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[Gofriends] FW: Alert: proposal to remove underscores from rootterm names

Petri, Victoria vpetri at mcw.edu
Thu Jun 4 07:47:27 PDT 2009


Hello,

I'm forwarding the e-mail I got from our developer(s) - on our side the change will create problems and we too are short at the time in available developers. So, I suggest waiting. I agree that it may be inconsistent but we 'lived' with it w/out much if any problems. If the change happens as dated, we will/may be unable to load newer version of the ontologies.

Thanks,

Victoria

Victoria Petri, Ph.D.
Research Scientist
Rat Genome Database 
(http://rgd.mcw.edu)
Bioinformatics Program
Human and Molecular Genetics Center
Medical College of Wisconsin 
8701 Watertown Plank Road, Milwaukee, WI 53226
(414) 456-7507
Fax (414) 456-6595 
vpetri at mcw.edu

 


-----Original Message-----
From: Stoddard, Alexander 
Sent: Thursday, June 04, 2009 9:40 AM
To: Petri, Victoria; Bakir, Burcu; De Pons, Jeff
Cc: Shimoyama, Mary; Patzer, Andrew
Subject: RE: [Gofriends] Alert: proposal to remove underscores from rootterm names

A quick check of the code base shows that it does depend on the term name (NOT the stable GO id) to look up the root terms.
In the ontology loading code the file "createDBMFiles.pl" uses a search for the terms "biological_process" etc to look up the root.

At least that file will need to be updated or our ontology stuff will break.

I have not checked the website code yet, just the ontology loading code.

Our ontology updates are currently on a manual schedule, not an automatic update, so I can coordinate testing of our ontology / Portal code with the change without the risk of the public site breaking.

Given the timing of the change (I may be the only RGD developer here) and the possibility that it won't happen at all I propose waiting to see if it actually happens. If so, I can then spend time to patch our code and test it. 


Thank you,
Alex



-----Original Message-----
From: Petri, Victoria 
Sent: Thursday, June 04, 2009 8:53 AM
To: Stoddard, Alexander; Bakir, Burcu; De Pons, Jeff
Subject: FW: [Gofriends] Alert: proposal to remove underscores from rootterm names

Hello,

I don't know who is going to take care of uploading ontologies, but here is a proposal for changing the root terms of the three GO ontologies from underscore to space (and reaction to it). I know that in the past when such a change was introduced - I believe it was the opposite - we had problems loading the ontologies. 

Please let me know and/or reply to this forwarded message.

Thanks,

Victoria

Victoria Petri, Ph.D.
Research Scientist
Rat Genome Database 
(http://rgd.mcw.edu)
Bioinformatics Program
Human and Molecular Genetics Center
Medical College of Wisconsin 
8701 Watertown Plank Road, Milwaukee, WI 53226
(414) 456-7507
Fax (414) 456-6595 
vpetri at mcw.edu

 

-----Original Message-----
From: gofriends-bounces at genome.stanford.edu [mailto:gofriends-bounces at genome.stanford.edu] On Behalf Of Midori Harris
Sent: Thursday, June 04, 2009 8:34 AM
To: GO Friends
Subject: Re: [Gofriends] Alert: proposal to remove underscores from rootterm names

We have received one comment so far:

   Date: Thu, 04 Jun 2009 08:31:29 -0400
   From: Barry Zeeberg <zeebergb at mail.nih.gov>
   To: Midori Harris <midori at ebi.ac.uk>
   Subject: Re: [Gofriends] Alert: proposal to remove underscores from root
   term names

   Dear Midori,

   I agree the underscores are inconsistent, but that inconsistency
   should not have been introduced in the first place. Given that it
   unfortunately was introduced, I think that you should not change it
   at this late date, as that could lead to a lot of effort, by us and
   other developers, to change existing software that relies on that
   format. We have lost most of our software team, and it would add to
   our problems to have to track down all the potential places for
   problems (or to have users run into these problems).

   So I really hope you can re-consider this action.

   Thanks,
   Barry

Note that the proposed change would affect only the 'name' tag in an OBO 
stanza, and the 'name' field of the 'term' table in the MySQL database; 
these fields are changed fairly frequently for non-root terms.

Midori

On Thu, 4 Jun 2009, Midori Harris wrote:

> Dear GO and Friends,
>
> A proposal has been made to remove the underscores from the names of the 
> three ontology roots in GO:
>
>  name: biological_process	-->	name: biological process
>  name: cellular_component	-->	name: cellular component
>  name: molecular_function	-->	name: molecular function
>
> The reason for this change is consistency: at present these are the only term 
> names that contain underscores instead of spaces.
>
> The namespaces will be unaffected; i.e. they will still contain underscores.
>
> This will affect you if you are using the root name as a surrogate for the 
> ontology name (obo namespace) in a space-delimited file, or if you have any 
> sfotware that assumes that the root name is exactly the same as the ontology 
> name (note that OBO namespaces do not allow spaces, but in many ontologies, 
> including GO, spaces are allowed in term names).
>
> If there are no objections raised, we will make this change on Friday, June 
> 19, 2009.
>
> Thanks,
> Midori
> on behalf of GO's ontology developers
>
>
> ============================
> Midori A. Harris, Ph.D.
> GO Editor
> EMBL - EBI
> Wellcome Trust Genome Campus
> Hinxton
> Cambridge CB10 1SD UK
>
> Tel: +44 (0) 1223 494667
> Fax: +44 (0) 1223 494468
> Email: midori at ebi.ac.uk
>
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