search

Ensembl / schemas

Work on data models and APIs for Genomic data.
http://ga4gh.org/#/api
Apache License 2.0
1 stars 0 forks source link

Use cases feedback - find biosamples by phenotype/disease #2

Open mcourtot opened 7 years ago

mcourtot commented 7 years ago

I would rephrase "Find all biosamples for an individual with an annotation of polydactyly (phenotype)" to "Find all biosamples for an individual with a specific phenotype or disease" to be a little bit broader. We should also keep in mind that usually disease are only at the individual level, while phenotypes can be both individual and sample.

mcourtot commented 7 years ago

Maybe also consider positive/negative queries, e.g. all individuals that have X and NOT Y

kozbo commented 7 years ago

Logical operations move us in the direction of implementing an SQL query, which we will never do as a direct SQL portal. Is there a level of implementation that provides enough functionality without taking on all the complexity of a full featured logical query language?

mcourtot commented 7 years ago

Phenopackets support negation - so if we were able to export from GA4GH to PXF we should be able to support that type of query. Other option is to have the negation as part of the characteristics objects following a similar model, i.e. prefixing ontologTerm(s) by "not" in the array.

lairdm commented 7 years ago

I agree with Melanie, negation doesn't necessarily mean exposing the underlying implementation. I can see allowing negative server side filtering on result sets.