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new term request: profundal placode #693

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ANiknejad opened this Issue May 1, 2015 · 3 comments

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ANiknejad commented May 1, 2015

Hi Chris,

Currently we only have this term for 'profundal' stuff:

id: XAO:0004093
name: profundal placode (Xenopus)

'profundal placode' sounds to be egal to 'ophtalmic placode'
http://www.ncbi.nlm.nih.gov/pubmed/?term=22512454
" [In vertebrates] The lens placode, which generates the crystalline-containing cells of the lens, is also associated with the forebrain but forms more posteriorly alongside the region of the diencephalon that will give rise to the optic cup. More caudally, the trigeminal placodes, the ophthalmic (or profundal) and maxillomandibular, emerge at the level of the midbrain-hindbrain boundary....clearly distinct profundal and trigeminal placodes giving rise to correspondingly distinct ganglia are readily observable in shark embryos (O’Neill et al. 2007)."

In Uberon we have an 'optic placode' exact synonym of
UBERON:0003071
name: eye primordium

However I guess, that does not match the 'profundal placode' as defined here for Shark
http://www.ncbi.nlm.nih.gov/pubmed/?term=17234174

Cheers,

Anne

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cmungall commented May 3, 2015

Interesting. See also: UBERON:0003070 ! trigeminal placode

Figure 9-5 of Butler and Hodos seems to use Profundal as synonymous with trigeminal... but this may only be true of their distal end; from XAO: "The profundal and the trigeminal ganglia are separate distally but fused at their proximal end as they condense around NF stage 24"

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mellybelly commented May 3, 2015

The placodes are notoriously diverse across species. here is a great review with many key citations:
http://www.ncbi.nlm.nih.gov/books/NBK53171/

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cmungall commented May 10, 2015

See this
model
for a first pass.

In this model we have a single class for each 'lobe' of the trigeminal complex, whether that 'lobe' is completely fused, partly fused or a distinct ganglion unto itself. We could split this and have separate classes, and then link via a cross-class homology assertion, but this seems like inflation.

The ontology is more complex than the diagram as we follow EMAPA in introducing an intermediate 'preganglion', but if this does no work for us should we merge it?

Nerves need work.

cmungall added a commit that referenced this issue May 27, 2015

This release incorporates a first pass at organism subdivisions for
the acorn worm (enteropneust). We would like to bud this off into an
external ontology that is federated with the core Uberon. For more
information, see [692](#692)

We also clarified the distinctinction between trigeminal and profundal
placodes and the structures they give rise to. For more information,
see [693](#693), and the following diagram:

![trigeminal](https://raw.githubusercontent.com/obophenotype/uberon/master/docs/trigeminal.png)
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