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Request class "Mesoaxial fingers" #592

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drseb opened this Issue Oct 22, 2014 · 2 comments

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drseb commented Oct 22, 2014

has_part some
('manual digit 2'
or 'manual digit 3'
or 'manual digit 4’)

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cmungall Oct 22, 2014

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For this and #593 we have the following:

[Term]
id: UBERON:4200015
name: inner digits of foot
namespace: none
def: "The medial most digits of the pes." []comment: In most tetrapods this corresponds to digits II-IV, but the exact identiy of digits in this region varies taxonomically based on digit numbering.
xref: PHENOSCAPE:ad
is_a: UBERON:0005445  ! segment of pes
relationship: part_of UBERON:0012142 ! pedal digitopodium region

[Term]
id: UBERON:4200094
name: inner digits of hand
namespace: none
def: "The medial most digit of the manus skeleton." []
comment: In most taxa this is digits II-IV, but this varies based on the number of digits and thier identity in the taxa examined.
is_a: UBERON:0005451  ! segment of manus
relationship: part_of UBERON:0012140 ! digitopodium region

These were added as part of the ext project. I will modify in the following way which is consistent with the text def and intent: these will be made subclasses of the relevant digit class.

We also want digits2,3,4 to be a subclass of this in humans. We could do this using this pattern https://github.com/obophenotype/uberon/wiki/Evolutionary-variability-GCIs

But this is quite complex. What I suggest doing instead is adding distinct classes:

  • digit 1 or 5 {manus,pes,generic}
  • digit 2,3 or 4 {manus,pes,generic}

drseb would use these for defining the human phenotype classes.

These would be inferred to be subclass of "lateral" or "mesoaxial" in different species. We would also add taxon-specific syns to the newly added classes (lateral, mesoaxial)

Thus the new classes would be 'rigid' and the existing classes would remain fluid, with different digits in different taxa classifying under them.

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cmungall commented Oct 22, 2014

For this and #593 we have the following:

[Term]
id: UBERON:4200015
name: inner digits of foot
namespace: none
def: "The medial most digits of the pes." []comment: In most tetrapods this corresponds to digits II-IV, but the exact identiy of digits in this region varies taxonomically based on digit numbering.
xref: PHENOSCAPE:ad
is_a: UBERON:0005445  ! segment of pes
relationship: part_of UBERON:0012142 ! pedal digitopodium region

[Term]
id: UBERON:4200094
name: inner digits of hand
namespace: none
def: "The medial most digit of the manus skeleton." []
comment: In most taxa this is digits II-IV, but this varies based on the number of digits and thier identity in the taxa examined.
is_a: UBERON:0005451  ! segment of manus
relationship: part_of UBERON:0012140 ! digitopodium region

These were added as part of the ext project. I will modify in the following way which is consistent with the text def and intent: these will be made subclasses of the relevant digit class.

We also want digits2,3,4 to be a subclass of this in humans. We could do this using this pattern https://github.com/obophenotype/uberon/wiki/Evolutionary-variability-GCIs

But this is quite complex. What I suggest doing instead is adding distinct classes:

  • digit 1 or 5 {manus,pes,generic}
  • digit 2,3 or 4 {manus,pes,generic}

drseb would use these for defining the human phenotype classes.

These would be inferred to be subclass of "lateral" or "mesoaxial" in different species. We would also add taxon-specific syns to the newly added classes (lateral, mesoaxial)

Thus the new classes would be 'rigid' and the existing classes would remain fluid, with different digits in different taxa classifying under them.

cmungall added a commit that referenced this issue Oct 26, 2014

cmungall added a commit that referenced this issue Oct 27, 2014

2014-10-26 release
 * NTs: skin crease {palmar,plantar}. Fixes issue #591
 * NTs: digits1,5 and 2,3,4 of manus and pes - Fixes issue #592 #593 #594
 * subcapsular polar regions. Addresses #599. Requires expert input. It seems the subcapsular regions are not specifically part of the pole?
 * NT: chorioretinal region. drseb. Fixes issue #600
 * thyroid fixes - relationship to neck is species specific
 * merged false add of colorectal mucosa, added bto xref instead
 * bto and emapa xrefs
 * NTs: gemellus
 * NTs: skin of anterior chest; lateral chest. Fixes issue #588
 * added disjointness axiom between splenic and celiac arteries. Issue #268
 * Made relationship between celiac artery supply of various organs to be indirect. This will fix issue #268
 * Added definition of indirectly supplies. Fixes #587
 * syn for jugal bar. PHENOSCAPE:wd.\nFixed issue #586
 * EMAPA xrefs
 * NTs: dorsal nerve of penis/clitoris
 * improved multiple defs. Fixed otic capsule to use endochondral pattern
 * NT: nursing stage. Fixes issue #576
 * splanchnic nerve tidying
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drseb Oct 28, 2014

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Thanks a lot

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drseb commented Oct 28, 2014

Thanks a lot

@drseb drseb closed this Oct 28, 2014

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