"Long fingers" vs. "Short toe" vs. "Arachnodactyly"

sivarajankumar / phenotype-ontologies

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"Long fingers" vs. "Short toe" vs. "Arachnodactyly" #16

Closed GoogleCodeExporter closed 8 years ago

GoogleCodeExporter commented 8 years ago

In Uberpheno@charite I see that "Long fingers" is a subclass of "Short toe" 
which is definitely wrong.

IMHO it is the definition of Arachnodactyly that causes the problems but I am 
not sure.  I attached a screenshot of the first two explanations.

Does somebody have any idea? Should we maybe just delete the logical definition 
of Arachnodactyly!

Original issue reported on code.google.com by dr.sebas...@gmail.com on 4 Apr 2014 at 9:02

Attachments:

[Screen Shot 2014-04-04 at 10.59.36.png](https://storage.googleapis.com/google-code-attachments/phenotype-ontologies/issue-16/comment-0/Screen Shot 2014-04-04 at 10.59.36.png)

GoogleCodeExporter commented 8 years ago

A related problem (see screenshot), but I still don't get it where the mix of 
toe/finger is coming from. Anybody any ideas?

Original comment by dr.sebas...@gmail.com on 4 Apr 2014 at 2:09

Added labels: Priority-High
Removed labels: Priority-Medium

Attachments:

[Screen Shot 2014-04-04 at 16.06.42.png](https://storage.googleapis.com/google-code-attachments/phenotype-ontologies/issue-16/comment-1/Screen Shot 2014-04-04 at 16.06.42.png)

GoogleCodeExporter commented 8 years ago

In MPO "arachnodactyly" is a direct subclass of "abnormal digit morphology".
The MPO-arachnodactyly is asserted by us to be equivalent to HPO-Arachnodactyly.
IMHO the problem comes from HPO-hierarchy, where Arachnodactyly:
is_a: HP:0001238 ! Slender finger
is_a: HP:0010511 ! Long toe
is_a: HP:0100807 ! Long fingers

Does anybody agree that this might be the root of the problem?
If yes, does anybody have an idea how to solve this?

Original comment by dr.sebas...@gmail.com on 4 Apr 2014 at 2:21

GoogleCodeExporter commented 8 years ago

Yes! HP is definitely wrong here.

HP:0001166 ! Arachnodactyly ***  [DEF: "Abnormally long and slender fingers 
("spider fingers")."]

Nothing about toes

Original comment by cmung...@gmail.com on 16 Apr 2014 at 3:33

GoogleCodeExporter commented 8 years ago

Ok I'll fix this in HPO. MP is correct here? They refer to the more general 
class 'digit' here.

Original comment by dr.sebas...@gmail.com on 16 Apr 2014 at 3:59

GoogleCodeExporter commented 8 years ago

Original comment by dr.sebas...@gmail.com on 16 Apr 2014 at 4:05

Changed state: Fixed