GA4GH Connect Virtual Meeting Report
This year, over 200 attendees worldwide participated in the virtual connect meeting to advance key deliverables and cross-Work Stream initiatives.
Gap Analysis Summary
Recording | Presentation | Gap Analysis Summary
Starting in 2019, Heidi Rehm and Andrew Morris conducted a Gap Analysis Survey to identify successes and gaps with GA4GH. In this opening session, Rehm and Morris shared key findings and themes from the Gap Analysis, and attendees voted on the top six areas that GA4GH should focus on addressing first. These are:
- Collaborate with healthcare, EHRs, and HL7
- Improve Interoperability and alignment between standards
- Create tooling and testbeds to support implementation
- Highlight end-to-end implementation demonstrations
- Harmonize terminologies, data models, definitions of maturity, and versioning across the organization
- Increase facilitation, training, and support for implementations
Assurance Levels
Agenda & Presentations | Recording
The Data Use & Researcher Identities (DURI) and Data Security Work Streams met to raise awareness about assurance levels and shared a state-of-the-art solution for strong ID proofing used in ELIXIR. The teams aim to use the information discussed to improve the Data Security Infrastructure Policy and to consider assurance levels across Data Security and DURI products.
Contact: Melissa Konopko
Beacon v2
Agenda & Presentations | Recording
The team presented the current status of Beacon v2 and explored how Beacon can work with other GA4GH standards developed by the Clin/Pheno, Genomic Knowledge Standards (GKS), and Data Use & Researcher Identities (DURI) Work Streams. The team also discussed ways to better align initiatives within the Discovery Work Stream.
Contact: Rishi Nag
Building Tooling
Agenda & Presentations | Recording
The session focused on streamlining the process of standards development to make it easier for work streams to publish their standards. These include: 1) an automated documentation builder to convert OpenAPI specifications to HTML, 2) cross work-stream, consolidated approaches to compliance testing and reporting, and 3) human-friendly introduction to standards.
Contact: Rishi Nag
DURI Connector
Agenda & Presentations | Recording
The Data Use & Researcher Identities Work Stream met to discuss connecting the Data Use Ontology (DUO) and GA4GH Passports standards in the data access request systems. The team collected user workflows to see how DUO and GA4GH Passports can fit into different processes to further streamline and automate data access processes.
Contact: Melissa Konopko
Federated Analysis Systems Project (FASP)
Agenda & Presentations | Recording
The Discovery, Cloud, Data Use & Researcher Identities (DURI), and Data Security Work Streams met to further work on FASP—a project demonstrating the utility of GA4GH APIs working together in an ecosystem. The team saw an updated "golden demo" using the DNAstack/Google software, and implementers shared feedback on building systems that support these APIs. The team will continue to collect feedback and expand the current "golden demo" to include more data sources and complexity.
Contact: Rishi Nag
FHIR Implementation Guide
Agenda & Presentations | Recording
During the session, teams from Children's Hospital of Philadelphia (CHOP) and Johns Hopkins University shared the outcomes of test implementations of the Phenopackets-FHIR guide and a JSON-LD method for validating & roundtripping phenopackets to FHIR, respectively. Next, the team aims to refine Phenopackets-FHIR mappings.
Contact: Lindsay Smith
Future of Variant Data Representation
Agenda & Presentations | Recording
The Varation Representation Specification (VRS) and VCF teams met to discuss similarities between their specifications, particularly around the construction and representation of CNVs and SVs. The teams will schedule regular touchpoints between the specifications on CNV/SV representation to harmonize where possible, and record similarities and dissimilarities in public-facing documentation.
Contact: Rishi Nag
htsget: Interactions with DRS & other projects
Agenda & Presentations | Recording
The session focused on extending features of htsget and discussing cross-Work Stream integration. These include: define service-info vocabulary for htsget endpoints, clarify Data Use & Researcher Identities (DURI)/Passport flows, extend interoperability testing to registered htsget servers, and explore opportunities for a FHIR Genomics htsget pilot.
Contact: Rishi Nag
Key Management
Agenda & Presentations | Recording
The Cloud, Large Scale Genomics (LSG), and Data Security Work Streams discussed the system architecture and rationale behind key management. The team arrived at two crucial points: 1) embed geographic distribution and national constraints in the system, and 2) make key management itself more manageable.
Contact: Melissa Konopko
Machine Readable Consents
Agenda & Presentations | Recording
The group discussed the Machine-Readable Consent Drafting Guidance, which aims to eliminate ambiguity between data sharing consent language in consent forms and machine-readable data use terms (DUO) to enable more efficient and ethical data sharing. The community is encouraged to read the Machine-Readable Consent Drafting Guidance and comment on clarity, value, and feasibility.
Contact: Adrian Thorogood
Pedigree
Agenda & Presentations | Recording
During the session, the team shared a pilot case for managing integration of patient-reported and clinician-curated health data, cross-collaborated with the VCF team, and arrived at a consensus on data modeling priorities for the Pedigree standard. The team will continue work on a Minimum Core Data Set, to result in a new FHIR profile, and will aim to have a draft Pedigree standard ready by 8th Plenary.
Contact: Lindsay Smith
Phenopackets: Treatment Course + VRS Integration
Agenda & Presentations | Recording
The Genomc Knowledge Standards (GKS) and Phenopackets team met to discuss implementation of the Variation Representation Specification (VRS) alongside the Variant building block in Phenopackets. The team also identified a potential new cross-Work Stream effort on Treatment Course, with plans to continue discussion post-Connect.
Contact: Lindsay Smith
Sequence Annotation
Agenda & Presentations | Recording
Large Scale Genomics (LSG) and Genomic Knowledge Standards (GKS) Work Streams discussed the current status of the Sequence Annotation standard. The group aims to harmonize existing approaches to feature-level annotation, and will work closely with the Variation Representation Specification (VRS) team to follow best data-modeling practices.
Contact: Rishi Nag
With the launch of the first GA4GH Strategic Roadmap in 2018, GA4GH is now undergoing a Gap Analysis project to identify successes and gaps within GA4GH and to update the Strategic Roadmap. During Virtual Connect, each work stream met to discuss their Gap Analysis feedback and continue finalizing their 2020 roadmaps.
Clininical & Phenotypic Data Capture Roadmap
Recording | Draft Clin/Pheno Roadmap
Clin/Pheno identified next steps for advancing the Phenopackets standard and will aim to have a draft of the Pedigree standard ready by 8th Plenary. The team also reiterated the importance of connecting with labs, healthcare systems, and patients.
Contact: Lindsay Smith
Cloud Roadmap
For the Virtual Connect meeting, the Cloud Work Stream did not host a roadmap session—but rather chose to invest time in cross-Work Stream initiatives such as the Federated Analysis Systems Project (FASP).
Contact: Rishi Nag
Data Security Roadmap
Recording | Draft Data Security Roadmap
Data Security reviewed Gap Analysis feedback and agreed with most of the findings. They will aim to provide better implementation support and create guides for performing security audits. The team also received good cross-Work Stream feedback, and aims to work with REWS on data sharing in the realm of rapidly evolving patient privacy standards and work with the Federated Analysis Systems Project (FASP) on security-by-design.
Contact: Melissa Konopko
Data Use & Researcher Identities (DURI) Roadmap
Recording | Draft DURI Roadmap
DURI aims to continue advancing its key deliverables: the Data Use Ontology (DUO), GA4GH Passports, and computable Consent Forms (in partnership with REWS). The team is also developing a plan to connect these standards together to optimize the data access request workflow.
Contact: Melissa Konopko
Discovery Roadmap
Recording | Draft Discovery Roadmap
Discovery discussed the advancement of roadmap deliverables, including Networks (Service Registry Standard and GA4GH Service Registry), Search Implementation, Schemablocks, and Beacon v2, as well as ways to integrate across Discovery products. The team is also focused on integration across Work Streams, and is involved in FASP (Federated Analysis Systems Project).
Contact: Rishi Nag
Genomic Knowledge Standards (GKS) Roadmap
From the gap analysis, GKS will address content and technical gaps in its standards, as well as increase cross-Work Stream and pan-SDO communications. GKS noted no significant issues for proposed Variation Representation Specification (VRS) and Variation Annotation roadmaps, and has support for current activities and direction.
Contact: Melissa Konopko
Large Scale Genomics (LSG) Roadmap
LSG focused on cross-Work Stream activities, including mapping data structures from the file formats group to GKS initiatives and exploring DURI-Cloud-LSG workflows. Moving forward, the team aims to conduct outreach to community tool developers for input and explore potential for clinical engagement.
Contact: Rishi Nag
Regulatory & Ethics (REWS) Roadmap
Recording | Draft REWS Roadmap
REWS has made progress on deliverables and has community support on key initiatives such as standard data licenses, machine readable consents, the Consent Task Force, the Your DNA, Your Say survey, patient engagement practices, and the GDPR and Data Sharing Forum. REWS also discussed developing a position statement on data sharing during the COVID-19 pandemic.
Contact: Adrian Thorogood
Report Backs
During the Report Backs, each session shared their key accomplishments from the meeting and next steps. You may refer to the following timestamps to locate each session's report back slide:
- 01:22: Regulatory & Ethics Update
- 05:02: Data Security Update
- 06:13: Large Scale Genomics Update
- 09:23: Genomic Knowledge Standards Update
- 11:57: Data Use & Researcher Identities Update
- 14:56: Discovery Update
- 19:26: Cloud Update
- 21:28: Clin/Pheno Update
- 23:19: Pedigree
- 25:23: Phenopackets: Treatment Course + VRS Integration
- 26:48: FHIR Implementation Guide
- 29:02: Key Management
- 31:16: Assurance Levels
- 33:04: Machine Readable Consents
- 36:45: Beacon V2
- 39:34: Future of Variant Data Representation
- 42:04: Sequence Annotation
- 44:03: htsget: Interactions with Other Projects
- 49:38: Building Tooling
- 53:31: Federated Analysis Systems Project (FASP)
