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Re: [Obi-role-branch] is host a disposition (new name for thread)
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From: Barry S. <phi...@bu...> - 2009-04-28 13:54:56
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Will do my best to get myself up to speed on this conversation soon. In the mean time, the best we have been able to come up with regarding definitions for 'dispotion' etc., is in the attached. We are working on adding a new subtype of realizable called 'capability' as in: this horse has the capability to pull 300 kg. This seems not to be a function, role or disposition. Getting clear on capability may help us to get clear also on susceptibility. BS At 04:15 PM 4/27/2009, Fostel, Jennifer (NIH/NIEHS) [C] wrote: >i suspect that we disagree. > >in the malaria example, >the pathogen Pfalciparum is a human pathogen because it has pfEMP1 >which are able to bind to human cells. >the generic human is a host for Pf because he or she contains cells >with surface receptors for Pf. > >there are also presumably mutant humans lacking such surface >receptors and mutations of Pf without the virulence factor; not >clear if these are viable, but they do not inform the >discussion. the generic human with the receptor has the disposition >to be a host for Pf with or without meeting and Pf. > >Definition: A realizable entity [snap:RealizableEntity] that >essentially causes a specific process or transformation in the >object [snap:Object] in which it inheres, under specific >circumstances and in conjunction with the laws of nature. A general >formula for dispositions is: X (object [snap:Object] has the >disposition D to (transform, initiate a process) R under conditions C > >X= human cells (or more generically the human) >R = infection process >C = when encoutering P falciparum in blood stream > >in an experiment, the human could also bear the (OBI role) host role >for Pf, and Pf could bear pathogen role > >does this match your thinking? > >...jennifer > > > >---------- >From: Lindsay G Cowell [mailto:cow...@mc...] >Sent: Monday, April 27, 2009 2:44 PM >To: Richard H. Scheuermann, Ph.D. >Cc: OBI Developers; obi...@li... >Subject: Re: [Obi-role-branch] disposition branch call today 11 >eastern on centra > > >hmmm. my first thought was that there is probably a disposition (D) >to participate in a process (P) and a role (R) played by an entity >when participating in P so that in many cases these are two sides of >the same coin. but based on the bfo definitions for role and >disposition (below), i would say that being a host, for example, "is >not essential to a continuant in virtue of the kind of thing that it >is" but that some continuants can serve as host in some contexts. i >would say host is not a disposition because being a host does not >"essentially cause a specific process or transformation" in the >entity in which it inheres. > >i am hoping barry will comment ... > >name: role >comment: Definition: A realizable entity [snap:RealizableEntity] the >manifestation of which brings about some result or end that is not >essential to a continuant [snap:Continuant] in virtue of the kind of >thing that it is but that can be served or participated in by that >kind of continuant [snap:Continuant] in some kinds of natural, >social or institutional contexts. > >name: disposition >comment: Definition: A realizable entity [snap:RealizableEntity] >that essentially causes a specific process or transformation in the >object [snap:Object] in which it inheres, under specific >circumstances and in conjunction with the laws of nature. A general >formula for dispositions is: X (object [snap:Object] has the >disposition D to (transform, initiate a process) R under conditions C. > >------------------------------------- >Lindsay G. Cowell >Assistant Professor >Department of Biostatistics and Bioinformatics >Duke University Medical Center >2424 Erwin Road, Suite 1102, 11086 >Durham, NC 27705 >(919) 681-6226 > > >"Richard H. Scheuermann, Ph.D." ><ric...@ut...> wrote on 04/27/2009 02:08:30 PM: > > > I actually think that they should be dispositions rather than roles. > > > > Richard > > > > On Apr 27, 2009, at 12:44 PM, Lindsay G Cowell wrote: > > > > > > thanks for the forward. we have all of these although as roles > > rather than dispositions. i can add the disposition terms if you > > think we should have terms for both. > > ------------------------------------- > > Lindsay G. Cowell > > Assistant Professor > > Department of Biostatistics and Bioinformatics > > Duke University Medical Center > > 2424 Erwin Road, Suite 1102, 11086 > > Durham, NC 27705 > > (919) 681-6226 > > > > > > Barry Smith <phi...@bu...> wrote on 04/27/2009 12:13:25 PM: > > > > > > > > >Delivered-To: phi...@ma... > > > >Delivered-To: phi...@bu... > > > >From: "Richard H. Scheuermann, Ph.D." <richard. > > > sch...@ut...> > > > >Date: Mon, 27 Apr 2009 11:02:49 -0500 > > > >To: "Fostel, Jennifer (NIH/NIEHS) [C]" <fo...@ni...> > > > >X-Mailer: Apple Mail (2.753.1) > > > >X-Scan-Signature: 74018b61a7b96a3c6dc22d0d41014132 > > > >X-Spam-Score: -3.7 (---) > > > >X-Spam-Report: Spam Filtering performed by mx.sourceforge.net. > > > > See http://spamassassin.org/tag/ for more details. > > > > -4.0 RCVD_IN_DNSWL_MED RBL: Sender listed at http://www. > > dnswl.org/, > > > > medium trust [199.242.236.197 listed in list.dnswl.org] > > > > 0.0 HTML_MESSAGE BODY: HTML included in message > > > > 0.3 AWL AWL: From: address is in the auto white-list > > > >X-Headers-End: 1LyTIS-0000ue-Au > > > >Cc: OBI Developers <obi...@li...>, > > > > "obi...@li..." > > > > <obi...@li...> > > > >Subject: Re: [Obi-role-branch] dispositoin branch call today > 11 eastern on > > > > centra > > > >X-BeenThere: obi...@li... > > > >X-Mailman-Version: 2.1.9 > > > >List-Id: <obi-role-branch.lists.sourceforge.net> > > > >List-Unsubscribe: > > > ><https://lists.sourceforge.net/lists/listinfo/obi-role-branch>, > > > > > > > ><mailto:obi...@li...?subject=u > nsubscribe> > > > >List-Archive: > > > ><http://sourceforge.net/mailarchive/forum.php?forum_name=obi-ro > le-branch> > > > >List-Post: <mailto:obi...@li...> > > > >List-Help: <mailto:obi...@li...? > > subject=help > > > > > > > >List-Subscribe: > > > ><https://lists.sourceforge.net/lists/listinfo/obi-role-branch>, > > > > > > > ><mailto:obi...@li...?subject=subscribe> > > > >X-PM-Spam-Prob: : 8% > > > > > > > >None of these seem to be in the OBI domain. They appear to be > > > >natural dispositions, which I believe are being handled by the > > > >Infectious Disease Ontology. > > > > > > > >Richard > > > > > > > >On Apr 27, 2009, at 8:52 AM, Fostel, Jennifer (NIH/NIEHS) [C] wrote: > > > > > > > >>material for starting discussion > > > >>host disposition = disposition to allow pathogen to enter the > > host organism > > > >>pathogen disposition = disposition to enter the host organism and > > > >>cause damage to host > > > >>symbiote disposition = disposition to enter host orgasnism and > > > >>benefit host organism and symbiote organism > > > >>carrier disposition = disposition to allow entry for organism that > > > >>is pathogen to another species, without harm or benefit to > > carrier organism > > > >> > > > >>The host range or host specificity of a parasite is the collection > > > >>of hosts that an organism can utilize as a partner > > > >>quality of pathogen > > > >> > > > >>Jennifer Fostel, Ph.D. > > > >>CEBS Scientific Administrator > > > >>Global Health Sector, SRA International, Inc > > > >> > > > >>Laboratory of Respiratory Biology > > > >>NIEHS, NIH > > > >>PO Box 12233 Mail Drop F1-05 > > > >>111 Alexander Drive > > > >>Research Triangle Park NC 27709-2233 > > > >> > > > >>phone 919 541 5055 > > > >>fax 919 541 1460 > > > >> > > > >> > > > >><dispositions.pdf> > > > > > >>---------------------------------------------------------------- > -------------- > > > >>Crystal Reports - New Free Runtime and 30 Day Trial > > > >>Check out the new simplified licensign option that enables unlimited > > > >>royalty-free distribution of the report engine for > externally facing > > > >>server and web deployment. > > > >><http://p.sf. > > > net/sfu/businessobjects_______________________________________________ > > > >http://p.sf. > > > net/sfu/businessobjects_______________________________________________ > > > >>Obi-role-branch mailing list > > > >><mailto:Obi...@li...>Obi-role- > > > br...@li... > > > >>https://lists.sourceforge.net/lists/listinfo/obi-role-branch > > > > > > > > > >----------------------------------------------------------------- > ------------------------------- > > > > > > > >Richard H. Scheuermann, Ph.D. > > > >Chief, Division of Biomedical Informatics > > > >Director, Division of Translational Pathology > > > >John H. Childers Professorship in Pathology > > > >Department of Pathology > > > >U.T. Southwestern Medical Center > > > >5323 Harry Hines Blvd. > > > >Dallas, TX 75390-9072 > > > > > > > >phone: 214-648-4115 > > > >FAX: 214-648-4070 > > > >email: > > > ><<mailto:ric...@ut...>mailto:richard. > sch...@ut...>richard. > > > sch...@ut... > > > >http://pathcuric1.swmed.edu/Research/scheuermann.html > > > > > > > > > > > > > > > > > >----------------------------------------------------------------- > ------------- > > > >Crystal Reports - New Free Runtime and 30 Day Trial > > > >Check out the new simplified licensign option that enables unlimited > > > >royalty-free distribution of the report engine for externally facing > > > >server and web deployment. > > > >http://p.sf.net/sfu/businessobjects > > > >_______________________________________________ > > > >Obi-role-branch mailing list > > > >Obi...@li... > > > >https://lists.sourceforge.net/lists/listinfo/obi-role-branch > > > > > > > > > > > ------------------------------------------------------------------------------------------------ > > > > > Richard H. Scheuermann, Ph.D. > > Chief, Division of Biomedical Informatics > > Director, Division of Translational Pathology > > John H. Childers Professorship in Pathology > > Department of Pathology > > U.T. Southwestern Medical Center > > 5323 Harry Hines Blvd. > > Dallas, TX 75390-9072 > > > > phone: 214-648-4115 > > FAX: 214-648-4070 > > email: ric...@ut... > > > <http://pathcuric1.swmed.edu/Research/scheuermann.html>http://pathcuric1.swmed.edu/Research/scheuermann.html > |
