[go] Fwd: [Obo-discuss] biological processes & molecular functions

[Chris Mungall]

For anyone who is interested: the function vs process issue has come  
up again, this time on the obo-discuss list

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Begin forwarded message:

> From: Mike Bada <mike.bada at UCHSC.edu>
> Date: January 12, 2008 7:13:23 PM PST
> To: obo-discuss at lists.sourceforge.net
> Subject: [Obo-discuss] biological processes & molecular functions
> Reply-To: obo-discuss at lists.sourceforge.net
>
> Hi all,
>
> Like Colin Batchelor, who has recently posted to this list, we are
> trying to extensively use OBOs in the annotation of journal articles
> (i.e., NLP annotation, not annotation in the sense of that done by the
> various model-organism databases).  And, like Colin, we are  
> experiencing
> issues in trying to use these OBOs (although I won't speak for him!).
>
> One issue that has caused us trouble is the dichotomy between GO
> biological processes and molecular functions, and this leads to a
> reexamination of the nature of these concepts.  My understanding from
> that written by Barry Smith and others is that a biological process is
> an actual process and that a molecular function is a functionality
> inherent in a gene/gene product that is realized in a corresponding
> process.  (Please correct me if I'm wrong.)  This makes sense, I  
> think,
> when examining the GO transport and transporter terms:  The  
> transporter
> terms in the MF subontology are of the form "Enables the transport  
> of *
> into, out of, within or between cells", while the transport terms  
> in the
> BP subontology are of the form "The directed movement of * into,  
> out of,
> within or between cells".  So drug transporter activity is the
> functionality inherent in a given gene/gene product that is  
> realized in
> a drug-transport process.  I assume that this is the reason for so  
> many
> parallel BP transport and MF transporter activity terms.  But if  
> this is
> the case, then why isn't there a corresponding BP term for each MF  
> term?
>
> Arguing on the other side, most of the MF terms are not defined as
> inherent functionalities but rather sound like processes to me:  Most
> binding terms are defined as "Interacting selectively with *"; most
> catalytic-activity terms are defined as "Catalysis of the reaction:  
> *";
> many enzyme-regulator-activity terms are defined as "Modulates *";  
> etc.
> Furthermore, on the GO Web site, molecular functions are described as
> "activities, such as catalytic or binding activities, that occur at  
> the
> molecular level", which to me sound like processes (at a molecular
> level) rather than functionalities inherent in genes/gene products  
> that
> are realized in processes.
>
> The specific issues we're having and how we deal with them depend  
> on the
> nature of the relationship between BPs and MFs, so I won't go into  
> more
> detail until this is clear.  We're hoping someone from GO/OBO could
> clear this up for us.
>
> Cheers,
> Mike
>
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