From: Alan R. <ala...@gm...> - 2014-05-27 13:12:18
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Or you could just use the RO term directly instead of unnecessarily having a duplicate IRI. -Alan On Fri, May 23, 2014 at 5:55 PM, Michel Dumontier < mic...@gm...> wrote: > Hi Chris, > all good points. i would be open to changing the definition as you > suggest. adding the transitive/non-transitive form to RO would be nice, and > we could add the SIO-RO mapping. > > m. > > > Michel Dumontier > Associate Professor of Medicine (Biomedical Informatics), Stanford > University > Chair, W3C Semantic Web for Health Care and the Life Sciences Interest > Group > http://dumontierlab.com > > > On Fri, May 23, 2014 at 2:51 PM, Chris Mungall <cjm...@lb...> wrote: > >> >> This followed from the original definition in the RO paper, in which the >> derived must have a significant portion of matter from the derivee. There >> is no guarantee that this property holds transitively. >> >> In practice this has not been a problem as this relation is not widely >> used (at all?). The most common derivation use case for RO is development, >> and the develops from hierarchy follows the intuitive nomenclature of >> having the non-transitive subtype be prefixed with "immediately" >> >> See for example: >> http://purl.obolibrary.org/obo/RO_0002207 >> >> For non-developmental use cases: I think the cleanest thing to do here is >> obsolete http://purl.obolibrary.org/obo/RO_0001000 'derives from' and to >> introduce two new properties, with clear labels indicating the transitive >> or lack of transitive characteristic. >> >> Michel, for SIO has >> >> + derives into [Transitive] >> +--- immediately derives into >> >> With defs: >> >> "a derives to b if and only if a or some part thereof is consumed in the >> formation of b" >> >> "a immediately derives into b if and only if a or some significant part >> thereof is consumed in the formation of b and there are no identifiable >> intermediate entities between a and b." >> >> Is this correct? >> >> Let's say we have a chain of IDI relations, a1 IDI a2 IDI a3 …. IDI a_n >> >> It follows that a_1 DT a_n, by the OWL axioms. >> >> However, this may contradict the definition of DT; the formation of a_n >> may be significantly temporally downstream of the consumption of a_1. >> >> Maybe the def of DT should read: >> >> "a derives to b if and only if a or some part thereof is consumed in the >> formation of b *or as part of a causal series of events leading to the >> formation of b*" >> >> Or simply >> >> "this is the transitive form of IDI" >> >> >> >> >> On 23 May 2014, at 14:30, Michel Dumontier wrote: >> >> Hi Ramona, >>> SIO has a derives into transitive relation: >>> http://semanticscience.org/resource/derives-into >>> >>> along with the non-transitive relation >>> http://semanticscience.org/resource/immediately-derives-into >>> >>> best, >>> >>> m. >>> >>> >>> >>> Michel Dumontier >>> Associate Professor of Medicine (Biomedical Informatics), Stanford >>> University >>> Chair, W3C Semantic Web for Health Care and the Life Sciences Interest >>> Group >>> http://dumontierlab.com >>> >>> >>> On Fri, May 23, 2014 at 2:25 PM, Ramona Walls <rlw...@gm...> >>> wrote: >>> >>> Can someone clarify why the derives from relation is not transitive? I >>>> need to use a derivation relation that is transitive, and would rather >>>> not >>>> create my own. Is there something else I should be using in RO? >>>> >>>> Ramona >>>> ------------------------------------------------------ >>>> Ramona L. Walls, Ph.D. >>>> Scientific Analyst, The iPlant Collaborative, University of Arizona >>>> Laboratory Research Associate, New York Botanical Garden >>>> >>>> >>>> ------------------------------------------------------------ >>>> ------------------ >>>> "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE >>>> Instantly run your Selenium tests across 300+ browser/OS combos. >>>> Get unparalleled scalability from the best Selenium testing platform >>>> available >>>> Simple to use. Nothing to install. Get started now for free." >>>> http://p.sf.net/sfu/SauceLabs >>>> _______________________________________________ >>>> Obo-relations mailing list >>>> Obo...@li... >>>> https://lists.sourceforge.net/lists/listinfo/obo-relations >>>> >>>> >>>> ------------------------------------------------------------ >>> ------------------ >>> "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE >>> Instantly run your Selenium tests across 300+ browser/OS combos. >>> Get unparalleled scalability from the best Selenium testing platform >>> available >>> Simple to use. Nothing to install. Get started now for free." >>> http://p.sf.net/sfu/SauceLabs_______________________________ >>> ________________ >>> Obo-relations mailing list >>> Obo...@li... >>> https://lists.sourceforge.net/lists/listinfo/obo-relations >>> >> > > > ------------------------------------------------------------------------------ > "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE > Instantly run your Selenium tests across 300+ browser/OS combos. > Get unparalleled scalability from the best Selenium testing platform > available > Simple to use. Nothing to install. Get started now for free." > http://p.sf.net/sfu/SauceLabs > _______________________________________________ > Obo-relations mailing list > Obo...@li... > https://lists.sourceforge.net/lists/listinfo/obo-relations > > |