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obophenotype / uberon

An ontology of gross anatomy covering metazoa. Works in concert with https://github.com/obophenotype/cell-ontology
http://obophenotype.github.io/uberon/
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unguals/ claws differentiate from nails #446

Closed alex-dececchi closed 3 years ago

alex-dececchi commented 10 years ago

Need to differentiate between a claw and a nail and between a ungual phalanx and a distal terminal phalanx. A claw encompasses the entire distal phalange, a nail only occupies the dorsal portion. Also a ungual (i.e. in a cat or a bird) is a different type of structure than a simple distal phalanx (i.e. in a human or a frog) and should be differentiate from the later.

cmungall commented 10 years ago

We had the start of a design doc here: https://docs.google.com/document/d/10rr9bU8FJ7px3ZaR2iqFMk_vXJ--Ab6HwhQ2K9-xyNI/edit?disco=AAAAAFgfUmU

I will copy this to the tracker so others can comment.

When you say "encompasses" do you mean physically covers, or physically forms the mass of?

Also, I have been taking as read certain assumptions, let me know if they are shared:

  1. skeletal tissue is disjoint from integument
  2. phalanxes are bones (and not, for example, bone plus integumentary part of claw)
  3. nails are always integument and contain no bone tissue
  4. the string "claw" is ambiguous and depending on the speaker, context and species may refer to an integumentary structure, a purely bone tissue extension of the phalanx, or a mixed structure encompassing both of the former
cmungall commented 10 years ago

Here is what we had:

Background

Many tetrapods have keratinized structures at the end of their digits. For example, humans have nails, together with associated structures such as nail beds, matrix, etc. Loosely speaking, the corresponding structure in some other tetrapods may be the claw or sometimes hoof but we must take care here, as ‘claw’ in many cases means a composite structure consisting of the some mix of the distal phalanx and the kertanized element.

Further confusion may arise from the use of ‘claw’ as a generic grouping ecompassing arthropods. We ignore this usage here.

Existing approaches

in XAO, ‘claw’ is an acellular structure on the hindlimb defined as ‘Anatomical structure consisting of a small, pointed keratinized appendage at the end of each of the three inner toes of the hind limbs’.

In MA, there is no ‘claw’ but there is a term ‘nail’. This has as parts the structures you might expect: nail bed, matrix, plate, etc

Approach

The term ‘claw’ can be ambiguous as to whether the keratinous sheath is being referred to, or the combination of keratin sheath plus bone. (or just bone)

Types of claw

We can classify claws by their constituent parts - presence or absence of keratin and bone. Where bone is present this is typically the entire distal (ungual) phalanx.

see Maddin et al. (2009); Xenopus non-homologous to amniote claws

Types of keratinous sheath

Hooves

TODO

Developmental biology

TODO

Applicability to other keratinized appendages

cmungall commented 10 years ago

comments?

alex-dececchi commented 10 years ago

I thought we had briefly discussed how the nail is only on the dorsal surface of the distal phalanx while a claw encompasses the entire (or minimally the large majority) of the phalanx. Alex

On Tue, Jun 10, 2014 at 2:15 PM, Chris Mungall notifications@github.com wrote:

comments?

— Reply to this email directly or view it on GitHub https://github.com/obophenotype/uberon/issues/446#issuecomment-45658636.

cmungall commented 10 years ago

this feels incomplete.

the nail isn't a phalanx surface - it's separated from the phalanx (which is composed of bone tissue), so isn't part of it.

we need to be sure this works for a variety of claws, including bone and keratin components

On Tue, Jun 10, 2014 at 12:57 PM, alex-dececchi notifications@github.com wrote:

I thought we had briefly discussed how the nail is only on the dorsal surface of the distal phalanx while a claw encompasses the entire (or minimally the large majority) of the phalanx. Alex

On Tue, Jun 10, 2014 at 2:15 PM, Chris Mungall notifications@github.com wrote:

comments?

— Reply to this email directly or view it on GitHub https://github.com/obophenotype/uberon/issues/446#issuecomment-45658636.

— Reply to this email directly or view it on GitHub https://github.com/obophenotype/uberon/issues/446#issuecomment-45663535.

alex-dececchi commented 10 years ago

I found this from Soligo and Muller 1999. "Traditionally, cheirideal appendages are categorized as claws (falculae) or nails (ungulae) according to their shape: claws are laterally compressed, longitudinally curved and have a sharp and pointed distal end; nails are more or less flat" While there is a continuum, I believe we could use a shape based definition to distinguish the majority of members of both categories.

On Tue, Jun 10, 2014 at 3:10 PM, Chris Mungall notifications@github.com wrote:

this feels incomplete.

the nail isn't a phalanx surface - it's separated from the phalanx (which is composed of bone tissue), so isn't part of it.

we need to be sure this works for a variety of claws, including bone and keratin components

On Tue, Jun 10, 2014 at 12:57 PM, alex-dececchi notifications@github.com

wrote:

I thought we had briefly discussed how the nail is only on the dorsal surface of the distal phalanx while a claw encompasses the entire (or minimally the large majority) of the phalanx. Alex

On Tue, Jun 10, 2014 at 2:15 PM, Chris Mungall notifications@github.com

wrote:

comments?

— Reply to this email directly or view it on GitHub < https://github.com/obophenotype/uberon/issues/446#issuecomment-45658636>.

— Reply to this email directly or view it on GitHub https://github.com/obophenotype/uberon/issues/446#issuecomment-45663535.

— Reply to this email directly or view it on GitHub https://github.com/obophenotype/uberon/issues/446#issuecomment-45665011.

spinosaur commented 10 years ago

Agreed, shape based definition is probably the best we can do.

Nizar

Nizar Ibrahim, PhD The University of Chicago Organismal Biology & Anatomy 1027 East 57th Street, Chicago

Email: nibrahim@uchicago.edu Office phone: 773-702-6025

From: alex-dececchi notifications@github.com<mailto:notifications@github.com> Reply-To: obophenotype/uberon reply@reply.github.com<mailto:reply@reply.github.com> Date: Wednesday, June 18, 2014 4:55 PM To: obophenotype/uberon uberon@noreply.github.com<mailto:uberon@noreply.github.com> Subject: Re: [uberon] unguals/ claws differentiate from nails (#446)

I found this from Soligo and Muller 1999. "Traditionally, cheirideal appendages are categorized as claws (falculae) or nails (ungulae) according to their shape: claws are laterally compressed, longitudinally curved and have a sharp and pointed distal end; nails are more or less flat" While there is a continuum, I believe we could use a shape based definition to distinguish the majority of members of both categories.

On Tue, Jun 10, 2014 at 3:10 PM, Chris Mungall notifications@github.com<mailto:notifications@github.com> wrote:

this feels incomplete.

the nail isn't a phalanx surface - it's separated from the phalanx (which is composed of bone tissue), so isn't part of it.

we need to be sure this works for a variety of claws, including bone and keratin components

On Tue, Jun 10, 2014 at 12:57 PM, alex-dececchi notifications@github.com<mailto:notifications@github.com>

wrote:

I thought we had briefly discussed how the nail is only on the dorsal surface of the distal phalanx while a claw encompasses the entire (or minimally the large majority) of the phalanx. Alex

On Tue, Jun 10, 2014 at 2:15 PM, Chris Mungall notifications@github.com<mailto:notifications@github.com>

wrote:

comments?

— Reply to this email directly or view it on GitHub < https://github.com/obophenotype/uberon/issues/446#issuecomment-45658636>.

— Reply to this email directly or view it on GitHub https://github.com/obophenotype/uberon/issues/446#issuecomment-45663535.

— Reply to this email directly or view it on GitHub https://github.com/obophenotype/uberon/issues/446#issuecomment-45665011.

— Reply to this email directly or view it on GitHubhttps://github.com/obophenotype/uberon/issues/446#issuecomment-46499563.

gouttegd commented 3 years ago

WARNING: This issue has been automatically closed because it has not been updated in more than 3 years. Please re-open it if you still need this to be addressed addressed addressed – we are now getting some resources to deal with such issues.