Re: [Phenoscape] Dealing with "absence of entities" in phenotype representations

[Hilmar Lapp]

Cartik, don't you think that there is a problem with the
lacks_part("process of basihyal bone") class? What is the genus here?

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.

So if you used, for example, lacks_part("body", "process of basihyal
bone"), then by inference:

lacks_part("body", "process of basihyal bone") is_a "body"
lacks_part("body", "process of basihyal bone") lacks_part "process of
basihyal bone"
lacks_part("body", "process of basihyal bone") lacks_part_of "basihyal
bone"

I don't follow how you infer from lacks_part("process of basihyal
bone") that

lacks_part("process of basihyal bone") is_a "absent"

Even if I add a genus term such as in

lacks_part("body", "process of basihyal bone") is_a "absent"

I'm not following how you arrive at that. But do we even need to infer
any of that?

Cheers,

-hilmar

On Aug 6, 2009, at 3:01 PM, Cartik Kothari wrote:

> Hello folks,
>
> At present, we handle "absence of entities" in phenotypes in a round
> about way. I put together some slides on the issue at hand, and I'd
> like you to go through these (there are 11 of them) and give me your
> thoughts. Further to that, I'll put in the possible implementation
> plans for our use cases.
>
> Cheers,
>
> Cartik
> <
> PhenotypesInPhenoscape
> .ppt>_______________________________________________
> Phenoscape mailing list
> Pheno...@nescent.org
> https://lists.nescent.org/mailman/listinfo/phenoscape

--
===========================================================
: Hilmar Lapp -:- Durham, NC -:- hlapp at duke dot edu :
===========================================================

[Chris Mungall]

Can you send the slides?

[Chris Mungall]

Cartik's analysis is largely correct and is why we recommend use of
relational qualities to indicate an increase, decrease of number of
parts (including the limit case, decrease to zero).

http://www.bioontology.org/wiki/index.php/PATO:Revised_2008#Absence_and_counting

Additional comments below

On Aug 6, 2009, at 6:41 PM, Hilmar Lapp wrote:

> Cartik, don't you think that there is a problem with the
> lacks_part("process of basihyal bone") class? What is the genus here?

I think we need to be more consistent with notation

R(X,Y) typically indicates a single proposition (aka statement,
sentence) involving a binary relation

In Cartik's slides he uses:
inheres_in(Q,E)

not to denote a proposition, but to denote a class expression: [Q and
inheres_in E]

lacks_part is a (binary) relation in ro_proposed. It also exists in
PATO as a relational quality or reified relation such that we can talk
directly of the lack.

I will choose to interpret lacks_part(X) as the class expression:

PATO:lacks_all_parts_of_type and towards X and inheres_in organism

Or equivalently

E=organism
Q=lacks_all_parts_of_type
E2=X

> 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.

Yes

(minor point: the differentia is the relation-relatum pair <inheres_in
basihyal_bone>)

> So if you used, for example, lacks_part("body", "process of basihyal
> bone"),

OK, here is where the notation becomes confusing. This is a
proposition stating 'all bodies lack a process of basihyal bone',
which is untrue

I will treat this as

PATO:lacks_all_parts_of_type and towards process-of-basihyal-bone and
inheres_in body

> then by inference:
>
> lacks_part("body", "process of basihyal bone") is_a "body"

inheres_in body

> lacks_part("body", "process of basihyal bone") lacks_part "process of
> basihyal bone"

towards basihyal-bone

> lacks_part("body", "process of basihyal bone") lacks_part_of "basihyal
> bone"

towards (anatomical_entity and part_of basihyal_bone)

> I don't follow how you infer from lacks_part("process of basihyal
> bone") that
>
> lacks_part("process of basihyal bone") is_a "absent"
>
> Even if I add a genus term such as in
>
> lacks_part("body", "process of basihyal bone") is_a "absent"
>
> I'm not following how you arrive at that. But do we even need to infer
> any of that?

My reading of the situation is as follows

From the proposition

[1] L-cornutus exhibits absence of (all) proc-of-basihyal-bone

we would like to infer

[2] L-cornutus exhibits absence of SOME process
[3] L-cornutus exhibits absence of SOME part of the basihyal-bone
[4] L-cornutus exhibits decreased number of processes
[5] L-cornutus exhibits decreased number of parts of the basihyal bone

but not

[2x] L-cornutus exhibits absence of (all) processes
[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

2-5 are all correct, 2x-5x are all wrong.

I use 'absence of' in the above propositions for readability, but
these would be translated to relational quality form.

Logically, absence is a non-quality cannot inhere in anything, and if
you attempt to treat like a quality that stands in an all-some
inheres_in relationship you will end up with false inferences such as
[2x].

To get the correct inferences, it's necessary to
- convert <absent inheres_in X> to the unambiguous relational
qualities (preferably as far upstream as possible); you can use the
reciprocal_of relation in PATO to help
- not treat 'towards' as an all-some relation
- add extra horn rules as sql views for these

For the phenotype analysis of OMIM we took a simplified approach and
just treated towards as an all-some relation, which made the
propositions weaker which we deemed to be ok for statistical matching