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Re: [Obi-role-branch] [Obi-devel] dispositoin branch call today 11eastern on centra
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From: Bjoern P. <bp...@li...> - 2009-04-27 19:21:04
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Melanie, I know what you are trying to say, and agree with that approach for terms that should clearly be in IDO or other ontologies. However, the 'vaccine' example is different: We had long discussions on it, and ended up saying that it should live in OBI. VO aims for placing all its terms into multiple relevant outside ontologies, similar to what I envision for the IEDB ontology. - Bjoern Melanie Courtot wrote: > I totally agree with that. I just think the primary location of the > term should be the relevant resource, which would maintain it, and > other could import it if needed. > So to take the example of the vaccine term, I would prefer to have it > live in VO, and then import it from OBI (using the mireot mechanism, > that VO is also using, for example with taxonomy terms) > They will then, as you mention, act as entry point and basis for > interaction. > > If we create an OBI class for a term we know we will import, we > duplicate the editing work, as the OBI class will need to be > deprecated when importing the new one. (see for example the classes > amino acids imported from CheBI and obsolete amino acid which was in OBI) > > Lindsay mentions a way to quickly get an ID for the proposed IDO > terms: using the correct IDO identifier directly will decrease our > curation load. > > Cheers, > Melanie > > > > > > > > > On 27-Apr-09, at 11:16 AM, Yongqun He wrote: > >> I agree with Bjoern. I think we still need some such terms in OBI >> since they are important terms for biomedical investigations in >> general. It is like some vaccine-specific terms (such as vaccine, >> vaccination). They are core terms in the Vaccine Ontology (VO) that I >> am leading to develop. I am happy to help and see them now being >> listed in OBI. These terms will be the linking points for OBI and VO. >> Parallel development of VO and OBI is important. I would think the >> same for many terms that may eventually go to the Infectious Disease >> Ontology (IDO) or other ontologies. >> Oliver >> >> >>> Bjoern Peters <bp...@li... <mailto:bp...@li...>> >> 4/27/2009 12:49 PM >>> >> In principle, I agree with Richard. We have had to add some such terms >> though to be able to reference them when describing experiments. >> Minimally they should be labeled though as being out of the primary >> scope and for future import (like we have also done for some molecules). >> >> - Bjoern >> >> Richard H. Scheuermann, Ph.D. wrote: >> > 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_______________________________________________ >> >> Obi-role-branch mailing list >> >> Obi...@li... >> <mailto:Obi...@li...> >> >> <mailto: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... >> <mailto:ric...@ut...> >> > <mailto:ric...@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-devel mailing list >> > Obi...@li... >> <mailto:Obi...@li...> >> > https://lists.sourceforge.net/lists/listinfo/obi-devel >> > >> >> >> ------------------------------------------------------------------------------ >> 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-devel mailing list >> Obi...@li... <mailto:Obi...@li...> >> https://lists.sourceforge.net/lists/listinfo/obi-devel >> >> ********************************************************** >> Electronic Mail is not secure, may not be read every day, and should >> not be used for urgent or sensitive issues >> ------------------------------------------------------------------------------ >> 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-devel mailing list >> Obi...@li... <mailto:Obi...@li...> >> https://lists.sourceforge.net/lists/listinfo/obi-devel > > --- > Mélanie Courtot > TFL- BCCRC > 675 West 10th Avenue > Vancouver, BC > V5Z 1L3, Canada > > > > |
