Discovery Strategic Roadmap 2022/2023
Brainstorming and Planning Document
Goal
Define the deliverables that Discovery will develop and disseminate starting in 2022.
General expectation is to be ready in second half of 2022
Contribution Guidelines
- Please use the designated template below to propose new ideas for the 2022/2023 Discovery Roadmap.
- It is ok to add ideas that are not fully fleshed out. The purpose of this document is to brainstorm and iterate on ideas. We welcome and encourage you to add any proposals/topics that come to mind.
- If you would like to make comments/suggestions to the text of an already proposed deliverable, please do so in suggestion mode (this mode is available via the drop-down in the top right corner - click the pencil. Please DO NOT write over the proposal or other suggestions/comments.
- If you would like to declare your interest in participating in a proposed topic/deliverable, please add your name to the “+1” list.
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Template (copy and paste as needed)
Proposed Deliverable Name/Topic: <Add name/topic here>
Standard (if applicable): <e.g. Beacon>
Proposed By: <Add your name here>
Proposal based on discussions at: <Plenary, Connect, Work Stream, Driver Project>
Collaborating Workstreams: <If applicable>
Driver Projects: <Please name fully>
Has a use case been identified (detail below in description) Y/N? <Y/N>
Description: <Please describe the proposed deliverable/topic to explore. For example, what are the gaps in this space? Why is this deliverable needed?>
+1: <If you are not the proposer and you support this deliverable, please add your name here>
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Document Contents
Template (copy and paste as needed)
Previous Roadmap Deliverables (completed and incomplete)
New Proposals - 2022
General Discovery proposals
Proposed Deliverable Name/Topic: Discovery-FASP use cases
Standard: Varied
Proposed By: Alice Mann
Proposal based on which discussions: Work Stream discussions
Collaborating Workstreams: FASP and any others as defined in the use cases
Driver Projects:
Has a use case been identified (detail below in description) Y/N?
Description: We discussed that to drive Discovery representation and standards usage in FASP, we would brainstorm some use cases from the Discovery work stream and bring them to the FASP working group. For this proposed deliverable, we could define use cases to take forward to FASP and define their outcomes or outline general areas to plan for specific use cases.
+1: <If you are not the proposer and you support this deliverable, please add your name here>
Proposed Deliverable Name/Topic: Data model registry service
Standard: New standard
Proposed By: Marc Fiume
Proposal based on which discussions: Schemablock requirements gathering discussions
Collaborating Workstreams:
Driver Projects:
Has a use case been identified (detail below in description) Y/N?
Description: Proposed library of components. They should be unique, stable, and referenceable. A UI for listing components in the library would be helpful, and encourage the community to re-use existing components vs. create net new ones. There should also be a way for the community to develop their own models (can we provide a codebase for hosting a library? Is there a need for a TRS like API? E.g. a “data model registry service”? Data Connect needs a library of referenceable concepts, frontend/website is optional
See here for more info.
+1: <If you are not the proposer and you support this deliverable, please add your name here>
Proposed Deliverable Name/Topic: Phenopackets as Beacon v2 model entity
Standard: Beacon v2
Proposed By: Michael Baudis
Proposal based on which discussions: Multiple discussions in Beacon and with Phenopackets developers; e.g. presented at ELIXIR All Hands 2022
Collaborating Workstreams: C/P, GKS
Driver Projects: Beacon
Has a use case been identified (detail below in description) Y/N?
Description: The approved Beacon v2 standard in its default data models already has been aligned to a large extent with the Phenopackets objects and parameters. With Beacon's flexible extensibility for additional data models, the next logical step would be to add a Phenopackets model as part of a Beacon v2.n specification. In the long run and based on implementer feedback it could be evaluated if Phenopackets could serve as the recommended Beacon data delivery entity.
+1: <If you are not the proposer and you support this deliverable, please add your name here>
Proposed Deliverable Name/Topic: Phenopackets over Beacon for matchmaking
Standard: Beacon v2, Phenopackets
Proposed By: Michael Baudis
Proposal based on which discussions:
Collaborating Workstreams: C/P
Driver Projects: Beacon
Has a use case been identified (detail below in description) Y/N?
Description:
+1: <If you are not the proposer and you support this deliverable, please add your name here>
Data Connect proposals
Proposed Deliverable Name/Topic: Data Connect Publication
Standard: Data Connect
Proposed By: Alice Mann
Proposal based on which discussions: Work Stream Discussions
Collaborating Workstreams:
Driver Projects:
Has a use case been identified (detail below in description) Y/N?
Description: Now that Data Connect is an approved standard, prepare a publication that would be used as a great reference and source of information for increasing awareness and usage.
+1: Alice Mann, Miro Cupak
Proposed Deliverable Name/Topic: Data Connect Use Cases/Implementations
Standard: Data Connect
Proposed By: Alice Mann
Proposal based on which discussions: Work Stream Discussions
Collaborating Workstreams:
Driver Projects:
Has a use case been identified (detail below in description) Y/N?
Description: Interest from GA4GH Plenary and Connect as well as DP check ins identified potential new DPs that would be interested in implementing DC. We could start by having tailored sessions with the DP use case to support new implementations of DC.
+1: Miro Cupak
Proposed Deliverable Name/Topic: Data Connect Getting Started Artifacts
Standard: Data Connect
Proposed By: Ian Fore
Proposal based on which discussions: Work Stream Discussions
Collaborating Workstreams:
Driver Projects:
Has a use case been identified (detail below in description) Y/N?
Description: Enhance materials for getting started with Data Connect as a researcher and data custodian, select from:
- Starter Kit
- Videos
- Case studies - tiered model for adoption, harmonizing in a network of DC implementations
- Session at GA4GH meetings
+1: Miro Cupak
Proposed Deliverable Name/Topic: Data Connect and BioMart exploration
Standard: Data Connect
Proposed By: Susan Fairley
Proposal based on which discussions: Work Stream Discussions
Collaborating Workstreams:
Driver Projects:
Has a use case been identified (detail below in description) Y/N?
Description: Biomart is used at EBI for things like Ensembl but also a bunch of other resources at other places. It lets you ‘build’ queries on relational databases. How does Biomart relate to Data Connect and can anything be learnt from either functionality?
Tab/Comma delimited file == relational table == R data frame == BioMart output == DataConnect API
BiomaRt package in R is a highly used scheme. Should we look to write a R package to the DataConnect API that makes a data frame, and potentially a DataConnect end point to BioMart
+1: <If you are not the proposer and you support this deliverable, please add your name here>
Proposed Deliverable Name/Topic: Passport support for Data Connect and Networks
Standard: Data Connect and Networks
Proposed By: Miro Cupak
Proposal based on which discussions: Work Stream Discussions
Collaborating Workstreams: FASP, DURI, Cloud?
Driver Projects: ASI
Has a use case been identified (detail below in description) Y/N?
Description: Over the last year and half, DRS has been exploring support for Passports through FASP. When this integration is ready, work with FASP to learn from the DRS use case and similarly provide a standard way of supporting Passports in Data Connect for access to datasets, including controlled access datasets. Additionally, provide guidelines for using OAUTH 2.0 to secure Data Connect implementations.
+1: <If you are not the proposer and you support this deliverable, please add your name here>
Proposed Deliverable Name/Topic: Data Connect and Beacon alignment
Standard: Data Connect
Proposed By: Miro Cupak
Proposal based on which discussions: Work Stream Discussions
Collaborating Workstreams: N/A (within Discovery WS)
Driver Projects:
Has a use case been identified (detail below in description) Y/N?
Description: Data Connect and Beacon are two complementary Discovery Workstream standards that sound similar on paper. For a long time, adopters have been asking why both standards are needed, what the differences are, how they complement each other, and when to use one over the other. We haven’t done a good job explaining this clearly. As part of this deliverable, we think it would be useful for adopters to:
- Create an implementation guide describing the relationship between Beacon and Data Connect.
- Provide an implementation of Beacon on top of Data Connect to support both standards.
+1: <If you are not the proposer and you support this deliverable, please add your name here>
Proposed Deliverable Name/Topic: Data Connect for Computable Cohort Representation
Standard: Data Connect
Proposed By: Ian Fore
Proposal based on which discussions: Work Stream Discussions
Collaborating Workstreams:
Driver Projects:
Has a use case been identified (detail below in description) Y/N?
Description: Data Connect is an approved GA4GH API capable of performing operations like cohort selection. Explore alignment with the Computable Cohort Representation effort in GA4GH.
+1: Miro Cupak
Proposed Deliverable Name/Topic: Networks landscape analysis/usage/implementation survey
Standard: Data Connect
Proposed By: Miro Cupak
Proposal based on which discussions: Work Stream Discussions
Collaborating Workstreams:
Driver Projects:
Has a use case been identified (detail below in description) Y/N?
Description: Discovery Networks standards (Service Registry and Service Info) have been stable for a couple of years and have gotten substantial adoption. The goal of this deliverable would be to understand who is using Networks and how they are using it, and what the gaps are that new developments the specifications could address. The Work Stream Manager could lead this approach, by devising a survey or questions and who to approach both within and outside GA4GH. Then analyse the results and discuss in the Work Stream to feed into ideas about what the team could do with Networks in the future.
+1: <If you are not the proposer and you support this deliverable, please add your name here>
Roadmap Deliverables 2022
Data Connect
Type | Status | Description | |
Previous Roadmap Deliverables (completed and incomplete)
Beacon
Type | Status | Description | |
v2 | API Draft specification | WIP | Review draft 4 Generate Release Candidate (RC) of the spec |
v2 | API Real world testing | WIP | Real tests with early adopters Shown to DP along the process from Draft1 to Draft4 GHIF workshop planning Stronger testing Autumn 2021 |
v2 | API Support for MME | WIP | Several meetings with MME DP, their requirements are an integral part of the specification |
v2 | API Major version | WIP | Submission for January Steering Committee |
V2 | Publication | WIP | Beacon v2 publication |
Data Connect
Type | Status | Description | |
v1.0 | API Draft specification | Complete | Draft specification of Table API + Query API and companion products e.g. service registry API |
v1.0 | API Implementations | Complete | Specification implemented by at least 2 DPs |
v1.0 | API FASP integration | Complete | Functional demo of the integration of DC and DURI and Cloud WS APIs to enable federated search and analysis of controlled access data |
v1.0 | API Major release | Complete |
Service Registry/Service Info
Type | Status | Description | |
v1.0 | API Major Version | Complete | Complete product approval for Service Info and Registry |
v1.0 | API Implementation | Complete | A reference implementation of Service Registry with mixed service types e.g. Beacons and Matchmakers. The GA4GH service registry contains a mix of GA4GH services. |
v1.0 | API Implementation | Delayed | A reference implementation of an indexer that recursively crawls connected Service Registries to compile a list of services in the Internet of Genomics. This aligns closely with a Secretariat goal or providing this information on ga4gh.org |
v1.1 | API Feature Set | Not delivered | 1.1 release of Service info to aid use of authentication methods to access services and service description discovery Suggested to wait for DRS + passports to crystallise so we can modify and translate to a Service Registry and passports solution |
v1.1 | API Feature Set | WIP | Registry writable endpoints PR branch requires reviewer feedback. Discussed in 2020 but not picked up in a while |
v1.1 | API Implementation | Not delivered | FASP integration with Service Registry |
v1.1 | API Implementation | Not delivered | A reference implementation of a cross-service registry query engine |