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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 understand how data is organized: Projects, Studies and Cohorts . For details on the query parameters, please refer to the Swagger documentation linked above.

Getting information about genomic variants

Getting variant data from a given study:

http://bioinfodev.hpc.cam.ac.uk/hgva-1.0/webservices/rest/v1/analysis/variant/query?studies={project}:{study}

An extensive list of filtering parameters allow great flexibility on the queries (check Swagger documentation link above). For example, get TTN variants from the Genome of the Netherlands study, which is framed within the reference_grch37 project. We will also limit the number of returned results to 3:

http://bioinfodev.hpc.cam.ac.uk/hgva-1.0/webservices/rest/v1/analysis/variant/query?gene=TTN&studies=hgvauser@reference_grch37:GONL&limit=3

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

Getting information about studies

Get all available studies and their metadata. Please note, of special interest will be here the field alias which contains the study identifier to be used as an input whenever a study must be passed as a parameter:

http://bioinfodev.hpc.cam.ac.uk/hgva-1.0/webservices/rest/v1/studies/search

For example, getting all metadata for all available studies:

http://bioinfodev.hpc.cam.ac.uk/hgva-1.0/webservices/rest/v1/studies/search

Getting summary data from a particular study:

http://bioinfodev.hpc.cam.ac.uk/hgva-1.0/webservices/rest/v1/studies/{project}:{study}/summary

For example, getting summary data for study 1kG_phase3 which is framed within project reference_grch37:

http://bioinfodev.hpc.cam.ac.uk/hgva-1.0/webservices/rest/v1/studies/reference_grch37%3A1kG_phase3/summary

Getting all available metadata for a particular study:

http://bioinfodev.hpc.cam.ac.uk/hgva-1.0/webservices/rest/v1/studies/{project}:{study}/info

For example, getting all metadata for study GONL  which is framed within the project reference_grch37:

http://bioinfodev.hpc.cam.ac.uk/hgva-1.0/webservices/rest/v1/studies/reference_grch37:GONL/info

Getting all samples metadata for a given study:

http://bioinfodev.hpc.cam.ac.uk/hgva-1.0/webservices/rest/v1/studies/{project}:{study}/samples

For example, getting all samples metadata for study 1kG_phase3 which is framed within project reference_grch37. Please, note that not all studies contain samples data, e.g. GONL, ExAC, among others, only provide variant lists and aggregated frequencies, i.e. no sample genotypes.

http://bioinfodev.hpc.cam.ac.uk/hgva-1.0/webservices/rest/v1/studies/reference_grch37:1kG_phase3/samples

Getting genomic variants from a given study. This is probably the most popular web service among HGVA users:

http://bioinfodev.hpc.cam.ac.uk/hgva-1.0/webservices/rest/v1/studies/{project}:{study}/variants

For example, getting missense_variants from the Chronic Myeloid Leukemia project of the Russian Academy of Medical Sciences, which is framed within the cancer_grch37 project. Lets also limit the number of results to 3 and exclude the study field from the results:

http://bioinfodev.hpc.cam.ac.uk/hgva-1.0/webservices/rest/v1/studies/cancer_grch37%3ARAMS_CML/variants?gene=BRCA2&annot-ct=missense_variant&exclude=studies&limit=3

Getting information about samples

Get all metadata for a particular sample:

http://bioinfodev.hpc.cam.ac.uk/hgva-1.0/webservices/rest/v1/samples/{sample}/info?study={project}:{study}

For example, get all metadata for sample HG00096 of the 1kG_phase3 study which is framed within the reference_grch37 project:

http://bioinfodev.hpc.cam.ac.uk/hgva-1.0/webservices/rest/v1/samples/HG00096/info?study=reference_grch37:1kG_phase3

Getting information about cohorts

Getting all samples metadata in a given cohort:

http://bioinfodev.hpc.cam.ac.uk/hgva-1.0/webservices/rest/v1/cohorts/{cohort}/samples?study={project}:{study}

For example, get all samples metadata for cohort GBR from study 1kG_phase3 which is framed within project reference_grch37:

http://bioinfodev.hpc.cam.ac.uk/hgva-1.0/webservices/rest/v1/cohorts/GBR/samples?study=reference_grch37:1kG_phase3

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