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Re: [Obi-role-branch] [Obi-devel] dispositoin branch call today 11easternon centra
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From: Yongqun H. <yon...@me...> - 2009-04-27 19:50:22
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It's true that VO will include many terms (e.g., disease, pathogen) that are from other ontologies. However, I envision that VO will have its own set of terms as a reference ontology, for example, various vaccine names. Currently it has included more than 100 vaccine names in a carefully defined hierarchy. I am in the process of adding all ~400 vaccines curated from our VIOLIN database (http://www.violinet.org) to VO. We target to add all vaccines licensed in the world, in clincial trial, or in research. These will include vaccines for both human and animal vaccines. Eventually we will have thousands of vaccine items at minimal. In VO, we treat all these vaccines as classes instead of instances. Therefore, this is an area which may not be suitable for OBI to handle. As a vaccine reference ontology, I think any vaccine deserves a unique VO id. This is some envision I have which may be different from Bjoern's. Oliver >>> Bjoern Peters <bp...@li...> 4/27/2009 3:20 PM >>> 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 th at 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 > > > > ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues |
