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[Gofriends] Alert: proposal to remove underscores from root term names

Sorin Draghici sorin at
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,

Sorin Draghici

Midori Harris wrote:
> We have received one comment so far:
>   Date: Thu, 04 Jun 2009 08:31:29 -0400
>   From: Barry Zeeberg <zeebergb at>
>   To: Midori Harris <midori at>
>   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
>> Wellcome Trust Genome Campus
>> Hinxton
>> Cambridge CB10 1SD UK
>> Tel: +44 (0) 1223 494667
>> Fax: +44 (0) 1223 494468
>> Email: midori at
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