[go] Fwd: [Obo-discuss] 3 forwarded messages on MF vs BP from obo-discuss
Midori Harris
midori at ebi.ac.uk
Tue Jan 15 04:21:34 PST 2008
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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