change primary name for UBERON:2000088

[hdrabkin]

The primary term name of UBERON:2000088 is YSL with an exact synonym of yolk sac layer. Could we get the primary name and synonym swapped so yolk sac layer is the term name and YSL is the synonym? The primary term name should be spelled out.

Two other term might also need to be changed similarly
E-YSL UBERON_2000309
I-YSL UBERON:2000712

[cmungall]

@wdahdul are you Ok to make this edit (in the phenoscape-ext module)?

[cmungall]

Do we get any useful generalization out of the two subclasses in Uberon?

@hdrabkin is this for annotation or ontology axiomatization?

[hdrabkin]

The latter. If I want to make a logical def for a requested term yolk sac layer development.

[cmungall]

Thanks for linking the tracker items!

I think we should make the change straight away, and we should also add taxon constraints and make sure the definition is suitably generalized. @sabrinatoro provided some links here:
geneontology/go-ontology#16536 (comment)

Also, e.g: Structure of the Yolk Syncytial Layer in Teleostei and Analogous
Structures in Animals of the Meroblastic Type of Development
https://link.springer.com/article/10.1134%2FS1062359016030055

[wdahdul]

@cmungall Would you add two taxon constraints in this case? e.g., 1) only_in_taxon some 'Vertebrata ' for Teleostei, Myxini, Chondrichthyes, and Lepisosteiformes, and 2) only_in_taxon some Cephalopoda

[hdrabkin]

But from saying only in taxon 1, could you also then say 'only in taxon 2'? Sounds contradictory.
Also, it's not all vertebrata, right?; only some fish and , not mammal, bird, repitile, etc.?

[cmungall]

I would treat this as a union.

Seems like an odd union though. Are there meaningful similarities between cephalopod and fish here?

[doughowe]

YSL, I-YSL, and E-YSL are terms in ZFA as well. Is it important to have consistency in term naming across these ontologies? Not sure if our anatomy editors would want to make that change. There are other terms handled in a similar way, at least in ZFA, having the abbreviated form as the primary term name when the community uses that format predominantly.

Also, I believe it would be yolk syncytial layer, rather than yolk sac layer? I am assuming those two terms are referring to the same thing...

[cmungall]

@doughowe - see the linked ticket in ZFA tracker above.

Standard ontology naming conventions are to spell out abbreviations in the primary name. Tools can still choose to use an abbreviation

• https://scholar.google.com/scholar?hl=en&as_sdt=0%2C5&as_vis=1&q=YSL++zebrafish&btnG= YSL 1350
• "yolk syncytial layer" https://scholar.google.com/scholar?q=%22yolk+syncytial+layer%22+zebrafish&hl=en&as_sdt=0&as_vis=1&oi=scholart 2110

[doughowe]

Stellar..looks like you guys are at least a day ahead of me!

[cmungall]

on second thoughts for TCs I think we should be conservative and only add negative constraints.

Really we should have an ontology class somewhere for "mereoblastic cleavage" and add some TCs there. This could be a subclass of GO:0040016 embryonic cleavage, or of UBERON:0000107 cleavage stage. The uberon YSL would then be an output of this and inherit it's TCs..