aortic (valve) stenosis

[cmungall]

Originally reported on Google Code with ID 3

MP has:

[Term]
id: MP:0010463
name: aorta stenosis
def: "diffuse constriction or narrowing of the aorta" [MGI:csmith]
****comment: Do not confuse with aortic valve stenosis.
synonym: "aortic stenosis" RELATED []
is_a: MP:0000272  ! abnormal aorta morphology
is_a: MP:0006135  ! artery stenosis

HP has:

[Term]
id: HP:0001650
name: Aortic valve stenosis
def: "The presence of a stenosis (narrowing) of the aortic valve." [HPO:probinson]
comment: Aortic stenosis can lead to a pressure gradient between the left ventricle
and the aorta and may result in left ventricular hypertrophy and decreased left ventricular
compliance.
*****synonym: "Aortic stenosis" EXACT []
synonym: "Valvular aortic stenosis" EXACT []
is_a: HP:0001646  ! Abnormality of the aortic valve

The HP exact syn contradicts the MP comment.

Note there is a separate term: MP:0006117 ! aortic valve stenosis

Recommendations:

1. HP demotes the syn from EXACT OR adds aortic stenosis as a separate term
2. (optional) the MP comment is represented explicitly as an OWL disjointness axiom

Reported by cmungall on 2013-10-31 00:38:26

[cmungall]

This usage is standard in the medical community, and thus I think it is appropriate
to have this as an exact synonym. Nobody should be using text mining to match between
HP and MP (hmm....., at least not after we finish all of the logical definitions :-0).

Reported by peternro on 2013-11-16 21:51:54

[cmungall]

OK, that suggests the MP should have a different primary label for the grouping class.

I agree text mining is best avoided. But unless we are striving for 100% sensitivity
then it's the best strategy to complement the logical defs. There are 766 pairs of
matching labels (many of which are problematic of course) for which there is no logical
def for at least one of the partners.

Many of these are simply too hard to give a meaningful OWL logical definition to, so
the best we can do is a verified direct equivalence axiom between the two ontologies.

Our strategy is much better than most other text mining efforts. We have a strategy
for overriding spurious matches (the disjoints file), and of course having the logical
definitions override.

Reported by cmungall on 2013-11-18 01:39:18

[cmungall]

An example of a difficult class to define using an OWL pattern using PATO:

[Term]
id: MP:0004110
name: transposition of great arteries
namespace: MPheno.ontology
alt_id: MP:0006127
def: "cardiovascular structural anomaly in which the aorta arises from the right ventricle
while the pulmonary artery arises from the left ventricle" [MGI:monikat]
subset: CvDC_Terms  ! NHLBI Cardiovascular Development Consortium (CvDC) Terms
synonym: "TGA" EXACT []
synonym: "discordant VA connections" EXACT []
synonym: "transposition of great vessels" RELATED []
is_a: MP:0010426  ! abnormal heart and great artery attachment

But I suspect the equivalence to the identically labeled HP:0001669 ! Transposition
of the great arteries is correct.

In fact I think it *is* possible to do good OWL definitions for defects such as this,
but it involves creating an abnormal anatomy ontology -- https://github.com/cmungall/vmao
-- but is it worth this extra effort if we can make a direct link and infer the basic
anatomical axioms from the parent....

Reported by cmungall on 2013-11-18 01:46:55