From: Peter M. <pet...@gm...> - 2013-11-12 15:55:36
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Ok, got it - and there are certainly terms in NBO (and the portion of ABO that we want to add to it) that need to address the cardinality issue. Agree that this doesn't help much with binary interactions between individuals. Is the relationship a composition of has_participant in a process that is part_of a population level process, or is that over simplifying? I think there are a fair number of cases where population level processes might be treated as collections of behavioral (or physiological) processes. -Peter On Nov 12, 2013, at 9:56 AM, David Osumi-Sutherland <dj...@ge...> wrote: > Hi Peter and Ramona > > v. good point re population level processes. Here are some thoughts on how to formalise: > > I've been playing around with definitions like this: > > multi-organism process > EquivalentTo 'biological process' that has_participant min 2 organism > > multi-organism behavior > EquivalentTo behaviour that has_participant min 2 organism > > My initial assumption was that it would be semantically equivalent to use PCO 'collection of individuals' instead: > > multi-organism process > EquivalentTo 'biological process' that has_participant some PCO:'collection of individuals' > > This would have the advantage of keeping cardinality constraints (outside EL) out of the GO - pushing it into PCO (where I think it could happily live, given PCO's small size): As suggested here https://code.google.com/p/popcomm-ontology/issues/detail?id=6, it might make sense to define 'collection of organisms' as > 'collection of organisms' EquivalentTo: has_member min 2 organism and has_member only organism. > > With this formalisation strategy, we could take advantage of the PCO hierarchy, e.g. > > GO:'intraspecies interaction between organisms' EquivalentTo: biological_process that has_participant some PCO:'collection of organisms of same species' > > However, given the need to distinguish population level processes from interactions between 2 individuals, perhaps we should reserve "has_participant some ' collection of individuals'" for population level processes like swarming: > > PCO:population process > EquivalentTo 'biological process' that has_participant some PCO:'collection of individuals' > > I notice that the text definition of 'population process' is quite close to this: "A process that has as primary participant a population." But this term also has the coment: "Population processes may depend on the processes of individual organisms… but cannot be described for an individual organism. Perhaps we need something stronger than just has_participant, as individual population members clearly participate in population processes even if the process 'cannot be described for an individual organism'. Not sure what to suggest though > > Note that GO has a few processes that probably belong under this class, for example 'quorum sensing', but mostly its multi-organism processes are binary interactions. So, it is no longer clear that PCO provides a route for defining these terms - although the host, parasite, symbiont roles etc could come in handy. > > - David > > > > > On 12 Nov 2013, at 13:33, Ramona Walls <rlw...@gm...> wrote: > >> Peter, >> >> I agree with the distinction you describe between a behavior and a population or community process, although the boundary is not always so easy to determine. Thank for bringing that up. >> >> Ramona >> >> ------------------------------------------------------ >> Ramona L. Walls, Ph.D. >> Scientific Analyst, The iPlant Collaborative, University of Arizona >> Laboratory Research Associate, New York Botanical Garden >> >> >> On Tue, Nov 12, 2013 at 6:22 AM, Peter Midford <pet...@gm...> wrote: >> Hi David and Ramona, >> There is a line to be drawn between behavior and population processes, but I don't think it is at the level between 1 individual and 2. For example, courtship and mating (and other forms of communication) are properly behavior, whereas processes with larger number of individuals (e.g., leks, swarms, etc.) are arguably population level events. Likewise, social learning is a type of learning, but culture, tradition, etc. are population level processes. >> >> -Peter >> >> >> On Nov 12, 2013, at 6:01 AM, dosumis <do...@gm...> wrote: >> >>> Hi Ramona, >>> >>> I think that PCO may be a more natural home for these terms: >>> It doesn't have the limitations of terms needing some relationship to human disease that IDO does. >>> There is good potential for GO to use other terms in your ontology to define various other flavours of multi-organismal process such as mating and courtship. >>> >>> We've actually been working with PATO to define multi-organismal process terms - axiomatising them using cardinality constraints in OWL. But I think a solution with PCO would be much cleaner and more intuitive. I can also think of other use cases for PCO in defining phenotype ontology terms. >>> >>> Lindsay - would you be amenable to mapping the IDO terms to PCO? >>> >>> Cheers, >>> David >>>> >>>> On 11 Nov 2013, at 18:25, Ramona Walls <rlw...@gm...> wrote: >>>> >>>>> Jane and Lindsay: >>>>> >>>>> This is a very useful discussion, which I was just able to read today. I suggest that perhaps the Population and Community Ontology (PCO) could include some of the more general terms you are looking for. The scope of the PCO (http://code.google.com/p/popcomm-ontology/) is specifically terms related to collections of interacting organisms. Although the PCO is still fairly sparse, we consider terms such as host role, predator role, role of organism producing venom, etc. to be well within our scope. I am very much aware of the existing terms in the IDO, but have not yet tried to coordinate with IDO, simply for lack of time. I am quite happy to re-use existing terms from IDO, but I think if there is a real need for more general classes, the PCO may be a more appropriate home. >>>>> >>>>> I am actually in the process of looking for funding to hold a PCO workshop, to help ramp up development. The plan was to focus on core classes related to describing population-level phenotypes, but I was also planning to devote at least part of the workshop to coordination with other ontologies such as GO and OBI. Perhaps coordination with IDO could also be a part of this. In any case, I would love to participate in a discussion about roles of interacting organisms and what is needed for the GO. >>>>> >>>>> Ramona >>>>> >>>>> ------------------------------------------------------ >>>>> Ramona L. Walls, Ph.D. >>>>> Scientific Analyst, The iPlant Collaborative, University of Arizona >>>>> Laboratory Research Associate, New York Botanical Garden >>>>> >>>>> >>>>> On Mon, Nov 11, 2013 at 8:54 AM, Lindsay Cowell <Lin...@ut...> wrote: >>>>> >>>>> On Nov 11, 2013, at 7:49 AM, Jane Lomax wrote: >>>>> >>>>>> Hi Lindsay >>>>>> >>>>>> In fact your definition of host role is broad enough to encompass the venom/toxin situations so we could use that. >>>>>> >>>>>> I think it's also broad enough to use for pheromomes which is the other scenario we need to consider. >>>>>> >>>>>> The difficulty comes when you need to talk specifically about the role of being the host that participates in a symbiotic relationship, as opposed to the more general sense. Also, we need a role to designate to the organism producing the vemon/toxin/pheromome because the definition of symbiont role is too narrow to encompass this. >>>>>> >>>>>> Perhaps we need multiple classes e.g. 'host' in the broad sense, and a more specific 'host as part of symbiosis'? >>>>> >>>>> yes that I what I was thinking too. >>>>> >>>>>> >>>>>> Anyhow, let's arrange a call. I'll set up a Doodle poll. >>>>> >>>>> I'll keep my eye out for it. >>>>> >>>>> thanks >>>>>> >>>>>> Jane >>>>>> >>>>>> On 08/11/2013 01:27, Lindsay Cowell wrote: >>>>>>> Dear Jane, >>>>>>> >>>>>>> Thank you for your email. >>>>>>> >>>>>>> On Nov 7, 2013, at 6:00 AM, Jane Lomax wrote: >>>>>>> >>>>>>>> Hi Lindsay >>>>>>>> >>>>>>>> We are hoping to use some IDO classes in GO logical definitions and annotations. This will probably be just symbiont and host to begin with, with possibly symbiont role, host role and some of the subclasses of symbiont being used further down the line. >>>>>>> >>>>>>> That's great. And please let us know if the definitions work for you or if you suggest revisions. We tried to be consistent with the GO process terms, so hopefully we are in good shape, but let us know if some adjustment is needed. >>>>>>> >>>>>>> There are a lot of host and host role terms floating around, so it would be great to have a concerted effort to reconcile these. >>>>>>> >>>>>>> Some uses are indeed more general than the infectious disease domain, but we didn't find an existing term that we thought was appropriate so included one in IDO. >>>>>>> >>>>>>> Most of the versions I have seen focus on "host" as used in the context of symbiosis. We defined the term more broadly, both to accommodate usage in our domain but also to avoid clashing with other domains. An example of an alternative use is host as someone who has received a transplant or medical implant of some kind. Thus, we defined host very generally, too generally some would say, but we could think of counter examples for all narrower definitions we came up with. >>>>>>> >>>>>>>> >>>>>>>> What we really need, however, is a class for an organism that is the 'recipient' of a venom or toxin, where that organism is not a host. So for example the recipient of a snake bite, or bacterial toxin. >>>>>>> >>>>>>> Interesting that you raise this issue, as when we were first developing IDO, disease caused by bacterial or fungal toxins when there is no infection (the toxin is consumed but the bacteria or fungi are not, or the bacteria/fungi are consumed but are not alive, or are consumed but are cleared from the digestive track without establishing an infection), caused some difficulty for us. In the first two cases, the affected organism is not a host to the organisms that produced the toxin (but may be a host to the toxin, see below). >>>>>>> >>>>>>> I would have to re-read some of our definitions to remind myself how we handled this, but I think we may have decided to ignore these. It can be argued that these are not infectious diseases, but they are relevant for us because the source of the toxin is in many cases an infectious agent. >>>>>>> >>>>>>>> >>>>>>>> In GO we currently use 'other organism' which is unsatisfactory because, first, it really isn't a cell component and second, because it doesn't communicate the role the organism is playing. >>>>>>>> >>>>>>>> Do you think this is in scope for IDO? Not sure what you might call the class - bitten organism? poisoned organism? >>>>>>> >>>>>>> We defined host role and host in a general enough way that more specific types could accommodate the cases you mention. It is open for discussion of course whether people agree with this approach, but as things currently stand this could be done relatively easily. >>>>>>> >>>>>>> Scope is an interesting question. Many of the terms you will need probably fall outside the scope IDO, but I don't know of another ontology that seems more appropriate. We could certainly include in IDO the upper level terms, since we will need them as parents to some terms that are within our scope. We could also create a small ontology specifically for organism roles (or something) that works for all of our use cases. >>>>>>> >>>>>>> Perhaps we should arrange a call to discuss the best approach. >>>>>>> >>>>>>> Thanks, >>>>>>> >>>>>>> Lindsay >>>>>>> >>>>>>>> >>>>>>>> thanks, >>>>>>>> >>>>>>>> Jane >>>>>>>> >>>>>>> >>>>>>> ------------------------------------------------------------------- >>>>>>> Lindsay G. Cowell, PhD >>>>>>> Division of Biomedical Informatics >>>>>>> Department of Clinical Sciences >>>>>>> University of Texas Southwestern Medical Center at Dallas >>>>>>> 5323 Harry Hines Blvd. >>>>>>> Dallas, TX 75390-9066 >>>>>>> >>>>>>> F4.212b, MC9066 >>>>>>> >>>>>>> phone: 214-648-2289 >>>>>>> fax: 214-648-2064 >>>>>>> Lin...@ut... >>>>>>> >>>>>>> >>>>>>> >>>>>>> UT Southwestern Medical Center >>>>>>> The future of medicine, today. >>>>>> >>>>> >>>>> ------------------------------------------------------------------- >>>>> Lindsay G. Cowell, PhD >>>>> Division of Biomedical Informatics >>>>> Department of Clinical Sciences >>>>> University of Texas Southwestern Medical Center at Dallas >>>>> 5323 Harry Hines Blvd. >>>>> Dallas, TX 75390-9066 >>>>> >>>>> F4.212b, MC9066 >>>>> >>>>> phone: 214-648-2289 >>>>> fax: 214-648-2064 >>>>> Lin...@ut... >>>>> >>>>> >>>>> ------------------------------------------------------------------------------ >>>>> November Webinars for C, C++, Fortran Developers >>>>> Accelerate application performance with scalable programming models. Explore >>>>> techniques for threading, error checking, porting, and tuning. Get the most >>>>> from the latest Intel processors and coprocessors. 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