usecases.rst

Use Cases

Variants

• Allow one or more filters to be specified using logical operators
• Fetch all variants for males between 40 and 50 years old
• Find all variants by RSID

Phenotype

• Find all features associated with sensitivity of GIST
• Find all associations with sensitivity of GIST in gene KIT
• Find all associations with non-Hodgkin's lymphoma, with RNA sequencing evidence in gene CD20
• Find all associations with disease <http://purl.obolibrary.org/obo/DOID_4> in a given feature

Sample queries

• Query for individuals in cohorts using logical operators
• Fetch all biosamples for an individual X
• Fetch all biosamples for male individuals X
• Fetch ancestry and/or ethnicity for an individual X
• Find all biosamples for an individual with a specific phenotype or disease (eg annotation of polydactyly)
• Find all biosamples by tissue or cell line
• Find all individuals that have X and not Y (negative filtering of result sets)
• Find all individuals with X using method Y (eg AML diagnosis with CGH array data and RNA-Seq)

Lookup

• For a given name, what else is this feature known as (synonym lookup)

Metadata

• For a dataset, what use restrictions apply (DUO ontology <https://github.com/EBISPOT/DUO> )
• Filter above result sets based on creation/update time (exact or range)

Reads/Sequence

• Fetch associated reads/sequence for results set from above filters (second query or parameter to first query?)

Federated queries

• Allow user to request recursive lookups, which queries all servers it knows about to aggregate results (similar to DNS recursive queries)
• In returned results for recursive lookups, list the servers queries and success/failure of each
• Returns a list of peer/other servers that a server knows about, to assist with data discovery
• Return what servers would be queried for a recursive query

Data discovery

• What subset of the schema does query server provide, endpoints, object types returned
• Does server queried provide recursive lookups
• Return a list of servers recursive lookups are performed against (will this be by endpoint, as different servers may provide different subsets of defined endpoints?)