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animal hemisphere and zyogote #153

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mellybelly opened this Issue Nov 16, 2012 · 3 comments

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mellybelly commented Nov 16, 2012

'animal hemisphere' in ext should probably be defined as an equivalent class something like:
dorsal compartment part_of some zygote

Since this requires spatial.obo and core uberon classes, should be moved to uberon core and declared there.

Note that while we have a zygote stage, we don't seem to have a zygote (e.g. fertilized egg) in uberon core, though there is a class for this in ext.

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cmungall Nov 16, 2012

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I have obsoleted UBERON:3010325, it's confused about whether it's referring to a direction or a region, and whether that region is restricted to the zygote stage or past the zygote stage.

Agreed, best to keep the v difficult early embryogenesis stuff in core. A lot more work needs done here.

Doing the same for vegetal.

TODO: same terms in blastomere. More clarification on the original XAO terms required. Perhaps some of this is difficult to generalize above Xenopus and is best left ungeneralized until we need it?

Note:

CL:0000365 ! zygote is in CL and is auto-merged into uberon/merged which is owl-imported into ext.

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cmungall commented Nov 16, 2012

I have obsoleted UBERON:3010325, it's confused about whether it's referring to a direction or a region, and whether that region is restricted to the zygote stage or past the zygote stage.

Agreed, best to keep the v difficult early embryogenesis stuff in core. A lot more work needs done here.

Doing the same for vegetal.

TODO: same terms in blastomere. More clarification on the original XAO terms required. Perhaps some of this is difficult to generalize above Xenopus and is best left ungeneralized until we need it?

Note:

CL:0000365 ! zygote is in CL and is auto-merged into uberon/merged which is owl-imported into ext.

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Note: another known source of confusion is the definition of embryo & when it starts. in EHDAA2 it isn't considered to start until around morula, the conceptus is too hard to discriminate into extra and embryonic parts until then. But other considerations apply for non-mammals. For simplicity is is useful to have a general grouping class that covers a single-celled zygote through morula etc to organism at later stages.

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cmungall commented Nov 16, 2012

Note: another known source of confusion is the definition of embryo & when it starts. in EHDAA2 it isn't considered to start until around morula, the conceptus is too hard to discriminate into extra and embryonic parts until then. But other considerations apply for non-mammals. For simplicity is is useful to have a general grouping class that covers a single-celled zygote through morula etc to organism at later stages.

cmungall added a commit that referenced this issue Nov 19, 2012

* additional definitions, synonyms and clarification comments for se…
…rous membranes and mesothelia, incl. tunica vaginalis

 * NTs for animal and vegetal poles, plus parent class. Addresses #153
 * fixes from MP
 * new terms for mapping to MTB
 * Epithelium overhaul
 * moved cannon bone syn to metacarpa/tarsal 3
 * fixes #150
 * NT: digestive syncytial vacuole; additional invertebrate taxon relationships for statocyst and other classes
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