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monarch-initiative / monarch-legacy

Monarch web application and API
BSD 3-Clause "New" or "Revised" License
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faq for how to interpret data on our site #560

Open nlwashington opened 10 years ago

nlwashington commented 10 years ago

We need some documentation about how to interpret data on our site. This easily lends itself to a FAQ. I think the FAQ should be broken up into several parts based on the primary data that can be explored.

Some questions: What kind of data is available in Monarch? How do I interpret the phenogrid? Can I search for diseases using a custom list of phenotypes? Can I put the phenogrid into my own website?

What do the different values mean for frequency of human phenotypes? Why do I sometimes see the same disease listed in a table with slightly different names?

Why can't I search for my favorite gene? Sometimes my search term is both a "disease" and a "phenotype". Why? What's the difference?

*I don't understand the nomenclature for the genotypes of this other species. Can you explain it to me?

What are ontologies, and why should I care? What ontologies and vocabularies are used?

*What is the "sufficiency score"?

nlwashington commented 10 years ago

related to #556

pnrobinson commented 10 years ago

This is a good idea. Maybe we should start a google doc? I could contribute to the disease vs phenotype FAQ -Peter

mellybelly commented 10 years ago

That would be great Peter. Will send something around, maybe it can even go into the next release.

nlwashington commented 10 years ago

we should definitely add a link to description for clinical significance, and perhaps even a hover to some of this information when presenting on variant tab.
http://www.ncbi.nlm.nih.gov/clinvar/docs/clinsig/#standard

we might also consider creating a standardized vocabulary (SO?) that holds these kinds of terms, and apply them to the other organisms too.