digits

[wdahdul]

We have a few proposed changes to definitions, labels, and synonyms of 'digit' UBERON:0002544 and related terms, summarized in this google doc: https://docs.google.com/spreadsheets/d/1LEYEUyVukLErqbUEDOUPTA8ZEvze0zAw0tJCHz4olRo/edit?usp=sharing

Note the proposed change to the definition of 'digit' to include the metapodial elements in addition to phalanges, an arrangement that is perhaps less human-centric and requires coordination with other ontologies. Additional comments and references to follow.

Phenoscape (Nizar, Alex, Wasila, Paula)

[cmungall]

This is a continuation of https://github.com/obophenotype/uberon/issues/341#issuecomment-25503610

[cmungall]

I think this will cause a lot of confusion, as digits are commonly thought to connect to extend as far as the metacarpal/metatarsal parts, not as far as the wrist/ankle. This is certainly the case in medical usage (although I don't think this necessarily shows a human bias - I would like to survey comparative anatomists).

If it truly is the case that "digit" is inherently ambiguous then we will have to give up on it as a primary label. Unfortunately this will result in some ugly terminology - e.g. "acropodial appendage" for what is commonly called a finger or toe. But even this is not ideal, as Wagner uses acropodium to encompass both phalangeal and metapodial. So perhaps "phalangeal appendage" for what is commonly called fingers or toes.

One possibility is to have different naming schemes depending on whether we are in a skeletal or organism subdivision context. But this would create a confusing terminological misalignment as "skeleton of digit 1" would not be part of digit 1.

Of course, it's always possible to have community specific primary labels, but there is the scope for confusion here where the same term is used for a different concept.

Either way, changing the existing documented scheme will be a massive refactoring so it would be good to get as wide a range of opinions possible before commencing.

[cmungall]

Additional fixes in r4086 of ext

[alex-dececchi]

Also I was wondering can we include a "has_part" relationship so that all instances of skeleton of digit x absent denotes that the digit itself is absent? I do not believe you can have a digit without its skeleton, but since for fossil data we will be annotation to the skeletal terms, it would be nice to have the absences of a skeleton mean the absent of the digit to facilitate the linking to extant/ MOD or medical data.

On Sun, May 4, 2014 at 10:16 PM, Chris Mungall notifications@github.comwrote:

Additional fixes in r4086 of ext

— Reply to this email directly or view it on GitHubhttps://github.com/obophenotype/uberon/issues/420#issuecomment-42156295 .

[cmungall]

Alex, see latest commit. Will be in core shortly. @balhoff this is using a subrelation of has_part, is this fine?

[balhoff]

That ought to work if Uberon has the subproperty axiom.

[cmungall]

row 5 of table (I can't edit): we already have:

• acropodium = set of all digits (sensu phalangeal) on an autopodial subdivision of appendage
• digitopodium = set of all digits (sensu phalangeal plus metapodials) on an autopodial subdivision of appendage

[cmungall]

row 32: why? I can add this to an anti-slim if you want it hidden.

[cmungall]

@alex-dececchi can you review?

I believe all classes required are in the correct structural place and have correct logical axioms and correct textual definitions.

The terminology can be resolved later. For now the classes you want for annotation typically have ugly labels like "{manual, pedal} digit N digitpodial skeleton". The IDs are stable.

[cmungall]

Jim - yes, it's there (not yet released though)

[alex-dececchi]

will review now, sorry to have been away for the earlier postings

On Wed, May 7, 2014 at 4:43 PM, Chris Mungall notifications@github.comwrote:

Jim - yes, it's there (not yet released though)

— Reply to this email directly or view it on GitHubhttps://github.com/obophenotype/uberon/issues/420#issuecomment-42487004 .

[alex-dececchi]

looks ok, I will call Wasila and Nizar tomorrow and we will confirm the changes. That ok? Alex

On Wed, May 7, 2014 at 8:30 PM, Alex Dececchi alex.dececchi@gmail.comwrote:

will review now, sorry to have been away for the earlier postings

On Wed, May 7, 2014 at 4:43 PM, Chris Mungall notifications@github.comwrote:

Jim - yes, it's there (not yet released though)

— Reply to this email directly or view it on GitHubhttps://github.com/obophenotype/uberon/issues/420#issuecomment-42487004 .

[cmungall]

in released version of core.owl

[gouttegd]

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