Step 1

Select which group(s) you would like to join based on the information in this document.

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Step 2

Email your group selection(s) to secretariat@ga4gh.org.

Terms/Concepts

Description

Work Streams (WS)

GA4GH WSs develop standards and tools that are designed to overcome technical and regulatory hurdles to international genomic data-sharing. Most WS meetings focus on high-level discussions, while in-depth standards development work is conducted within smaller subgroups.

Driver Project (DP)

GA4GH DPs are real-world genomic data initiatives that help guide development efforts and pilot tools. These global stakeholders advocate, mandate, implement, and use GA4GH frameworks and standards in their local contexts.

Work Stream Members

Any individual who signs up to a GA4GH WS Google Group. WS members are encouraged, but not required, to join in on GA4GH discussions both asynchronously via email or slack as well as during virtual face-to-face meetings.

Work Stream Contributors

Any WS member who has also made a meaningful contribution to a GA4GH standard, policy framework, or other deliverable. All GA4GH contributors are expected to provide meaningful, documentable input on at least one GA4GH standard, policy framework, publication, or another deliverable.

Work Stream Managers

Each WS has one manager. This individual is an employed member of the GA4GH secretariat. They assist with WS-related coordination and project management while ensuring that the activities of the WS align with the goals of GA4GH.

Work Stream Leads

Each WS has one to two leads. Leads are contributors within the community and are responsible for achieving the high-level goals and vision of their respective WS.

Work Stream Meeting (All members)

At the main Clin/Pheno Work Stream meeting, you will be updated about the work being conducted in the subgroups listed below. You may also have the opportunity to discuss various community building topics including but not limited to, implementations, roadmapping, and event planning. The full WS meeting also poses an opportunity for discussion of new subgroups/working groups that are needed.

Meeting Schedule: Once every two months on Wednesdays at 20:00 UTC

Pedigree Subgroup

The group aims to standardize the way systems represent family health history and pedigree information. This will allow patients and care providers to share this information more easily between healthcare systems and help software tools to use this information to improve genome analysis and diagnosis.

Meeting Schedule: Biweekly on Thursdays at 20:00 UTC

Phenopackets Subgroup

The group focuses on the development of the Phenopacket standard. The Phenopacket Schema represents an open standard for sharing disease and phenotype information to improve our ability to understand, diagnose, and treat both rare and common diseases. A Phenopacket links detailed phenotype descriptions with disease, patient, and genetic information, enabling clinicians, biologists, and disease and drug researchers to build more complete models of disease.

No longer meeting for now as the v2 standard has been approved. Any topics/presentation related to Phenopackets will be discussed in the Full WS meetings.

Computable Cohort Representation Subgroup

This subgroup aims to create a computable cohort representation standard to computationally describe a cohort and execute the cohort definition as a query across a Cohort Beacon network. This group has not yet formally proposed a deliverable, and it is still exploring potential outputs.

Meeting Schedule: N/A. Ad hoc as the group explores topics.

Work Stream Meeting (All members)

At the main Discovery Work Stream meeting, you will be updated about the work being conducted in the subgroups listed below. The full WS meeting also poses an opportunity for discussion of new subgroups/working groups that are needed. Key strategic goals are discussed between group leads at this meeting.

Meeting Schedule: Monthly on the second Wednesday at 15:30 UTC

Data Connect/Networks Subgroup

This subgroup focuses on the ongoing development and potential new implementations of the Data Connect API which was approved by the GA4GH Steering Committee in April of 2021. The Data Connect API is a standard for the discovery and search of biomedical data. It provides a mechanism for 1) describing data and its data models and 2) searching the data with the given data model.

Meeting Schedule: Biweekly on Wednesdays at 16:00 UTC

Beacon API Subgroup

This meeting focuses on the development of the Beacon API. This API (sometimes extended with a user interface) allows for data discovery of genomic and phenoclinic data.

Meeting Schedule: Monthly on the second Wednesday at 15:00 UTC

Work Stream Meeting (All members)

At the main Data Security Work Stream meeting, you will be updated about the work being conducted in the subgroups listed below. The full WS meeting also poses an opportunity for discussion of new subgroups/working groups that are needed.

Meeting Schedule: Ad hoc

Passports/ Authorization and Authentication Infrastructure (AAI) Subgroup

The Passports/AAI Technical Working subgroup is a collaboration between the Data Security and DURI Work Streams. This group was formed with the aim of creating a small technical task force to discuss outstanding technical issues regarding v1.0 and migrating to a new version of the GA4GH Passports Standard named v1.2. AAI in security and DURI Passports are closely linked and therefore bring together those working in both areas.

Meeting Schedule: Weekly on Thursdays at 13:00 UTC.

Work Stream Meeting (Leadership only)

At the main LSG Work Stream meeting, leadership will meet to discuss the work being conducted in the subgroups listed below. The full WS meeting also poses an opportunity for discussion of new subgroups/working groups that are needed.

Once every 6 months

Future of VCF Subgroup

This project focuses on improvements to the VCF format as well as looking into potential future formats to handle the increasing scale of large sequencing projects more efficiently.

Meeting Schedule: Every 4 weeks on Tuesday alternating between 14:00 UTC and 21:00 UTC

Htsget API Subgroup

htsget is a protocol for secure, efficient and reliable access to sequencing read and variation data. This project describes ongoing improvements to the protocol and implementations to support ‘two-dimensional’ slicing of very large variant (VCF) datasets.

Meeting Schedule: Every 4 weeks alternating between Tuesday at 22:00 UTC and Wednesday at 17:00 UTC respectively

RNASeq Subgroup

This subgroup focuses on the development of the RNAget API. This API describes a common set of endpoints for search and retrieval of processed RNA data. This currently includes feature level expression data from RNA-Seq type assays and signal data over a range of bases from ChIP-seq, methylation or similar epigenetic experiments.

Meeting Schedule: Monthly on 3rd Wednesdays at 16:00 UTC

Refget API Subgroup

This subgroup focuses on the development of the refget API. The refget API enables access to reference genomic sequences without ambiguity from different databases and servers using a checksum identifier based on the sequence content itself. Currently, refget API focuses on single reference sequences uniquely identified by their checksums.

Meeting Schedule: Biweekly on Wednesdays at 15:00 UTC

File Formats Subgroup

This subgroup focuses on the SAM/BAM/CRAM file formats. It describes ongoing additions to SAM/BAM to improve efficiency and support new sequencing platforms. For CRAM the primary focus is on improved efficiency, random access for long reads and CRAM file sizes for short read data (with an expectation of 50–70% smaller than the corresponding BAM file).  Additionally improved indexing, and especially index documentation.

Meeting Schedule: Every 4 weeks on Tuesdays alternating between 16:00 UTC and 21:00 UTC

Encrypted file format Subgroup

This subgroup focuses on the methods that a file format can be used to store data in an encrypted and fully authenticated state,

Meeting Schedule: Every 4 weeks on Tuesdays at 15:00 UTC

VCF/VRS Alignment Subgroup

This meeting is to create alignment between the Variant Representation Schema and the Future of VCF teams from the GKS and LSG Work Streams respectively.

Meeting Schedule: Monthly on Wednesday at 20:000 UTC

Sequence Annotation Subgroup

The Sequence Annotation subgroup is developing a common model describing annotated genomic features such as transcripts and genes for use by others within GA4GH and in the general community.

Meeting Schedule: First Thursday of every month at 15:00 UTC

Variation Representation (VR) Subgroup

This subgroup discussed the VR specification - an extensible model for computational variation representation. The specification includes a data model, message schema, and methods for normalization of variants and computing identifiers.

Meeting Schedule: 

Meetings 3x a month:

2nd Monday, 11 am ET

3rd Monday, 5 pm ET

4th Monday, 11 am ET

Variant Annotation Subgroup

The VA Specification (VA Spec) will define extensible data models to support representation of diverse kinds of statements made about genetic variation, and the evidence and provenance supporting these statements. The specification will include information models, message exchange schema, and a formal framework for defining custom extensions to the core model. A more detailed description of these components can be found here.

Meeting Schedule: Every Wednesday at 16:00 UTC

Work Stream Meeting (All members)

At the main DURI Work Stream meeting, you will be updated about the work being conducted in the subgroups listed below. The full WS meeting also poses an opportunity for discussion of new subgroups/working groups that are needed. We also discuss new strategic aims for DURI including Roadmaps and seek feedback from any implementers or those with use cases that could inform DURI work and standard development.

Meeting Schedule: Every 6 weeks on Wednesdays at 13:00 UTC

Data Use Ontology (DUO) Subgroup

This subgroup focuses on the (DUO) standard. DUO allows semantic tagging of datasets with restrictions and permissions about their usage, making them automatically discoverable based on the users’ authorization level of users, or their intended data uses. This team focuses on developing a data use ontology to help determine if a researcher may be granted access to a particular data set.

Meeting Schedule: Meetings temporarily paused until the new phase of DUO activities begin again.

Passports Subgroup

GA4GH Passport specification aims to support data access policies and procedures within current and evolving data access governance systems. This specification defines Passports and Passport Visas as a standardized method of communicating the data access authorizations that a user has based on either their role (e.g. researcher), affiliation, or access status.

Meeting Schedule: On hold until Passports/AAI technical team work on v1.2 is completed.

Work Stream Meeting (All members)

Meeting Description: At the main Cloud Work Stream meeting, you will be updated about the work being conducted in the subgroups listed below. The full WS meeting also poses an opportunity for discussion of new subgroups/working groups that are needed.

Meeting Schedule: On the second and fourth Mondays of the month alternating between 18:00 UTC and 22:00 UTC respectively.

Workflow Execution Service (WES) Subgroup

The WES API describes a standard programmatic way to run and manage workflows. Having this standard API supported by multiple execution engines will let people run the same workflow using various execution platforms running on various clouds/environments.

Part of full Cloud WS meeting

Task Execution Schema (TES) Subgroup

The TES is a simple standardized interface for requesting long running asynchronous compute jobs.

Part of full Cloud WS meeting

Data Repository Service (DRS) Subgroup

The DRS provides a mechanism to read (and in the future, write) data objects across object stores in a cloud-agnostic way.

Part of full Cloud WS meeting

Tool Registry Service (TRS) Subgroup

The TRS API is one of a series of technical standards from the Cloud Work Stream that together allow genomics researchers to bring algorithms to datasets in disparate cloud environments, rather than moving data around.

Part of full Cloud WS meeting

Work Stream Meeting (All members)

At the main REWS General meeting, you will be updated about the work being conducted in the subgroups listed below. Occasionally, members will participate in a voting process to approve policies and frameworks. The full WS meeting also poses an opportunity for discussion of new subgroups/working groups that are needed.

Meeting Schedule: Once every 1-2 months

Data Access Committee Review Standards (DACReS) Subgroup

The DACReS work group leverages their expertise in bioethics, data privacy law, data science, and genomics to empirically investigate challenges and opportunities within Data Access Committees (via surveys and interviews) to develop an online, evidence-based Toolkit (“DACReS Toolkit”). We will build this resource through an international, consensus process with DACReS members during meetings and stakeholder workshops.

Meeting Schedule: Ad hoc

Genetic Discrimination (GD) Subgroup

The GD group within REWS is a collaborative effort supporting the work of the Genetic Discrimination Observatory (GDO). The subgroup aims to create specific tools that can be used by the community to combat genetic discrimination and provides contributions to the ongoing work at the GDO.

Meeting Schedule: Ad hoc, roughly once every 1-2 months

Ethical Provenance Toolkit Subgroup

The Ethical Provenance Toolkit aims to provide harmonized tools across research institutions and enable the clear oversight of biomedical data, throughout its lifecycle. The subgroup working meetings will discuss the progress of developing ethical provenance resources and identify where further efforts are needed.

Meeting Schedule: Ad hoc

Diversity in Datasets Subgroup

The Diversity in Datasets Subgroup aims to provide guidance on how to best promote diverse datasets in associated research, and also promote an international lens on meaningful diversity in datasets, a topic which is often limited to national discussion.

Meeting Schedule: Ad hoc, roughly once a month

Public Attitudes for Genomic Policy Subgroup

The Public Attitudes for Genomic Policy blog series aims to translate findings from the Your DNA Your Say Initiative, and other public attitudes studies, into useful outputs for stakeholders such as policymakers and other researchers.

Meeting Schedule: Ad hoc, roughly once every 1-2 months

Clinical Data Sharing and Consent Subgroup

The Clinical Data Sharing and Consent Subgroup is working to clarify the best practices for what level of detail of patient information, and for what purpose, can be shared without explicit consent from patients to inform variant classification for clinical purposes.

Meeting Schedule: Ad hoc, roughly once every 1-2 months

Consent Task Force

This group focuses on the collection, analysis, typology and harmonization of consent clauses from the different jurisdictions of the international genomic community. The goal is to provide sampled language to researchers and clinicians for clinical genetic testing, biobanking and population studies, genomic research, familial genomics and pediatrics.

Meeting Schedule: N/A. The consent toolkit has been completed.

General Data Protection Regulation (GDPR) Forum

The forum on the GDPR (EU) 2016/679 was launched in August 2018 as part of the REWS. The purpose of the forum is to discuss and disseminate information regarding European data protection law – specifically the GDPR – and its impact on international genomic and health-related data sharing. Monthly one-page GDPR briefs provide concise and timely guidance on specific topics relevant to health researchers, institutions, ethics bodies, and data sharing initiatives internationally.

Meeting Schedule: N/A. Almost all work happens asynchronously.

Technical Alignment Sub-Committee

The mission of TASC is to aid the harmonisation of aspects of GA4GH's products to ensure that they can be used together effectively. TASC provides mechanisms and recommendations to create internal consistency and technical alignment across GA4GH Work Streams and deliverables. While TASC functions as a central decision-making body, all of its decisions are informed by relevant stakeholders. The work of TASC, including all documentation and decisions, are regularly and openly communicated back to the GA4GH community.

TASC meeting attendance is by invitation only; however, anyone from the GA4GH community can propose an issue through the TASC GitHub repository. If you propose an issue, you can expect to be contacted by one or more members of TASC should your issue be accepted into the team’s workflow. As a key stakeholder, you may also be contacted for consultation activities.

Meeting Schedule: By invitation only

Equity, Diversity and Inclusion Advisory Group

This group supports GA4GH by finding equitable and inclusive ways to bring diverse ideas into the standards creation process. Pathways to EDI that the group explores include:

• Identifying opportunities to attract diverse talent to the GA4GH community;
• Helping new and existing contributors from all backgrounds feel welcomed and valued by the community; and
• Ensuring equitable access to leadership and speaking opportunities within GA4GH

Meeting Schedule: Quarterly

Quality Control

WGS Quality Control Standards describes a set of key quality control metrics and their detailed definitions that can be used as the basis for standardised guidelines for reporting quality control metrics for whole genome sequencing (WGS). Creating a common framework for QC of WGS results is needed to ensure that data generation adheres to published guidelines, and in turn, establishes confidence in the data quality and facilitates the exchange of results across initiatives

Meeting Schedule:

Monthly on fourth Tuesday at 12 PM GMT / 7 pm Singapore time

Experiments Metadata

Metadata on (epi)genomic experiments is crucial to understanding output data. Many initiatives have their own standards to describe experiments for the data that they are sharing; however, the level of detail, methods of organization and use of controlled vocabularies differ between these groups. Thus, there is a need to standardize a set of minimal metadata properties in order to increase shareability of (epi)genomic datasets. This is the problem statement that the experiments metadata study group aims to address.

Meeting Schedule: First Monday of every month

Ethical Preparedness for Pandemics and Epidemics

A collaboration between GA4GH and PHa4GE, this study group aims to address the ethical issues associated with data sharing during pandemics and epidemics. Topics of discussion include benefit sharing and risk analysis as it relates to infectious disease. The hope is to develop a policy or framework that will address challenges in this space.

Meeting Schedule: Ad hoc

Structural Variation Special Interest Group

The GKS Work Stream is convening clinicians, bioinformaticians, electronic health record vendors, researchers, testing laboratory representatives, genomic-knowledge-base maintainers, and anyone else involved in the reporting and exchange of patient genomic data in a Special Interest Group focused on structural variation. The group will undertake a time-limited effort to standardise structural variation modelling and development. It will cover fusions, rearrangements, and other classes as selected by group members.

The Special Interest Group will aim to develop a VRS model and schema for representing structural variations discretely and computably. To accomplish this, they will identify and review structural variation concepts from disparate use cases. The Special Interest Group will use this landscape analysis to define the scope and models for concepts supporting structural variations — including breakpoint coordinates, exon/intron identification, transcript junctions, segment phasing, impacted genes, and (de)composition of complex variants.

Meeting Schedule:  First Thursday of every month at 7 am EDT/ 4 am PDT / 12 pm BST/ 1 pm CET / 6 am CDT / 1 pm SAST / 7 pm CST /9 pm AEST

Federated Variant Matching

This GIF Project will focus on addressing barriers to gaining access to genotype and phenotype information, by hardening an API plan that can support multiple use cases in variant matching that range from data that is open to data that is only accessible with permissions. Also, some data may have query limitations (number of variant queries per day), others may be unlimited. Some sites may support narrow queries (exact variant match), others may wish to support broader queries by variant type or gene region. We also plan to determine if the platform would benefit from a centralized user interface to reduce node-to-node connections.

Meeting Schedule: On the third Wednesday of every month from 12pm EST to 1pm EST. To join contact ksocarra@broadinsitute.org

GDI Starter Kit

This GIF Project aims to implement an evolved version of this B1MG proof of concept, named the "GDI Starter Kit". The GDI team plans to leverage GIF to demonstrate that the starter kit can be successfully deployed in at least 5 other nodes. The project will demonstrate how a set of applications and components can be linked via GA4GH standards. Future projects will aim to address disease-specific use cases in cancer and rare disease.

Meeting Schedule:

eLwazi Federated Imputation

This GIF Project aims to enable meta imputation against more than one server by either providing a minimal user interface or an endpoint that Nextflow scripts can call. They hope to contribute to the imputation ecosystem by reducing barriers to end-user engagement. While the team further refines their project goals, they recognize that the outcome should be compatible with future developments such as homomorphic encryption and new imputation algorithms.

Meeting Schedule:

Cancer Community

The GA4GH Cancer Community promotes global cooperation, data sharing, collaborative cancer research, and better oncology care through implementation of GA4GH products.

Meeting Schedule: Every month on the second Monday

Infectious Disease Community

Bridging pathogen and host genomics, the GA4GH Infectious Disease Community brings together international groups that advance human genomics to better diagnose and treat infectious disease.

Meeting Schedule: Quarterly

Rare Disease Community

Researchers, clinicians, and technical experts meet in the GA4GH Rare Disease Community to discuss rare disease challenges that GA4GH products could help alleviate.

Meeting Schedule: Ad hoc