Difference between revisions of "Modeling Absence of Phenotypes"

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[[Media:PhenotypesInPhenoscape.ppt]]
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#REDIRECT [[Absence Phenotypes in OWL]]
  
'''Hilmar Lapp'''
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[[Category:Ontology]]
 
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[[Category:Reasoning]]
Cartik, don't you think that there is a problem with the lacks_part("process of basihyal bone") class? What is the genus here?
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[[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
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[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
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[4x] L-cornutus exhibits absence of (all) basihyal-bone
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[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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Latest revision as of 22:15, 3 September 2013