[go] Fwd: [Obo-discuss] 3 forwarded messages on MF vs BP from obo-discuss
David Hill
dph at informatics.jax.org
Wed Jan 16 11:37:15 PST 2008
I agree!
David
Michael Ashburner wrote:
> 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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