morbidmap.txt: 1 case of association w/ 2 mapping keys

[joeflack4]

Overview

I found one instance where there is an association with multiple mapping keys in morbidmap.txt.

Phenotype	Gene Symbols	MIM Number	Cyto Location
Neurodevelopmental disorder with hypotonia, stereotypic hand movements, and impaired language, 613443 (3)	MEF2C, C5DELq14.3, DEL5q14.3, NEDHSIL	600662	5q14.3
Chromosome 5q14.3 deletion syndrome, 613443 (4)	MEF2C, C5DELq14.3, DEL5q14.3, NEDHSIL	600662	5q14.3

Additional info

The gene MIM Number for this is 600662, and for Phenotype it is 613443.

Mapping key descriptions relevant to these two rows:

# 3 - The molecular basis for the disorder is known; a mutation has been found in the gene.
# 4 - A contiguous gene deletion or duplication syndrome, multiple genes are deleted or duplicated causing the phenotype.

Additional concerns

I don't yet know why for Phenotype, it these two rows have the same MIM# (613443), but different labels: Neurodevelopmental disorder with hypotonia, stereotypic hand movements, and impaired language and Chromosome 5q14.3 deletion syndrome.

Closing this issue

@matentzn Concerning what I need to do, I think that structurally this will be handled in the exact way as the reification structure you asked me to implement for gene::disease associations.
@sabrinatoro @matentzn So I think that we can close this issue whenever you and guys have looked at this and figured out if anything else (or nothing else) needs to be done w/ this case.

[sabrinatoro]

Taking the example above: (I don't know how to format it)
Phenotype Gene Symbols MIM Number Cyto Location
Neurodevelopmental disorder with hypotonia, stereotypic hand movements, and impaired language, 613443 (3) MEF2C, C5DELq14.3, DEL5q14.3, NEDHSIL 600662 5q14.3
Chromosome 5q14.3 deletion syndrome, 613443 (4) MEF2C, C5DELq14.3, DEL5q14.3, NEDHSIL 600662 5q14.3

1. there are 2 phenotypes that are represented by the same omim id, OMIM:613443
   "Chromosome 5q14.3 deletion syndrome" is an "included" entity in OMIM:613443.
   We decided to deal with these as follow: (create new axiom annotation to indicate an OMIM term is an included entry mondo#5507)

• "Neurodevelopmental disorder with hypotonia, stereotypic hand movements, and impaired language" = MONDO-1 (not the actual id) = MONDO:equivalentTo OMIM:613443
• "Chromosome 5q14.3 deletion syndrome" = MONDO-2 (not the actual id, but different from the one above) = MONDO:includedEntryInOMIM OMIM:613443

2. Each disease, (referred above to MONDO-1 and MONDO-2) that share the same OMIM id have different mapping keys because each diseases is associated to the gene in different ways (which makes sense since they are different diseases).
   Therefore I think that the "trick" will be to identify in the morbidmap which diseases are "included", and treat them as separate disease (=same OMIM id, but different MONDO:equivalentTo versus MONDO:incldedEntryinOMIM)

[joeflack4]

Hmm, interesting... We discussed the MIMs with ", INCLUDED" on the call today. There are lots of MIMs like that. However, this is the only one such case in all of morbidmap.txt for which there are 2 different evidence mapping keys in this way. Because of that, I wonder if there could be more to this. This data model has thoroughly scrambled my brain for the day.