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[Gofriends] Alert: proposal to remove underscores from root term names
sorin at wayne.edu
Thu Jun 4 12:52:53 PDT 2009
The Onto-Tools should be ok with the proposed changes. I bet that
somebody, somewhere did hard code these :-), but it should not be a
big deal to fix the source code since we know exactly what to look for.
However, if you decide to go ahead with it, I propose to make this
change together with other necessary changes, next time GO needs a
major overhaul. The overhead of switching somebody from whatever they
are doing to fixing this is not justified for this issue alone.
All the best,
Midori Harris wrote:
> 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.
> 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.
> 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
>> 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.
>> on behalf of GO's ontology developers
>> Midori A. Harris, Ph.D.
>> GO Editor
>> EMBL - EBI
>> Wellcome Trust Genome Campus
>> Cambridge CB10 1SD UK
>> Tel: +44 (0) 1223 494667
>> Fax: +44 (0) 1223 494468
>> Email: midori at ebi.ac.uk
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