consuming projects that are a
>>>>>>> higher priority. Would you agree?
>>>>>>>
>>>>>>> Thanks for thinking about it.
>>>>>>>
>>>>>>> Jen
>>>>>>>
>>>>>>>
>>>>>>> Judith Blake wrote:
>>>>>>>
>>>>>>>
>>>>>>>> not the least because they aren't synonyms....
>>>>>>>>
>>>>>>>> judy
>>>>>>>>
>>>>>>>> Jim Hu wrote:
>>>>>>>>
>>>>>>>>
>>>>>>>>> I agree with Judy that removing them from all terms is a good
>>>>>>>>> idea.
>>>>>>>>>  If us microbiologists ever get our act together and start 
>>>>>>>>> getting
>>>>>>>>> all the genes from metagenomics, you'll be glad you did! ;)
>>>>>>>>>
>>>>>>>>> Jim
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On Apr 2, 2008, at 6:06 PM, Judith Blake wrote:
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>> I agree with your proposal.
>>>>>>>>>>
>>>>>>>>>> Would you not remove gene symbols as synonyms from all terms?
>>>>>>>>>>
>>>>>>>>>> Judy
>>>>>>>>>>
>>>>>>>>>> Jennifer Deegan (nee Clark) wrote:
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>> Hi,
>>>>>>>>>>>
>>>>>>>>>>> A couple of GO terms currently contain a problematically large
>>>>>>>>>>> number of
>>>>>>>>>>>  gene symbols
>>>>>>>>>>> as related synonyms.
>>>>>>>>>>> The synonyms were imported into the OBO file during updates 
>>>>>>>>>>> from
>>>>>>>>>>> Enzyme
>>>>>>>>>>> Commission data.
>>>>>>>>>>>
>>>>>>>>>>> The synonyms are a problem because they mess up the display
>>>>>>>>>>> in GO
>>>>>>>>>>> browsers. For example:
>>>>>>>>>>>
>>>>>>>>>>> http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?
>>>>>>>>>>> term=GO:0004714&session_id=6392amigo1207145654
>>>>>>>>>>> <http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?
>>>>>>>>>>> term=GO:0004714&session_id=6392amigo1207145654>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> They are also confusing for users as they resemble annotations,
>>>>>>>>>>> but are
>>>>>>>>>>> only related synonyms.
>>>>>>>>>>>
>>>>>>>>>>> To resolve this problem, on 16th April we are going to remove
>>>>>>>>>>> the
>>>>>>>>>>> list
>>>>>>>>>>> of gene products as related synonyms from the following terms:
>>>>>>>>>>>
>>>>>>>>>>> GO:0004714 (transmembrane receptor protein tyrosine kinase
>>>>>>>>>>> activity)
>>>>>>>>>>> (201 gene symbols included as synonyms)
>>>>>>>>>>>
>>>>>>>>>>> GO:0004715 (non-membrane spanning protein tyro