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The "Clinical & Phenotypic Data Capture & Exchange" (GA4GH::CP) Work Stream is one of the elements of the Global Alliance for Genomics and Health (GA4GH), aimed at developing standard formats for the exchange of genomic data for research and biomedical applications. All members of this team must follow the GA4GH Standards of Professional Conduct.
This Work Stream supports the clinical adoption of genomics through establishing standard ontologies, best practices and information models to describe the clinical data for use in genomic medicine and research, including the capture and exchange of information between electronic health records and research systems.
This workstream has several project areas, focusing on different aspects of the mission:
While ontologies and terminologies provide the standard data concept definitions for capturing clinical information, an information model is required to successfully exchange that information between clinical information systems and with related information systems. A standardized structure for phenotypic data would catalyze integration from distributed sources such as authors, journals, data repositories and clinics when appropriately consented, and accelerate clinical utilization of this data to effect more precise health outcomes. The “Phenopackets” standard will provide information models with different levels of complexity to enable high level clinical phenotype information as well as deep clinical phenotype information to be exchanged. Note: This Subgroup currently does not have regular meetings, as the plan is to keep the standard stable in order to support implmentation.
The Phenopackets Schema FHIR Implementation Guide is an HL7 FHIR Implementation guide based on the approved Phenopackets standard. It will support the standardized exchange of phenotypic information from one health health information system to another through the FHIR API.
- Domain Analysis Github + Readthedocs
- Core Implementation Guide Github
- Phenopackets IG First Draft (1:1 mapping)
Pedigree data is currently represented in heterogeneous formats that frequently result in the use of lowest-common-denominator formats (e.g., PED) or custom JSON formats for data transfer. The need for high quality, unambiguous, computable pedigree and family history information is critical for informing genomic analysis as well as using the information to inform risk to family members. Standardizing the way systems represent family structure will allow patients to share this information more easily between healthcare systems and help software tools to use this information to improve genome analysis and diagnosis.
- Documentation (describes all of the links below)
- Use case collection
- Conceptual model
- Common dataset
- Draft FHIR IG
- KIN Ontology
- Pedigree Tools
- Pedigree Validator
- Meeting Minutes
Exploring standardization around computable cohort representation. Several areas of interest have been identified: 1) MIACC (Minimum Information About Computable Cohort), aimed at describing sets of attributes required to describe a cohort consistently (eg. age, biological sex), 2) PHENO, aimed at looking at existing phenotypic standards, and combining phenotypic info into cohort representation (e.g. OMOP FIHR, i2b2 etc.), and 3) Cohort Summary Statistics, looking at how to define and query counts. This Subgroup is still in the landscape review/preliminary development phase, as a deliverable has not yet been formally proposed.
- Full Work Stream Monthly Calls: Every other month (bi-monthly) on Wednesdays at 12pm PST/3pm EST/8pm BST/9pm CEST/5am (Friday) AEST, etc. (19:00 UTC).
- Pedigree Technical Subgroup Calls: Bi-weekly/fortnightly Thursdays at 1pm PST/4pm EST/9pm BST/10pm CEST/6am (Friday) AEST, etc. (20:00 UTC).
- Cohort Representation Subgroup Calls: Currently ad hoc as topics are explored.
- Phenopackets Subgroup Calls: Ad hoc.
Please email Lindsay Smith for meeting invitations.
- Draft 2022-2023 Roadmap Refresh
- 2020-2021 Roadmap
- 2019 Roadmap
- 2023-2024 Meeting Minutes
- 2021-2022 Meeting Minutes
- 2019-2020 Meeting Minutes
- Slack - Clin/Pheno channel is #clin_pheno_full
- GA4GH Plenary in Barcelona, September 2022. See here for meeting slides and recordings.
- GA4GH Connect Montreal (Hybrid), April 2022. See here for the meeting report.
- GA4GH Virtual Connect, October 2021. See here for the meeting report.
- GA4GH Virtual Connect, March 2021. See here for the meeting report.
- GA4GH Virtual 8th Plenary, September 2020. See here for Clin/Pheno working meeting notes and agendas, and here for Plenary session meeting materials
- GA4GH Virtual Connect, March 2020. See here for notes and presentations.
- GA4GH 7th Plenary in Boston, USA, October 2019. See here for notes and presentations.
- GA4GH Connect in Hinxton, UK, April 2019. See documentation.
- GA4GH 6th Plenary in Basel, Switzerland, October 2018. See here for more information.