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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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need to model variants as phenotypic markers #128

Open nlwashington opened 9 years ago

nlwashington commented 9 years ago

when generating model organisms for study, we often cross a line with another that harbors a marker for some kind of phenotype. for example, him-5 in C. elegans throws a higher percentage of males; many transgenics simply express GFP or other visual markers, flies often have eye color markers, etc

i would like a way of classifying these variants as special kinds of variations. @mbrush, what kind of class would they be mapped as instances of?

mellybelly commented 9 years ago

In zfin, the marker genes are classified as "engineered foreign genes" For example, http://zfin.org/action/marker/view/ZDB-EFG-070117-1 @mbrush has also done a lot of work on reporters in REO ontology in order to classify gene products.

nlwashington commented 9 years ago

only works, though, for foreign genes like GFP. but a human gene inserted into a fish would also be foreign. and in worms and flies, eye color or "roller" phenotypes are used as co-segregation markers. so we need something else.