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monarch-initiative / dipper

Data Ingestion Pipeline for Monarch
https://dipper.readthedocs.io/en/latest/
BSD 3-Clause "New" or "Revised" License
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THAS is not a gene #859

Closed pnrobinson closed 4 years ago

pnrobinson commented 4 years ago

Describe the problem

https://beta.monarchinitiative.org/disease/MONDO:0010742#variant

A clear and concise description of what the issue is.

The variant tab on this site is calling THAS a variant but it is the abbreviation for the disease.

kshefchek commented 4 years ago

We are attempting to model the linkage between THAS and Xq25-q26.1, in dipper we model OMIM:313850 as the disease (Mondo merged to Pentalogy of Cantrell), and type the NCBI mapping, https://www.ncbi.nlm.nih.gov/gene/7055, as a heritable phenotypic marker. SciGraph is categorizing the heritable phenotypic markers as variants, which does not seem correct, but this isn't really a genotype either. How should this be modelled and typed?

pnrobinson commented 4 years ago

Note that the Gene entry has Gene type: UNKNOWN, which is a clue that we should treat this differently from most other Gene entries

kshefchek commented 4 years ago

we do, we type it as a heritable phenotypic marker instead of a protein coding gene: http://www.sequenceontology.org/browser/current_svn/term/SO:0001500 or is there a better SO typing?

pnrobinson commented 4 years ago

We should filter out these "genes" from being considered as variants/genotypes

kshefchek commented 4 years ago

I'll fix this at the scigraph/neo4j level

kshefchek commented 4 years ago

this is fixed in our beta database, which will be pushed to production when our server issues are resolved, marking this as closed

https://beta.monarchinitiative.org/disease/MONDO:0010742