HGVA is powered by the Open Computational Genomic Analysis (OpenCGA) project. OpenCGA implements an exensive API that enables numerous operations over metadata, samples and genomic data. The whole API specification can be accessed at:
http://bioinfodev.hpc.cam.ac.uk/hgva-1.0/webservices
We will here focus on those end points of the API which are of more interest for HGVA users, giving examples of their use and pin pointing certain peculiarities of the parameters for HGVA. Data is hierarchically organised in Projects and Studies. Please, have a look at Data: sources and HGVA organization in order to fully understand the behaviour of the web services.
Getting information about projects
Getting all metadata from a particular project:
http://bioinfodev.hpc.cam.ac.uk/hgva-1.0/webservices/rest/v1/projects/{projects}/info
For example, getting all metadata for the reference_grch37 project:
http://bioinfodev.hpc.cam.ac.uk/hgva-1.0/webservices/rest/v1/projects/reference_grch37/info
Getting all metadata from all studies associated to a particular project:
http://bioinfodev.hpc.cam.ac.uk/hgva-1.0/webservices/rest/v1/projects/{projects}/studies
For example, getting all studies and their metadata for the cancer_grch37 project:
http://bioinfodev.hpc.cam.ac.uk/hgva-1.0/webservices/rest/v1/projects/cancer_grch37/studies
Studies
http://bioinfodev.hpc.cam.ac.uk/hgva-1.0/webservices/rest/v1/studies/search
http://bioinfodev.hpc.cam.ac.uk/hgva-1.0/webservices/rest/v1/studies/reference_grch37%3A1kG_phase3/summary
http://bioinfodev.hpc.cam.ac.uk/hgva-1.0/webservices/rest/v1/studies/reference_grch37%3A1kG_phase3/info?sid=wHO5F2FMmm5xFs0cg89Q
http://bioinfodev.hpc.cam.ac.uk/hgva-1.0/webservices/rest/v1/studies/reference_grch37%3A1kG_phase3/samples?sid=wHO5F2FMmm5xFs0cg89Q
http://bioinfodev.hpc.cam.ac.uk/hgva-1.0/webservices/rest/v1/studies/reference_grch37%3A1kG_phase3/variants?sid=wHO5F2FMmm5xFs0cg89Q&histogram=false&interval=2000&merge=false&limit=3
Samples
http://bioinfodev.hpc.cam.ac.uk/hgva-1.0/webservices/rest/v1/samples/search?sid=wHO5F2FMmm5xFs0cg89Q&study=reference_grch37%3A1kG_phase3&limit=3&lazy=true
http://bioinfodev.hpc.cam.ac.uk/hgva-1.0/webservices/rest/v1/samples/HG00096/info?sid=wHO5F2FMmm5xFs0cg89Q&study=reference_grch37%3A1kG_phase3&lazy=true