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− | [[Media:PhenotypesInPhenoscape.ppt]] | + | #REDIRECT [[Absence Phenotypes in OWL]] |
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− | '''Hilmar Lapp'''
| + | [[Category:Ontology]] |
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− | Cartik, don't you think that there is a problem with the lacks_part("process of basihyal bone") class? What is the genus here?
| + | [[Category:Database]] |
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− | When using inheres_in for the phenotype composition, such as inheres_in("flat", "basihyal bone"), there is a genus ("flat"), a relationship (inheres_in), and a differentia ("basihyal bone") term.
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− | So if you used, for example, lacks_part("body", "process of basihyal bone"), then by inference:
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− | lacks_part("body", "process of basihyal bone") is_a "body"
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− | lacks_part("body", "process of basihyal bone") lacks_part "process of basihyal bone"
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− | lacks_part("body", "process of basihyal bone") lacks_part_of "basihyal bone"
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− | I don't follow how you infer from lacks_part("process of basihyal bone") that
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− | lacks_part("process of basihyal bone") is_a "absent"
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− | Even if I add a genus term such as in
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− | lacks_part("body", "process of basihyal bone") is_a "absent"
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− | I'm not following how you arrive at that. But do we even need to infer any of that?
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− | '''Chris Mungall'''
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− | Cartik's analysis is largely correct and is why we recommend use of
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− | relational qualities to indicate an increase, decrease of number of
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− | parts (including the limit case, decrease to zero).
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− | http://www.bioontology.org/wiki/index.php/PATO:Revised_2008#Absence_and_counting
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− | Additional comments below
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− | On Aug 6, 2009, at 6:41 PM, Hilmar Lapp wrote:
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− | > > Cartik, don't you think that there is a problem with the
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− | > > lacks_part("process of basihyal bone") class? What is the genus here?
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− | I think we need to be more consistent with notation
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− | R(X,Y) typically indicates a single proposition (aka statement,
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− | sentence) involving a binary relation
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− | In Cartik's slides he uses:
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− | inheres_in(Q,E)
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− | not to denote a proposition, but to denote a class expression: [Q and
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− | inheres_in E]
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− | lacks_part is a (binary) relation in ro_proposed. It also exists in
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− | PATO as a relational quality or reified relation such that we can talk
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− | directly of the lack.
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− | I will choose to interpret lacks_part(X) as the class expression:
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− | PATO:lacks_all_parts_of_type and towards X and inheres_in organism
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− | Or equivalently
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− | E=organism
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− | Q=lacks_all_parts_of_type
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− | E2=X
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− | > > When using inheres_in for the phenotype composition, such as
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− | > > inheres_in("flat", "basihyal bone"), there is a genus ("flat"), a
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− | > > relationship (inheres_in), and a differentia ("basihyal bone") term.
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− | Yes
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− | (minor point: the differentia is the relation-relatum pair <inheres_in
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− | basihyal_bone>)
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− | > > So if you used, for example, lacks_part("body", "process of basihyal
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− | > > bone"),
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− | OK, here is where the notation becomes confusing. This is a
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− | proposition stating 'all bodies lack a process of basihyal bone',
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− | which is untrue
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− | I will treat this as
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− | PATO:lacks_all_parts_of_type and towards process-of-basihyal-bone and
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− | inheres_in body
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− | > > then by inference:
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− | > >
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− | > > lacks_part("body", "process of basihyal bone") is_a "body"
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− | inheres_in body
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− | > > lacks_part("body", "process of basihyal bone") lacks_part "process of
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− | > > basihyal bone"
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− | towards basihyal-bone
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− | > > lacks_part("body", "process of basihyal bone") lacks_part_of "basihyal
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− | > > bone"
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− | towards (anatomical_entity and part_of basihyal_bone)
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− | > > I don't follow how you infer from lacks_part("process of basihyal
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− | > > bone") that
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− | > >
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− | > > lacks_part("process of basihyal bone") is_a "absent"
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− | > >
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− | > > Even if I add a genus term such as in
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− | > >
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− | > > lacks_part("body", "process of basihyal bone") is_a "absent"
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− | > >
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− | > > I'm not following how you arrive at that. But do we even need to infer
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− | > > any of that?
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− | My reading of the situation is as follows
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− | From the proposition
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− | [1] L-cornutus exhibits absence of (all) proc-of-basihyal-bone
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− | we would like to infer
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− | [2] L-cornutus exhibits absence of SOME process
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− | [3] L-cornutus exhibits absence of SOME part of the basihyal-bone
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− | [4] L-cornutus exhibits decreased number of processes | |
− | [5] L-cornutus exhibits decreased number of parts of the basihyal bone | |
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− | but not
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− | [2x] L-cornutus exhibits absence of (all) processes
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− | [3x] L-cornutus exhibits absence of (all) parts of the basihyal-bone | |
− | [4x] L-cornutus exhibits absence of (all) basihyal-bone | |
− | [5x] L-cornutus exhibits decreased number of basihyal-bone
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− | 2-5 are all correct, 2x-5x are all wrong.
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− | I use 'absence of' in the above propositions for readability, but
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− | these would be translated to relational quality form.
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− | Logically, absence is a non-quality cannot inhere in anything, and if
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− | you attempt to treat like a quality that stands in an all-some
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− | inheres_in relationship you will end up with false inferences such as
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− | [2x].
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− | To get the correct inferences, it's necessary to
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− | - convert <absent inheres_in X> to the unambiguous relational
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− | qualities (preferably as far upstream as possible); you can use the
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− | reciprocal_of relation in PATO to help
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− | - not treat 'towards' as an all-some relation
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− | - add extra horn rules as sql views for these
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− | For the phenotype analysis of OMIM we took a simplified approach and
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− | just treated towards as an all-some relation, which made the
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− | propositions weaker which we deemed to be ok for statistical matching
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