HP_0000175 Cleft palate and HP_0410004 Cleft secondary palate are inferred to be equivalent

[nicolevasilevsky]

HP_0000175 Cleft palate and HP_0410004 Cleft secondary palate are inferred to be equivalent

HP_0000175 Cleft palate
'has part' some
('closure incomplete' and ('inheres in' some 'secondary palate') and ('has modifier' some abnormal))

text def
Cleft palate is a developmental defect of the palate resulting from a failure of fusion of the palatine processes and manifesting as a separation of the roof of the mouth (soft and hard palate).

HP_0410004 Cleft secondary palate
'has part' some
('closure incomplete' and ('inheres in' some 'secondary palate') and ('has modifier' some abnormal))

no text def

Suggested solution:
revise logical def for cleft palate to:
'has part' some
('closure incomplete' and ('inheres in' some 'roof of mouth') and ('has modifier' some abnormal))

Palate is a synonym of UBERON_0007375 roof of mouth

Related to #149

@cmungall @pnrobinson

[nicolevasilevsky]

same as obophenotype/human-phenotype-ontology#2431

@drseb and @pnrobinson
Should these be merged? Or should the logical definition of HP_0000175 Cleft palate be revised to include the hard and soft palate?

[nicolevasilevsky]

@drseb and @pnrobinson
I'm revisiting these old tickets - can you comment on my questions above? Thank you!

[sbello]

Hi Nicole,
We recently had this discussion for the MP as well. These should not be merged as cleft palate could mean cleft secondary palate and/or cleft primary palate. I'm trying to find the thread but haven't had any luck. There was an issue in UBERON with palate terms that needed to be resolved. Currently in the MP the term cleft palate does not have axioms attached. The closest UBERON term would be roof of mouth (UBERON:0007375) but I wasn't entirely comfortable with that one.

[nicolevasilevsky]

Hi @sbello- Perhaps @markengelstad can weigh in here, he is a craniofacial surgeon. I feel like this topic came up before too. I wonder if we need a new term in Uberon?

[mellybelly]

the logical def for cleft palate is incorrect as it includes too specific an anatomical term (secondary palate). Your suggestion seems correct to me Nicole, it is the parent of the other palate terms: http://purl.obolibrary.org/obo/UBERON_0007375

[cmungall]

I think we should start with HPO definitions - looks like there are none for primary and second? It's often dangerous axiomatizing ahead of the text definitions as the danger is you have different mental models of what the term means and you end up axiomatizing a different concept.

HP has

      is_a HP:0000175 ! Cleft palate [DEF: "Cleft palate is a developmental defect of the palate resulting from a failure of fusion of the palatine processes and manifesting as a separation of the roof of the mouth (soft and hard palate)."]
         is_a HP:0410003 ! Cleft primary palate *** 
         is_a HP:0410004 ! Cleft secondary palate *** 

I suggest getting a def for the 2 children first.

Note that the above hierrachy doesn't seem compatible with axiomatizing HP:0000175 with RoM in uberon. RoM is formed in part by SP, in part by PP. The HPO def of 'Cleft palate' says it's the failure of fusion of the palatine processes which would make it SP in Uberon (PP is premaxillary, which has a different developmental origin?)

Caveat: it's a while since I looked at this and I always found the skull a total nightmare.

I think this is all important for having developmentally sound groupings. It would be good to tie areas of ontology evolution here with improving annotations and comparing before and after.

See also discussion in GO
geneontology/go-ontology#11680
(but this pertains to abstracting across vertebrates, we're just concerned with mammals here)