GA4GH Discovery Work Stream¶
The GA4GH Discovery Work Stream builds and coordinates standards for federated, secured networks of data and services, to form an “Internet of Genomics” for enabling data discovery and retrieval in health research and clinical genomics.
The Discovery Work Stream is lead by Marc Fiume and Michael Baudis. For details on how this Work Stream operates please read the Discovery Work Stream Organizational Structure & Vision document.
This group meets at a high-level monthly. In addition, the sub-groups listed below meet on their own schedules. Participation in these groups is open but requires adherence to the GA4GH Standards for Professional Conduct.
Transitional Status of Website & Work Stream Structure
Following the 2023 April GA4GH Connect meeting we're currently in a phase of workstream "refactoring", incuding this site.
Please be patient and check back frequently!
Products¶
Product development in GA4GH follows a process outlined in a GA4GH Product Approval Process Guide, in draft. Products developed by the work stream undergo an initial investigation phase, followed by a formal Proposed Product Phase, in which most of the work is done, followed by an formal Approval Phase during which the products gain GA4GH Approval. The formal steps require the approval of the Work Stream leads.
The following products are currently under development for this Work Stream.
Beacon API¶
The Beacon protocol defines the protocol details for implementing programming interfaces ("API") on genomic data resources, to enable the federated discovery and potential retrieval of genomic variations and associated biomedical information. The current version 2 ("v2") of the Beacon protocol is a GA4GH approved standard. It is being developed through the ELIXIR Beacon project and accessible there or directly trough its repository. Extensive documentation of the protocol and its implementation options is available at docs.genomebeacons.org.
Contact¶
- Responsible Discovery co-chair: Michael Baudis
- Product leads:
- Jordi Rambla
- Anthony Brookes
- Michael Baudis
Data Connect¶
Data Connect is a standard for biomedical data retrieval and analysis with support for federation across organizational boundaries.
Contact¶
- Product leads
- Miro Cupak
- Aaron Kemp
Networks¶
Networks group works on a collection of standards enabling discovery of services. This currently includes 2 GA4GH approved standards:
- Service Registry - API specification for services providing information about other GA4GH services, primarily for the purpose of organizing services into networks or groups and service discovery across organizational boundaries.
- Service Info - API specification for services to advertise information about themselves.
Contact¶
- Product leads
DaMaSC - Data Models and Schema Consensus Group¶
Contact¶
- Product lead:
- Kathy Reinold
{S}[B] SchemaBlocks¶
SchemaBlocks represents a cross work stream, cross driver project initiative to document object standards and prototypes with potenial use throughout the GA4GH ecosystem. This project does not attempt to develop a rigid, complete schema but rather to provide the object vocabulary and semantics for a large range of developments.
More information about the SchemaBlocks project as well as the current schema can be found on the project's site at schemablocks.org.
Before 2023 the {S}[B] site did also contain documentation about common GA4GH standards and practices related to genomics. This part has now been moved to the ga4gh-community-standards site.
Contact¶
- Responsible Discovery co-chair: Michael Baudis
- Product leads:
- Melanie Courtot
- Michael Baudis
News and Announcements¶
Discovery Co-Lead Appointed
GA4GH Discovery Work Stream welcomes new Co-Lead Nara Sobreira of Johns Hopkins Medicine
Nara Lygia De Macena Sobreira, associate professor of genetic medicine at Johns Hopkins University School of Medicine, joins the GA4GH Standards Steering Committee as Discovery Work Stream Co-Lead.
Continue readingDiscovery Co-Lead Nominations
Opening for a new work stream co-lead
With the announcement of Marc Fiume's retreat from his Discovery leadership role there is now an opportunity for a person with experience in "-omics" data in biomedical settings as well as a strong interest to shape the future of GA4GH and genommic data exchange in general to step up to the challenge of a workstream leadership position!
Continue readingBeacon v2 standard highlighted during the GA4GH April Connect 2023
Last month Beacon was present at the GA4GH Connect 2023, the working meeting to advance the GA4GH Roadmap and gather feedback on product development and needs.
Beacon v2 at the International Congress of Human Genetics
Hands-on sessions on genomic data discovery
These Hands-on workshops will take place on February the 26th and 27th, in the framework of the International Congress of Human Genetics (ICHG), that is being held in Cape Town from February 22 – 26.
Continue readingBeacon training course: How to make COVID-19 sensitive data discoverable using Beacons
The online workshop BEACON - How to make sensitive data discoverable will take place on November 2 and 3. The European Genome-phenome Archive (EGA) Beacon Team will provide a special hands-on training session for the BY-COVID partners for "Beaconising" the datasets.
Progenetix & BeaconPlus - An open cancer genomics resource on a stack of Beacon code...
ELIXIR All Hands Amsterdam 2022
Michael Baudis¶
Here Michael provides some overview of the multi-year trajectory of the Beacon API development, and how BeaconPlus & Progenetix have been utilized for "implementation driven design".
Continue readingBeacon implementations: Beaconize your genomics data
Beacon v2 Workshop at ELIXIR All Hands
Hosts: Lauren Fromont, Michael Baudis & Jordi Rambla¶
Amsterdam, 7th June 2022 Link to webpage¶
One of the main bottlenecks in human genomics research is the lack of tools for federated discovery of identifiable genomics data that requires tight privacy controls. This problem needs even more attention since genomics data sees an ever greater application in clinical settings, such as for medical diagnostic or prognostic purposes, in rare diseases or cancer. Continue reading
Beacon v2 submitted to GA4GH
Beacon v2 was submitted to the Global Alliance for Genomics and Health and is now available for public review! Our specification is available on Github and several implementations are already available!
The GA4GH Beacon Protocol at BC2
Michael Baudis presenting Beacon in the session Federating computational analyses with GA4GH standards
BC2 Basel 2021¶
During the "Federating computational analyses with GA4GH standards" workshop at
BC2 2021 Michael presented history and the current status of the Beacon
project, as well as its integration with specific data resources and analysis initiatives.
Progenetix, Beacon and GA4GH at RDA
ELIXIR Beacon Project - Concepts | Status | History | Outlook
Michael Baudis¶
Research Data Alliance - RDA Virtual Plenary 17¶
This seminar gives an overview of current state of the Progenetix Beacon project and the overall connection to the Global Alliance for Genomics and Health (GA4GH).
Continue readingELIXIR Beacon Project - Networking Resources Across and Beyond ELIXIR Human Data Communities
ELIXIR Open Day 2020 - Wellcome Trust Genome Campus Hinxton
Michael Baudis¶
In this presentation I introduce the Beacon project and provide my opinions about its future trajectory, and especially its role in driving the alignment of ELIXIR and GA4GH projects in related to (human) genome data sharing.
Links¶
Continue readingDNAstack Launches Clinical Evidence Beacons
DNAstack Launches Clinical Evidence Beacons to Drive Crowdsourcing for Genetic Disease Discovery
TORONTO, Ont. (Oct. 15, 2019) — DNAstack today announced the launch of "Clinical Evidence Beacons" on the Beacon Network, a real-time search engine for finding genetic mutations across a global network of genomic datasets. These additions will enable medical laboratories to crowdsource the interpretation of variants through a secure social network.
Continue readingFederated discovery and sharing of genomic data using Beacons
Beacon publication at Nature Biotechnology
Marc Fiume, Miroslav Cupak, Stephen Keenan, Jordi Rambla, Sabela de la Torre, Stephanie O. M. Dyke, Anthony J. Brookes, Knox Carey, David Lloyd, Peter Goodhand, Maximilian Haeussler, Michael Baudis, Heinz Stockinger, Lena Dolman, Ilkka Lappalainen, Juha Törnroos, Mikael Linden, J. Dylan Spalding, Saif Ur-Rehman, Angela Page, Paul Flicek, Stephen Sherry, David Haussler, Susheel Varma, Gary Saunders and Serena Scollen¶
Today, Nature Biotechnology published the Beacon manuscript "Federated discovery and sharing of genomic data using Beacons". This was accompanied by a GA4GH press release. Enjoy!
Continue readingPress Release: GA4GH and ELIXIR Release Beacon API v1...
GA4GH and ELIXIR Release Beacon API v1 with increased security measures
ELIXIR and the Global Alliance for Genomics and Health (GA4GH) have announced the release of the first genomic data interoperability standard from the GA4GH 2018 Strategic Roadmap.
Continue readingGA4GH Beacon v1.0
Release of the first official GA4GH Beacon product
The official Beacon API v1.0.0 has been approved through the GA4GH Product Approval Process.
Continue readingGlobal network of Beacons - Beacon v0.4
Global network of Beacons lighting up the world of genomic data
The Beacon Project has released new Beacon API v0.4 specifications to provide greater search functions and richer search results.
These API specifications are available through the new Beacon website which will provide up-to-date support and regular updates on the project developments. v0.4 of Beacon has been developed with support from ELIXIR and constitutes the basis for the upcoming GA4GH approval process towards a "v1".
Continue reading