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

Benjamin Hitz hitz at genome.stanford.edu
Thu Jun 4 10:01:47 PDT 2009


I object too as I am sure we have this hard coded somewhere.  I agree  
with the sentiment, however.
It's a special case - but the root terms ARE special cases (especially  
since they now essentially mean "unknown")


Ben
On Jun 4, 2009, at 7:47 AM, Petri, Victoria wrote:

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






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