poles/hemispheres

[obophenotype-user]

What is the difference between these two?

..is_a XAO:0003186 ! anatomical region ...is_a XAO:0000202 ! animal hemisphere ...is_a XAO:0004088 ! animal pole

hemisphere is defined "In developmental biology, the embryo is divided into two hemispheres: the animal pole or hemisphere and the vegetal pole or hemisphere. The animal hemisphere is the actively dividing hemisphere of the embryo, opposite the vegetal hemisphere, and is pigmented dark brown."

pole is not defined, and the only relationship it has is is_a; no start/end

Consider renaming XAO:0000297 ! animal to "animal direction"

same applies to vegetal

..is_a XAO:0003186 ! anatomical region [DEF: "A region of the whole organism that contains a recognizable set of structures or anatomical entities."] ...is_a XAO:0000280 ! vegetal hemisphere ...is_a XAO:0004113 ! vegetal pole

Note that neither of these terms are defined.

There are further problems. Look at the start/end stages:

[Term] id: XAO:0000202 name: animal hemisphere namespace: xenopus_anatomy def: "In developmental biology, the embryo is divided into two hemispheres: the animal pole or hemisphere and the vegetal pole or hemisphere. The animal hemisphere is the actively dividing hemisphere of the embryo, opposite the vegetal hemisphere, and is pigmented dark brown ." [ISBN:3-921015-04-9] xref: AAO:0010325 is_a: XAO:0003186 ! anatomical region relationship: end_stage XAO:1000021 ! NF stage 11 relationship: part_of XAO:0000035 ! zygote relationship: start_stage XAO:1000001 ! NF stage 1 relationship: start_stage XAO:1000017 ! NF stage 7

Why are there 2 start stages?

If this is truly part of the zygote, does it not also end in stage 1?

there is also the continuation into the blastomere:

[Term] id: XAO:0000200 name: animal blastomere namespace: xenopus_anatomy def: "Pigmented, smaller blastomere of the animal (upper) hemisphere of the cleaving embryo." [ISBN:0471209627] synonym: "micromere" RELATED [] xref: AAO:0010283 is_a: XAO:0003016 ! blastomere relationship: develops_from XAO:0000202 ! animal hemisphere relationship: end_stage XAO:1000019 ! NF stage 9 relationship: start_stage XAO:1000011 ! NF stage 2 (2-cell)

currently the temporal stages of 'animal hemisphere' cover animal blastomere. It seems "animal hemisphere" is trying to do double duty as both being a general class that is the is_a parent of all the stage-specific animal hemispheres and also being the zygote stage version..

My xenopus embryogenesis is pretty poor so I may have misunderstood something, but it's clear something isn't quite right here

Reported by: cmungall

Original Ticket: obo/xenopus-anatomy-xao-term-requests/16

[obophenotype-user]

I think these could be merged (they are definitely related synonyms), or the hemisphere is sometimes used only for the zygote whereas the pole term is used for multicellular early stage embryos (e.g. animal blastomere would be part_of animal pole, which would develop from animal hemisphere of the zygote, if the two terms are kept separate). If you decide to keep both terms, perhaps relabel "animal hemisphere of zyogote" or somesuch. Just some thoughts.

Original comment by: mellybelly

[obophenotype-user]

• assigned_to: nobody --> seger
• status: open --> open-accepted

Original comment by: seger

[obophenotype-user]

• Description has changed:

Diff:

--- old
+++ new
@@ -1,4 +1,3 @@
-
 What is the difference between these two?

 ..is\_a XAO:0003186 \! anatomical region

• status: open-accepted --> closed-fixed
• Group: -->

Original comment by: seger

[obophenotype-user]

For Xenopus a distinction was made between hemisphere (one half of embryo) vs. pole (top- or bottom-most part, i.e. the regions near the "poles" where the axis intercepts the surface).

An in situ could detect mRNA say in the top half of the embryo or more so at the top most part. Some of Janet Heasman's maternal transcript in situ hybridizations come to mind.

This distinction could also be used to describe protein localization in a sectioned egg or embryo showing a protein localized to the animal/vegetal pole as opposed to being distributed more evenly throughout the animal/vegetal half (hemisphere).

I have tried to clarify the definitions. Also, the hemispheres (existing from stages 1 to 11) have been made part_of embryo (existing from stages 1 to 44).

Fixed in edit files in https://code.google.com/p/xenopus-anatomy-ontology/source/browse/trunk/src/ontology/

[Term] id: XAO:0000202 name: animal hemisphere def: "Anatomical region comprising the upper, darkly pigmented, and actively dividing half of the developing early embryo." [XAO:EJS] xref: UBERON:0012284 is_a: XAO:0003186 ! anatomical region relationship: end_stage XAO:1000021 ! NF stage 11 relationship: part_of XAO:0000113 ! embryo relationship: start_stage XAO:1000001 ! NF stage 1

[Term] id: XAO:0004088 name: animal pole def: "Anatomical region comprising the top-most part of the animal hemisphere of the developing early embryo." [XAO:EJS] is_a: XAO:0003186 ! anatomical region relationship: end_stage XAO:1000021 ! NF stage 11 relationship: part_of XAO:0000202 ! animal hemisphere relationship: start_stage XAO:1000001 ! NF stage 1

[Term] id: XAO:0000280 name: vegetal hemisphere def: "Anatomical region comprising the lower, lightly pigmented half of the developing early embryo." [XAO:EJS] xref: UBERON:0012285 is_a: XAO:0003186 ! anatomical region relationship: end_stage XAO:1000021 ! NF stage 11 relationship: part_of XAO:0000113 ! embryo relationship: start_stage XAO:1000001 ! NF stage 1

[Term] id: XAO:0004113 name: vegetal pole def: "Anatomical region comprising the bottom-most part of the vegetal hemisphere of the developing early embryo." [XAO:EJS] is_a: XAO:0003186 ! anatomical region relationship: end_stage XAO:1000021 ! NF stage 11 relationship: part_of XAO:0000280 ! vegetal hemisphere relationship: start_stage XAO:1000001 ! NF stage 1

Original comment by: seger