#506 jointed, unjointed

phenoscape
open
5
2013-09-12
2013-01-24
No

Jointed
definition: A structural quality inhering in a bearer by virtue of the bearer's being articulated with another entity to permit movement.

Unjointed
definition: A structural quality inhering in a bearer by virtue of the bearer's not being articulated with another entity,

Related

Phenotypic quality (PATO) requests: #506

Discussion

  • Chris Mungall

    Chris Mungall - 2013-01-24

    I think it's useful to have examples of use here.

    Consider a verstigial limb that no longer articulates with the body of the organism, but has skeletal joints as part. Is this jointed?

    I understand the need for all these terms for phenoscape but I'm not sure PATO is the best way to do this in the long term.

    If I want to query an anatomy ontology for all pato:jointed or unjointed structures, I don't get any results, despite the fact that the AO states the articulation relations and the presence of joints.

    I would instead try and use a relation such as articulates_with, or I would just use the presence or absence of UBERON:0000982 ! skeletal joint (or a more general class if you are using 'jointed' more generally). This may involve some precoordination on the part of the AO.

    If the terms do go into PATO then there needs to be a strategy for eventually axiomatizing these terms so they connect to other ontologies.

    E.g.

    jointed (sense 1): EquivalentTo inheres-in some articulates_with some Thing
    jointed (sense 2): EquivalentTo inheres-in some (has-part some joint)

    (your text def is sense 1, which is more of a relational quality - hence my question about the vestigial limb which satisfies sense 2 but not sense 1)

    It would help to record some of the OWL required in these requests (for a subset of requesters of course!)

     
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    Anonymous - 2013-02-01

    I would say that jointed should be retained because it captures something slightly different from "articulates with". The relational nature of "articulates with" requires two distinct entities, but you can have a jointed single entity. The example from curation is "radials, jointed or unjointed". In the "jointed" category, each individual radial has a articulation with another, but the exact nature of whom articulates with whom is never specified. Another example, the appendage of a beetle is said to be jointed compared to the appendage of a polycheate worm, but we do not have to specify which element(or elements) articulate with which other element (or elements).

    For these reasons I would prefer to keep these two classes separate.

    Thanks
    Alex

     
  • Georgios V. Gkoutos

    Hi Alex,

    makes sense that sometime the secondary entity is unknown or not defined. I see no problem in using an relational quality and not define an E2. This is the strategy we follow for HPO, MP etc

    Best wishes,

    George

     
  • Wasila Dahdul

    Wasila Dahdul - 2013-09-12

    Hi George, Chris,

    We think adding 'jointed' and 'unjointed' to PATO, with documentation that these need to be linked to Uberon terms, would be preferable for curator consistency. We commonly see these terms used to describe characters in the literature. Ok to add them to PATO?

    There are similar classes in PATO (e.g., articulates with) which crossover to an anatomical domain. Is there a system set up to record axioms for these, from PATO to Uberon?

    Thanks,
    Wasila and Alex

     
  • Chris Mungall

    Chris Mungall - 2013-09-12

    I think we need reciprocal equivalence axioms

    jointed SubClassOf inheresIn some ('skeletal element' and overlaps some
    'skeletal joint' and 'connected to' some 'skeletal element')
    'skeletal element' and connected_to some 'skeletal element' SubClassOf
    bearerOf some jointed

    I have to say I think it's a bad idea having two ways of saying something.
    You can't always determine equivalence. But insofar as we have these terms
    in PATO we need axioms defining and connecting them.

    Uberon has a generic 'articulation' as a superclass of 'skeletal joint'

    On Thu, Sep 12, 2013 at 10:34 AM, Wasila Dahdul wdahdul@users.sf.netwrote:

    Hi George, Chris,

    We think adding 'jointed' and 'unjointed' to PATO, with documentation that
    these need to be linked to Uberon terms, would be preferable for curator
    consistency. We commonly see these terms used to describe characters in the
    literature. Ok to add them to PATO?

    There are similar classes in PATO (e.g., articulates with) which crossover
    to an anatomical domain. Is there a system set up to record axioms for
    these, from PATO to Uberon?

    Thanks,
    Wasila and Alex


    [phenotypic-quality-pato-requests:#506] jointed, unjointed

    Status: open
    Labels: new term request
    Created: Thu Jan 24, 2013 08:00 PM UTC by Wasila Dahdul
    Last Updated: Thu Jan 24, 2013 08:00 PM UTC
    Owner: Georgios V. Gkoutos

    Jointed
    definition: A structural quality inhering in a bearer by virtue of the
    bearer's being articulated with another entity to permit movement.

    Unjointed
    definition: A structural quality inhering in a bearer by virtue of the
    bearer's not being articulated with another entity,


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    Phenotypic quality (PATO) requests: #506


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