[go] Fwd: [Obo-discuss] 3 forwarded messages on MF vs BP from obo-discuss
Michael Ashburner
ma11 at gen.cam.ac.uk
Wed Jan 16 10:38:54 PST 2008
I suggest this to be an agenda item for Salt Lake City.
Michael
On 15 Jan 2008, at 04:21, Midori Harris wrote:
> Hi Chris,
>
> I'm really glad you're paying attention to this thread, and I agree
> that the annotators' point of view will be valuable. I have a bit
> more from the ontology front ...
>
> What struck me about Mike's most recent message is that his
> examples of parallel terms list exactly those terms that have been
> the subject of the most intense discussions on the GO list and at
> GOC meetings. I think Jen is working on another detailed response,
> though, so I'll stick to the bigger picture.
>
> I found this exchange from yesterday rather alarming:
>
>>>> Mike: My understanding ... 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.)
>>>
>>> Barry:
>>> You are not wrong.
> [snip]
>>
>> Mike:
>> OK, it is as I thought. Does this mean that there will be many
>> more parallel BP and MF terms, even a one-to-one correspondence?
>
> Although Jen's email has probably got Mike sorted out on this
> point, I still think it's worth pointing out specifically that we
> have no intention whatsoever of aking MF and BP parallel each other
> completely -- I can't see how that would be a sensible use of our
> time.
>
> With respect to Mike's most recent:
>> However, it seems there's not even consensus within the GO/OBO
>> Consortium concerning the relationship between MFs and BPs. I
>> originally asked whether the MFs were inherent functionalities of
>> genes/gene products that get realized as processes or as
>> "elementary" processes themselves. What you describe agrees with
>> the documentation on the GO Web site and with most of the MF term
>> names and their definitions, i.e.,
>> with the latter view, while Barry takes the former view.
>
> I think it's quite clear that there is consensus within GO on what
> the distinction between MF and BP is at present. We've long
> acknowledged that the split was arbitrary, and done for pragmatic
> reasons (which Jen might go into). Accordingly, there is still a
> lot of discussion, sometimes outright argument, about exactly where
> the boundary lies, and whether a given term/entity belongs in MF or
> BP, but the inherent functionality vs. actual "process" question
> hasn't come up.
>
> Barry's "you are not wrong" statement was therefore not an accurate
> description of GO's present content, documentation or practices.
> Perhaps GO will move towards distinguishing inherent
> functionalities from molecular-scale processes, but it's early days
> -- the issue is still very much under discussion, implementation
> has barely begun (if at all; it's probably fairer to simply say
> this is not what we're doing now) and it's certainly not what we've
> done historically. If anything, we have occasionally tried to speak
> and think of MF terms as events (and annotation could be thought of
> as making a statement about a particular gene product's inherent
> functionality).
>
> It's been a long, long time since I've done any gene product
> annotation, so I hope more people chime in. But one thing I can say
> is that when I was doing annotation, I was definitely among that
> majority of biologists who (as Mike correctly surmises) don't care
> about the inherent functionality/execution of function distinction.
> I might even stick my neck out and say that in many papers Mike's
> "A transports B to the nucleus" example would refer to both the
> process "B transport" and to the corresponding inherent
> functionality "B transporter activity" -- an experiment documents
> an actual instance of the process, and from that result the authors
> infer A's ability to do the deed.
>
> Sorry to be long-winded -- I thought mine was going to be the brief
> response!
>
> midori
>
> On Mon, 14 Jan 2008, Chris Mungall wrote:
>
>> [redirecting this part to GO, sorry if this confuses the thread,
>> but I want to ask a question of GO folks first]
>>
>> Thanks for responding Jen.
>>
>> I think Mike raises some interesting issues, many of which we've
>> raised internally. I have my ideas on how to answer Mike's
>> question, focusing on the signal transduction/transducer activity
>> example. But I'd like to get feedback, particularly from an
>> annotation perspective, before answering from an ontology-minded
>> perspective.
>>
>> It seems that we should have on the wiki as part of an annotation
>> SOP some rules/guidelines for when to annotate to "signal
>> transducer activity" vs "signal transduction" vs co-annotation of
>> both. (which would of course apply to analagous examples)
>>
>> We also need to start making P<->F links here.
>>
>> If it helps I have added an example query:
>> http://www.berkeleybop.org/goose
>>
>> select from the popup "genes annotated to signal transducer
>> activity but not signal transduction" (and change the DB if you
>> like - it's set to MGI in the example)
>>
>> you can also try swapping the terms around
>>
>> as you can see there is quite a lot
>>
>> Begin forwarded message:
>>
>>> From: Mike Bada <mike.bada at UCHSC.edu>
>>> Date: January 14, 2008 6:21:44 PM PST
>>> To: jdeegan at ebi.ac.uk, obo-discuss at lists.sourceforge.net
>>> Subject: Re: [Obo-discuss] 3 forwarded messages on MF vs BP from
>>> obo-discuss
>>> Reply-To: obo-discuss at lists.sourceforge.net
>>> Thank you for your detailed reply, Jennifer. However, it seems
>>> there's
>>> not even consensus within the GO/OBO Consortium concerning the
>>> relationship between MFs and BPs. I originally asked whether the
>>> MFs
>>> were inherent functionalities of genes/gene products that get
>>> realized
>>> as processes or as "elementary" processes themselves. What you
>>> describe
>>> agrees with the documentation on the GO Web site and with most of
>>> the MF
>>> term names and their definitions, i.e., with the latter view, while
>>> Barry takes the former view.
>>> Again, we are most concerned with all of the parallel terms
>>> between the
>>> two subontologies, which makes application toward NLP, among other
>>> tasks, much more difficult. This is not limited to the large
>>> number of
>>> corresponding transporter activity (MF) / transport (BP) terms; some
>>> other examples include:
>>> signal transducer activity (MF) ; signal transduction (BP)
>>> translation regulator activity (MF) ; regulation of translation (BP)
>>> enzyme regulator activity (MF) ; regulation of catalytic activity
>>> (BP)
>>> enzyme activator activity (MF) ; positive regulation of enzyme
>>> activity (BP)
>>> According to your explanation, all of these pairs of terms seem
>>> to mean
>>> essentially the same thing except for the fact that each of the
>>> former
>>> is a single-step process and each of the latter a multi-step
>>> process.
>>> It may be relatively easy to divide a metabolic pathway into its
>>> component biochemical reactions, but what constitutes an elementary
>>> single step of a process is often ambiguous. Any process can be
>>> recursively divided into component processes: Even a biochemical
>>> reaction can be divided into component processes of the reaction
>>> mechanism. This ambiguous nature of what an "elementary" step is
>>> makes
>>> it very difficult to determine whether a process mentioned in,
>>> say, a
>>> journal article is a single-step or multi-step process (and thus
>>> a MF or
>>> a BP, respectively).
>>> So there are two views, both of which hamper usability of the
>>> subontologies applied in combination: As to the view that MFs
>>> are the
>>> inherent functionalities of genes/gene products that are realized in
>>> BPs, it is often ambiguous whether a natural-language mention
>>> refers to
>>> the inherent functionality or to the process itself. As to the view
>>> that MFs are the "single-step" processes that make up multi-step
>>> BPs, it
>>> is often ambiguous whether a natural-language mention is a
>>> "single-step"
>>> or "multi-step" process. Wouldn't it be easier and clearer if there
>>> were one merged ontology of processes of all granularities and no
>>> parallel terms such as the aforementioned ones?
>>> Cheers,
>>> Mike
>>> Jennifer Deegan (nee Clark) wrote:
>>>> Hi Mike,
>>>> Midori forwarded this e-mail to me as I have been working on an
>>>> extensive overhaul of the transport terms in GO. I think that I
>>>> can help
>>>> clear up at least some of the confusion here, though it might
>>>> take a few
>>>> e-mails to get things completely clear.
>>>> In GO, as you have mentioned, we have transport terms in the
>>>> function
>>>> and process ontologies, and as you mention, they are really quite
>>>> similar. However, this is partly because many of these terms
>>>> were made
>>>> in the early days of GO when we were really not too clear
>>>> ourselves on
>>>> the distinction between function and process. Now that we are much
>>>> clearer about the distinction I have been working through with a
>>>> number
>>>> of expert biologists and improving the terms.
>>>> Just to be clear, I will give a nice easy example of some
>>>> function and
>>>> process terms to get the distinction sorted out. We think of a
>>>> molecular
>>>> function as a single step reaction, whilst a process term
>>>> describes a
>>>> multistep event. You might think of a process term as being made
>>>> up of
>>>> several functions happening one after the other. We currently
>>>> make no
>>>> distinction between the actual execution of the function and the
>>>> potential execution of the function.
>>>> Function terms
>>>> ==============
>>>> An example of a function in GO is when a secondary active
>>>> transporter
>>>> molecule acts by changing
>>>> shape so as to propel a bound potassium ion across the membrane,
>>>> in a
>>>> single step chemical reaction. We would consider this reaction
>>>> to be a
>>>> molecular function that belongs in the molecular function
>>>> ontology. The
>>>> term could be 'secondary active potassium transporter activity',
>>>> though
>>>> in fact have the term:
>>>> potassium ion uniporter activity
>>>> def: Catalysis of the active transport of a potassium ion across a
>>>> membrane by a mechanism involving conformational change, where
>>>> energy
>>>> for active transport is derived from membrane potential if the
>>>> solute is
>>>> charged.
>>>> There is a picture here in case it helps anyone get the biology
>>>> clear:
>>>> http://www.ncbi.nlm.nih.gov/books/bv.fcgi?
>>>> highlight=carrier&rid=mboc4.figgrp.2000
>>>> Process terms
>>>> =============
>>>> An example of a process that is nice and straightforward is the
>>>> set of
>>>> photochemical reactions that occur in photosynthesis.
>>>> http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=mboc4.figgrp.2589
>>>> This is currently included in GO as 'photosynthesis, light
>>>> reaction'
>>>> def: The light reactions of photosynthesis, which take place in
>>>> photosystems II and I. Light energy is harvested and used to
>>>> power the
>>>> transfer of electrons among a series of electron donors and
>>>> acceptors.
>>>> The final electron acceptor is NADP+, which is reduced to NADPH.
>>>> NADPH
>>>> generated from light reactions is used in sugar synthesis in dark
>>>> reactions. Light reactions also generate a proton motive force
>>>> across
>>>> the thylakoid membrane, and the proton gradient is used to
>>>> synthesize
>>>> ATP. There are two chemical reactions involved in the light
>>>> reactions:
>>>> water oxidation in photosystem II, and NADP reduction in
>>>> photosystem I.
>>>> The thing that I think is confusing you is that we have process
>>>> terms
>>>> that look really a lot like the transport function terms. The
>>>> thing that
>>>> you need to know is that we have overhauled most of the function
>>>> terms
>>>> and given them proper definitions so that they are no longer
>>>> carrying
>>>> the very non-specific definitions that you saw before. Most of
>>>> them now
>>>> have very clear defs describing single step reactions as shown
>>>> above.
>>>> Process transport terms are defined as, for example:
>>>> The directed movement of potassium ions (K+) into, out of,
>>>> within or
>>>> between cells. (This is clearly a multistep affair, if we could
>>>> think of
>>>> a good example, though I think all these terms need a good
>>>> looking at too.
>>>> For example, do we really need a potassium transport process
>>>> term? This
>>>> is on my list to look at soon. )
>>>> In summary, the function terms are now better defined, to be
>>>> clearly a
>>>> single
>>>> step reaction, and the process terms have much more general
>>>> definitions
>>>> that
>>>> can cover a multistep reaction.
>>>> The other thing that I should mention, is that I am currently
>>>> working
>>>> with several transport experts to re-examine all of the
>>>> transport terms,
>>>> and to improve them to clearly represent the current state of
>>>> the biology.
>>>> I hope to improve the process terms considerably, and we still
>>>> have a
>>>> lot of work to do on the more granular function terms. If you
>>>> would like
>>>> to be involved in this then I would be very pleased to include you.
>>>> Here is a description of what we have done so far:
>>>> http://wiki.geneontology.org/index.php/Transporters
>>>> This is the documentation for the parts that we consider to be
>>>> rigorously logical, and up to date for the field, as it
>>>> currently stands:
>>>> http://wiki.geneontology.org/index.php/Docs
>>>> The process and function ontology docs may also help:
>>>> http://www.geneontology.org/GO.process.guidelines.shtml
>>>> http://www.geneontology.org/GO.function.guidelines.shtml
>>>> I hope this helps a bit. Please do write back to ask further
>>>> questions.
>>>> It is a tricky subject, and I have had to rattle this e-mail off
>>>> quite
>>>> quickly before diving into a meeting, ironically, with my transport
>>>> experts. Please could you also cc me, as I am not on the obo-
>>>> discuss list.
>>>> Thanks, and best wishes,
>>>> Jennifer
>>>> ---------- Forwarded message ----------
>>>> Date: Sat, 12 Jan 2008 20:13:23 -0700
>>>> From: Mike Bada <mike.bada at UCHSC.edu>
>>>> Reply-To: obo-discuss at lists.sourceforge.net
>>>> To: obo-discuss at lists.sourceforge.net
>>>> Subject: [Obo-discuss] biological processes & molecular functions
>>>> 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
>>>> -------------------------------------------------------------------
>>>> ------
>>>> Check out the new SourceForge.net Marketplace.
>>>> It's the best place to buy or sell services for
>>>> just about anything Open Source.
>>>> http://ad.doubleclick.net/clk;164216239;13503038;w?http://sf.net/
>>>> marketplace
>>>> _______________________________________________
>>>> Obo-discuss mailing list
>>>> Obo-discuss at lists.sourceforge.net
>>>> https://lists.sourceforge.net/lists/listinfo/obo-discuss
>>>> ---------- Forwarded message ----------
>>>> Date: Sat, 12 Jan 2008 23:24:15 -0400
>>>> From: "Smith, Barry" <phismith at buffalo.edu>
>>>> Reply-To: obo-discuss at lists.sourceforge.net
>>>> To: obo-discuss at lists.sourceforge.net, obo-
>>>> discuss at lists.sourceforge.net
>>>> Subject: Re: [Obo-discuss] biological processes & molecular
>>>> functions
>>>> At 11:13 PM 1/12/2008, Mike Bada wrote:
>>>>> 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.)
>>>> You are not 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?
>>>> I believe that the GO consortium has committed itself to creating
>>>> more consistency here. There are steps, also, to address the
>>>> issue of
>>>> functions at other (non-molecular) levels of granularity -- for
>>>> example cellular and organ-level functions, reflecting also a more
>>>> careful treatment of the granularities on the process side.
>>>>> 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.
>>>> This is a big issue -- resulting from an unfortunate decision to
>>>> label all function terms with the suffix 'activity'.
>>>> When you read 'activity' in GO, try to thing 'function'.
>>>>> 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.
>>>> Hope the above helps, at least somewhat.
>>>> BS
>>>>> Cheers,
>>>>> Mike
>>>>> ------------------------------------------------------------------
>>>>> -------
>>>>> Check out the new SourceForge.net Marketplace.
>>>>> It's the best place to buy or sell services for
>>>>> just about anything Open Source.
>>>>> http://ad.doubleclick.net/clk;164216239;13503038;w?http://
>>>>> sf.net/marketplace
>>>>> _______________________________________________
>>>>> Obo-discuss mailing list
>>>>> Obo-discuss at lists.sourceforge.net
>>>>> https://lists.sourceforge.net/lists/listinfo/obo-discuss
>>>> -------------------------------------------------------------------
>>>> ------
>>>> Check out the new SourceForge.net Marketplace.
>>>> It's the best place to buy or sell services for
>>>> just about anything Open Source.
>>>> http://ad.doubleclick.net/clk;164216239;13503038;w?http://sf.net/
>>>> marketplace
>>>> _______________________________________________
>>>> Obo-discuss mailing list
>>>> Obo-discuss at lists.sourceforge.net
>>>> https://lists.sourceforge.net/lists/listinfo/obo-discuss
>>>> ---------- Forwarded message ----------
>>>> Date: Sun, 13 Jan 2008 18:21:45 -0700
>>>> From: Mike Bada <mike.bada at UCHSC.edu>
>>>> Reply-To: obo-discuss at lists.sourceforge.net
>>>> To: obo-discuss at lists.sourceforge.net
>>>> Subject: Re: [Obo-discuss] biological processes & molecular
>>>> functions
>>>> Smith, Barry wrote:
>>>>> At 11:13 PM 1/12/2008, Mike Bada wrote:
>>>>>> 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.)
>>>>> You are not 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?
>>>>> I believe that the GO consortium has committed itself to creating
>>>>> more consistency here. There are steps, also, to address the
>>>>> issue of
>>>>> functions at other (non-molecular) levels of granularity -- for
>>>>> example cellular and organ-level functions, reflecting also a more
>>>>> careful treatment of the granularities on the process side.
>>>> OK, it is as I thought. Does this mean that there will be many
>>>> more
>>>> parallel BP and MF terms, even a one-to-one correspondence?
>>>> The crux of our difficulties is that, when analyzing and
>>>> attempting to
>>>> annotate a typical biological assertion found in a journal article,
>>>> we're often finding it extremely difficult to differentiate whether
>>>> something refers to a BP or a MF. A simple example is "A
>>>> transports B
>>>> to the nucleus." Does this refer to the process "B transport"
>>>> or to the
>>>> corresponding inherent functionality "B transporter activity",
>>>> i.e., to
>>>> the actual process or to the ability to effect the process? (I'm
>>>> using transport/transporter activity examples throughout, but
>>>> there are
>>>> many others.) The use of the simple verb might suggest that it's a
>>>> process, but of course, this is a generic statement about the
>>>> ability of
>>>> A to transport B to the nucleus, not about an actual reporting
>>>> of the
>>>> transport of a specific B to the nucleus by a specific A, so it
>>>> can be
>>>> seen as a MF as well. Frankly, I'd say that this is an ontological
>>>> distinction about which the large majority of biologists
>>>> understandably
>>>> wouldn't care, but it is something we have to consider because
>>>> we're
>>>> interested in getting computational systems to be able to
>>>> automatically
>>>> recognize GO (and other OBO) terms in natural-language text, and
>>>> the
>>>> distinctions between the two in text are often ambiguous to say the
>>>> least, which makes the task that much more difficult.
>>>> This leads me to ask, perhaps radically: Do we need both BPs
>>>> and MFs?
>>>> I'm not denying an ontological distinction between BPs and MFs as
>>>> they're defined now; I'm just wondering if it might be a
>>>> distinction
>>>> that is too subtle to be genuinely useful and too ambiguous to
>>>> differentiate in, for example, natural language. Even applied
>>>> to GO
>>>> annotations, if a gene or gene product has an annotation that
>>>> indicates
>>>> that it has the functionality to effect a drug-transport
>>>> process, is the
>>>> addition of another annotation that indicates that it
>>>> participates in
>>>> drug-transport processes useful? Wouldn't it be sufficient to
>>>> have only
>>>> processes or only functionalities in the GO? (I think processes
>>>> are
>>>> more straightforward and thus more generally useful.) This would
>>>> eliminate a huge amount of ambiguity in the application of terms
>>>> among
>>>> these two subontologies, I think.
>>>> Trepidatiously expecting a firestorm,
>>>> Mike
>>>>>> 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.
>>>>> This is a big issue -- resulting from an unfortunate decision to
>>>>> label all function terms with the suffix 'activity'.
>>>>> When you read 'activity' in GO, try to thing 'function'.
>>>>>> 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.
>>>>> Hope the above helps, at least somewhat.
>>>>> BS
>>>>>> Cheers,
>>>>>> Mike
>>>>>> -----------------------------------------------------------------
>>>>>> --------
>>>>>> Check out the new SourceForge.net Marketplace.
>>>>>> It's the best place to buy or sell services for
>>>>>> just about anything Open Source.
>>>>>> http://ad.doubleclick.net/clk;164216239;13503038;w?http://
>>>>>> sf.net/marketplace
>>>>>> _______________________________________________
>>>>>> Obo-discuss mailing list
>>>>>> Obo-discuss at lists.sourceforge.net
>>>>>> https://lists.sourceforge.net/lists/listinfo/obo-discuss
>>>>> ------------------------------------------------------------------
>>>>> -------
>>>>> Check out the new SourceForge.net Marketplace.
>>>>> It's the best place to buy or sell services for
>>>>> just about anything Open Source.
>>>>> http://ad.doubleclick.net/clk;164216239;13503038;w?http://
>>>>> sf.net/marketplace
>>>>> _______________________________________________
>>>>> Obo-discuss mailing list
>>>>> Obo-discuss at lists.sourceforge.net
>>>>> https://lists.sourceforge.net/lists/listinfo/obo-discuss
>>>> -------------------------------------------------------------------
>>>> ------
>>>> Check out the new SourceForge.net Marketplace.
>>>> It's the best place to buy or sell services for
>>>> just about anything Open Source.
>>>> http://ad.doubleclick.net/clk;164216239;13503038;w?http://sf.net/
>>>> marketplace
>>>> _______________________________________________
>>>> Obo-discuss mailing list
>>>> Obo-discuss at lists.sourceforge.net
>>>> https://lists.sourceforge.net/lists/listinfo/obo-discuss
>>> --------------------------------------------------------------------
>>> -----
>>> Check out the new SourceForge.net Marketplace.
>>> It's the best place to buy or sell services for
>>> just about anything Open Source.
>>> http://ad.doubleclick.net/clk;164216239;13503038;w?http://sf.net/
>>> marketplace
>>> _______________________________________________
>>> Obo-discuss mailing list
>>> Obo-discuss at lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/obo-discuss
>>
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