From: Michael A. <ma...@ge...> - 2012-01-30 15:09:51
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I apologise that I have not been folowing this issue closely. However, one statement from Suzanne does, in my opinion, rule this out as an OBO Foundry ontology: "The current work is part of my master’s project which will be finished this Spring semester" For and OBO Foundry Ontology there really must be a commitment to long term development. That is not what one would expect of a Master's project. Michael On 30 Jan 2012, at 12:58, Suzanne Santamaria wrote: > Responses between <sls> tags below... > Thanks, > Suzanne Santamaria > > On Thu, Jan 26, 2012 at 12:33 PM, WEBB, HOWARD M (AG/1000) <how...@mo... > > wrote: > I am a bit concerned about this ontology(s) being in the OBO. While > what you are defining is useful, I am not sure whether it is a > scientific domain, or more of an administrative ontology (ie U.S. > animal drug administration). Definitely you want to follow the OBO > design patterns, and leverage off of what it has. > <sls>The ontology was originally populated from animals needed by > the US Food and Drug Administration Center for Veterinary Medicine’s > (FDA CVM) and the United States Department of Agriculture - Animal > and Plant Health Inspection Services - Veterinary Services (USDA > APHIS VS). Since then other entities have wanted to use parts of the > ontology and the structure of the ontology allows for growth. Since > OBO includes “Biomedical” in its name, we have worked under the > assumption that classes of interest to medicine (including > veterinary medicine) and scientific research involving animals were > included in OBO’s scope. The ontology could also serve as a > knowledge bridge for scientists using animal models in biomedical > research to facilitate a better understanding of research in animal > science and veterinary medicine. We are encouraged to have received > positive feedback from multiple developers of other OBO ontologies > who have expressed interest in using this ontology. </sls> > > I see different subject areas in what you are discussing. One is a > species specific growth/life stage classification (calf, heifer), > the other is a husbandry role. > <sls>I agree that there might be a natural division of the current > work into three ontologies: 1. Animal life/development stages; 2. > Animals “in roles” group (production, husbandry, use); and 3. Common > non-Linnaean animal groupings. We will look into this and consider > dividing up the ontology in the near future. The current work is > part of my master’s project which will be finished this Spring > semester.</sls> > > For the first, I might suggest creating a mammalian development > ontology (similar to the plant PO), then making a restricted synonym > mapping between that and the NCBI Taxonomy (ie. 'calf' is the term > name of the mapping between 'youth' scoped by 'Bovinae', acting as > a restricted synonym). In think the PO simplifies this in places, > directly making them genus specific synonyms in the PO (cf. id: PO: > 0007095). > > <sls>We will investigate this during future development work. One of > the problems we encounter when trying to use the Linnaean classes is > that they lack contain common groupings which do not correspond with > one Linnaean class. Example: “Goose” does not correspond with one > Linnaean class – it refers to animals in multiple genera across the > three families of Anseriformes, but not all, as Anseriformes also > contains ducks and swans. Therefore, “Gosling” (young goose) cannot > be mapped to one Linnaean class. </sls> > > The husbandry issue strikes me as also a mapping (but maybe an > administrative mapping), it defines the 'role' of an animal in > relationship to the intended use ("broiler"), with a husbandry > practice associated to this role. Animals in relation to a zoo > (environment, business, ?) also have distinct husbandry practices. > Actual husbandry practices can vary zoo by zoo, though they may have > common patterns, my point here is that husbandry practices are not > consistent entities in a scientific domain. > > <sls>I agree that husbandry practices vary; however, we are not > attempting to define characteristics of certain husbandry practices, > we are just defining animals in those situations as participating in > those practices. For example, in the ontology a “Zoo bear” is > defined as a bear (“Family Ursidae”) that “lives in” a “Zoological > garden.” We are not attempting to define diets or other husbandry > practices associated with zoos. A “Beef calf” is defined as a “Calf” > that is “bearer of” a role to “Produce beef for human consumption.” > We are not attempting to define how this is carried out through > specific diet or management practices.</sls> > > The third ontology was common names. At best I would suggest making > these synonyms in the NCBI Taxonomy (and using the existing formal > hierarchy), but common names are definitely not 'scientific' > classifications. > > <sls>As mentioned above, animals are grouped by phenotypic and other > similarities in the “real world” and in scientific research, and > there is a demonstrated need to identify animals by these phenotypic > traits (duck, goose, deer, mouse, etc.) when the exact Linnaean > classification is not known or if there is not a 1:1 association > with a Linnaean class. Many common animal groupings do not > correspond with one class in NCBI Taxonomy or any other strict > Linnaean ontology. As mentioned in another post, let’s move this > part of the discussion to the OBO Taxonomy group . </sls> > > I like that you want to build off of the OBO, but I see the pattern > being more specific, closer to the relationship like that of > MaizeGDB to the OBO (MaizeGDB is referenced within within PO), than > being incorporated as an OBO ontology; it may be an 'ontology of > interest'. > > <sls>There is a definite need to identify animals as we have done in > this ontology. Where the ontology should rest is yet to be > determined. We will be sending a link for OBO folks to review the > ontology soon and will await guidance on future development and > placement on the OBO Foundry website. Thank you for your comments > and interest.</sls> > > Regards, > Howard Webb > This e-mail message may contain privileged and/or confidential > information, and is intended to be received only by persons entitled > to receive such information. 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