Re: [Obo-relations] derives from transitive

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Order of creation of the terms suggest that the SIO term is the duplicate.

On Tue, May 27, 2014 at 2:07 PM, Michel Dumontier <
mic...@gm...> wrote:

> Or you could just use the SIO term directly instead of unnecessarily
> having a duplicate IRI.
>
> hmm...
>
> 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 Tue, May 27, 2014 at 6:11 AM, Alan Ruttenberg
> <ala...@gm...> wrote:
> > 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
> >>>>>
> >>>>>
> >>>>>
> >>>>>
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> >>>>> _______________________________________________
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> >>>>> Obo...@li...
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> >>>>>
> >>>>>
> >>>>
> >>>>
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> >>
> >>
> >>
> >>
> >>
> ------------------------------------------------------------------------------
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> >
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