limb morphogenesis inconsistency

[ukemi]

In a recent ticket (#18624), we relaxed the logical definition of limb development so that it referred to the paired limb/fin term. This allows for automatic classification of fins under the appropriate terms in GO. The current textual definition for limb morphogenesis is restricted to tetrapods: The process in which the anatomical structures of a limb are generated and organized. A limb is a paired appendage of a tetrapod used for locomotion or grasping.

This is not consistent with the definition of the development term, but it and its children have been used for the annotation of zebrafish genes. @sabrinatoro and I discussed this and would like to propose that we relax the definitions of the GO terms so that they refer to the grouping classes for paired limbs/fins. We feel that this will allow for more powerful use of annotations across evolutionary space.

For example, limb morphogenesis would become 'anatomical structure morphogenesis' AND 'results in morphogenesis of' SOME 'paired limb/fin'. We would retain the GO term name and add a synonym, which is what we did with 'limb morphogenesis'. hindlimb morphogenesis would become 'anatomical structure morphogenesis' AND 'results in morphogenesis of' some 'pelvic appendage'. etc.

@balhoff and @cmungall do you see a problem with this plan where the nomenclature between GO and UBERON would not necessarily match? If there is, then we could use the UBERON strings, but they would not necessarily be intuitive labels for GO users.

[ukemi]

In addition we will lose some specificity in the information captured in tetrapod annotations that don't have extensions, but I'm not sure this is necessarily a problem.

[pgaudet]

Ontology call: @ukemi says paired fins are limbs - the definition needs to be relaxed.

@balhoff @cmungall Can you please reply to @ukemi 's question above ?

Thanks, Pascale

[pgaudet]

GO editors discussion:

@cmungall proposes to use limb/fin to match Uberon.

"Appendage/morphogenesis" and other terms with appendage are probably useless grouping terms - merge or obsolete ?

To be rediscussed.

@sabrinatoro @doughowe @hattrill your input is welcome !

Thanks, Pascale

[hattrill]

Not entirely clear what the proposal is here? What would we be left with?

From the FlyBase point of view, we are very attached to our appendages (insert joke) and we have many important pathways associated with appendage morphogenesis, so any changes could potentially be a lot of work.

From a user point of view, a couple of years a go Hugo Bellen made the point (quite strongly) that being able to compare human limb to appendage development had been vital in work for the rare disease network. Those gross anatomy terms are certainly useful to them.