are all epithelia part of the embryo?

[cmungall]

This is causing unsatisfiable classes when merged with uberon:

[Term]
id: EMAPA:32738
name: epithelium
namespace: anatomical_structure
comment: order=7 for EMAPA:16039norder=9 for EMAPA:25765
relationship: ends_at TS26 ! TS26
relationship: part_of EMAPA:16039 ! embryo
relationship: part_of EMAPA:25765 ! mouse
relationship: starts_at TS14 ! TS14

What about the extraembryonic endoderm? It's not classified as epithelium n EMAPA, but is in EHDAA2. If we have a structure that is part of both embryo and extraembryo then this causes a spatial disjointness violation in Uberon

[tfhayamizu]

First of all, EMAPA:32738 "epithelium" now ends at TS28, but would more appropriately not have "embryo" as a parent. This will be rectified.

Secondly, we have discussed classifying ectoderm as a germ layer but, for now, there is EMAPA:35986 "endoderm" (currently part of "mouse") with children EMAPA:16062 "embryonic endoderm" (part of "embryo") and EMAPA:16052 "extraembryonic endoderm" (part of "extraembryonic component") as well as EMAPA:16063 "primitive endoderm" which gives rise to embryonic and extraembryonic structures.

Finally, it seems that classifying endoderm as epithelium is like comparing apples and oranges. One could also assert that ectoderm and mesoderm can also be epithelia. Also, according to the the definition for UBERON:0000483, an epithelium is a "Portion of tissue, that consists of one or more layers of epithelial cells connected to each other by cell junctions and which is underlain by a basal lamina." Are the statements about cell junctions and basal lamina true for all endoderm at all times and all locations?

On May 18, 2014, at 5:29 PM, Chris Mungall wrote:

This is causing unsatisfiable classes when merged with uberon:

[Term] id: EMAPA:32738 name: epithelium namespace: anatomical_structure comment: order=7 for EMAPA:16039norder=9 for EMAPA:25765 relationship: ends_at TS26 ! TS26 relationship: part_of EMAPA:16039 ! embryo relationship: part_of EMAPA:25765 ! mouse relationship: starts_at TS14 ! TS14

What about the extraembryonic endoderm? It's not classified as epithelium n EMAPA, but is in EHDAA2. If we have a structure that is part of both embryo and extraembryo then this causes a spatial disjointness violation in Uberon

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[cmungall]

First of all, EMAPA:32738 "epithelium" now ends at TS28, but would more appropriately not have "embryo" as a parent. This will be rectified.

OK, great, if you commit to the RO definitions of the start and end relations it will be invalid to have a part child temporally extend beyond the part-parent.

I think I will pass on your germ layer question to @mellybelly

[tfhayamizu]

We are aware of this problem and have been working, in conjunction with our Edinburgh colleagues, to deal with this issue overall.

On 5/19/14 4:29 PM, "Chris Mungall" notifications@github.com<mailto:notifications@github.com> wrote:

First of all, EMAPA:32738 "epithelium" now ends at TS28, but would more appropriately not have "embryo" as a parent. This will be rectified.

OK, great, if you commit to the RO definitions of the start and end relations it will be invalid to have a part child temporally extend beyond the part-parent.

I think I will pass on your germ layer question to @mellybellyhttps://github.com/mellybelly

— Reply to this email directly or view it on GitHubhttps://github.com/obophenotype/mouse-anatomy-ontology/issues/3#issuecomment-43553630.

The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.