Open GoogleCodeExporter opened 8 years ago
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).
Original comment by peter...@gmail.com
on 16 Nov 2013 at 9:51
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.
Original comment by cmung...@gmail.com
on 18 Nov 2013 at 1:39
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....
Original comment by cmung...@gmail.com
on 18 Nov 2013 at 1:46
Original issue reported on code.google.com by
cmung...@gmail.com
on 31 Oct 2013 at 12:38