D9.3 Report on implementation of value-added user applications and cohort integration

A range of RESTful APIs have been developed by the EGA in order to allow powerful users, consortia and research institutions to programmatically interconnect with our system. Whilst the majority of the users perform discrete and limited queries/submissions to the system, the majority of the queries/submissions are performed by a limited and advanced set of users. Taking these handful of teams as reference, we are herein describing the different approaches EGA APIs can be used for a better, faster and complete experience.

As described in the previous deliverable (9.2), the following programmatic endpoints are available and documented for all EGA users: submission API, public metadata API and private metadata API. The main difference between the later two is the requirement of authentication for complete discovery of user-related metadata. 

EGA Submission API can be either directly used (https://ega-archive.org/submission/programmatic_submissions/submitting-metadata ) or by using a tool or interface mounted in the top of it. EGA developed its own interface (Submitter Portal - https://ega-archive.org/submission/tools/submitter-portal ) but it is great to see how other important partners are directly leveraging the API for their own solutions. We are focussing our attention on the ICGCsub, software provided by the ICGC consortia for all their projects worldwide for an harmonised and smooth submission to the EGA: https://github.com/icgc-dcc/egasub Metadata can also be retrieved programmatically and in a custom manner from the EGA: https://ega-archive.org/metadata/how-to-use-the-api . This flexible possibility of obtaining and filtering the results allows (1) the generation of reports by the user, who do not need to keep internal track of their submissions (and hence avoid duplications/mismatches), and (2) discovering crucial data information, a good filter before applying and downloading controlled access data. The first functionality can be either extended to the private metadata objects (i.e. in draft status) upon authentication (https://ega-archive.org/submission/programmatic_submissions/how-to-use-the-api ). Worldwide known research institutions with a consistent system of data/metadata submissions (Broad Institute, DKFZ) are consistently considering such feature as a main information gatherer for their submissions.