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#11257 OTR:scope of x formation terms
A CACAO student is annotating a paper about the role of Pitx-1 in hindlimb development
paper: http://dev.biologists.org/content/138/24/5301.full.pdf
annotation assessment: http://gowiki.tamu.edu/wiki/index.php/Special:Cacao/annotation/10172
In this case, the KO mutant does not form specific tendon and muscle, and we think the annotation is probably wrong based on the defect not reflecting the normal function, but rather how a mutant phenotype has a secondary effect on tendon formation.
But in the more general case: Does the term "tendon formation" or any other similar term, apply only when the gene product is required for formation of ALL tendons or do we use it when formation of ANY tendon is altered? In the latter case, should we be using a regulation term?
This is an annotation question, so really be on the annotation tracker.
Couple of suggestions anyway: It's always difficult to know how direct the relationship of a gene is to process messed up in phenotype. In this case, if there is good reason to believe that an upstream patterning process is effected, you could use (or request) a term referring to the process of develeopment of that region of the limb. If you still think it is justified to annotate to tendon, you could specify the precise tendons involved using annotation extensions to terms from UBERON.
Now closing ticket. Please shift to annotation issue tracker if you want to discuss further.
Cheers,
David