Need for terms to describe embryonic anterior/posterior commissure, longitudinal connective

[vjenkinsFB]

In FBrf0202065, here is part of Figure 1 and its caption:

Sli is present in the commissural tracts and longitudinal connectives. Anterior end is at top; midline is marked by vertical lines. AC, anterior commissure; PC, posterior commissure; LC, longitudinal connectives. (b) Wild-type embryo stained with anti-Sli-C antibody. Sli protein is present at very high levels in the midline, but it is also present at lower levels in the commissural tracts and longitudinal connectives (arrow with asterisk).

I'm not great at this anatomy, so I looked at the existing curation for Slit, but didn't find anything that reflected the terms the authors use. @SianGramates and Bev say these are very common terms and that we should have terms that are similar.

There are larval and adult longitudinal connective terms, but not embryonic. I don't know if "larval longitudinal connective" was more generic in the past, but there is curation in embryonic stages using this term, which is not ideal. It would be great to correct that by changing to a embryo-specific term.

Could I please have a term that could cover how the authors use anterior/posterior commissure, and one for embryonic longitudinal connective? Thank you!

[Clare72]

Hi Victoria, the 'larval' (and 'embryonic/larval') terms can be used for anything that is essentially the larval structure, but might be found at earlier or later stages. It is possible that these didn't used to have 'larval' in the name and I might have added it to make clear that they weren't adult structures ('longitudinal connective' sounds like it could apply to any stage, but I think the definition was always for the larval structure). I can add some 'embyronic/larval' synonyms if this helps clarify. Specific 'embryonic' terms are generally for structures that are still developing and have not yet reached their larval forms (I know this might sometimes be a bit subjective), these tracts are probably similar enough to those found in the larva that they do not need a separate term(?)

[vjenkinsFB]

On the CV page:

larval longitudinal connective

longitudinal tract of ventral nerve cord [EXACT] ventral nerve connective [EXACT]

Larval connective that extends in an anterior-posterior direction along the larval ventral nerve cord. These tracts continue forward into the subesophageal zone and bend laterally following the outline of the esophageal foramen (Hartenstein et al., 2018). They then converge, with their fibers forming a complex system of anastomoses before continuing into tracts of the supraesophageal ganglion (Hartenstein et al., 2017).

Would you please add some embryonic terms in the synonyms, or change the definition? I don't know how a user would realize that this was the term they wanted if they were thinking about larvae.

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For anterior and posterior commissure, there are larval terms:

larval anterior commissure larval posterior commissure

I can use them with the same logic, but there are no embryonic terms there, in definitions or as synonyms. Could they be added? Interestingly, I found these terms used only in the Pheno section rather than the Expn section.

[Clare72]

I added 'embryonic/larval' synonyms in the PR here: https://github.com/FlyBase/drosophila-anatomy-developmental-ontology/pull/1898/files will these be sufficient?

[vjenkinsFB]

That is great, thank you!

[SianGramates]

I do think that the terms currently named 'larval thing' that are valid during embryonic stages should be explicitly renamed 'embryonic/larval thing'. Most such terms are already named in that manner.

I do agree that these terms were probably renamed at some point to distinguish them from the adult structure; there's definitely expression curation that was likely done before then that currently has larval terms used inappropriately with embryonic stages.

[Clare72]

I do think that the terms currently named 'larval thing' that are valid during embryonic stages should be explicitly renamed 'embryonic/larval thing'.

This is ALL 'larval thing's - if it is essentially the mature larval structure, but just found in the late embryo, then the larval term is fine.

[Clare72]

same if it is still essentially the larval structure, but found in the early pupa

[SianGramates]

That would be acceptable for terms used only from embryonic stage 16, but not when, like the terms we're discussing, those used at embryonic stage 12.

[Clare72]

If the tracts are substantially different at earlier stages, then there should probably be different terms with definitions that reflect these differences (I do not know offhand how they arise and develop).