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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 14:39:59
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At 10:07 AM 4/28/2009, Fostel, Jennifer (NIH/NIEHS) [C] wrote: >how does this fit with tendency? it seems that the two might >overlap. i prefer capability in place of tendency. capability like function is somehow positive you may have a tendency that is not positive e.g. to go bald >the whole question seems to rest on stochastic outcomes, which may >or may not be known at the time of description. that is an epistemological matter BS >-----Original Message----- >From: Barry Smith [mailto:phi...@bu...] >Sent: Tuesday, April 28, 2009 9:50 AM >To: Fostel, Jennifer (NIH/NIEHS) [C]; 'Lindsay G Cowell'; Richard H. >Scheuermann, Ph.D. >Cc: obi...@li... >Subject: Re: is host a disposition (new name for thread) > >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 > =sub> > > >scribe> > > > > >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://pathcuri > > c1.swmed.edu/Research/scheuermann.html > > |
