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

Midori Harris midori at
Thu Jun 4 06:34:18 PDT 2009

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.


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 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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