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 phenotype for use in genomic medicine and research, including the capture and exchange of information between electronic health records and research systems.
This workstream has three 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.
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.
The complexity of implementing genomics into healthcare will require increasingly precise information to be captured about the patient to support clinical decision making and biomedical research. Since knowledge about clinical manifestations, their association with variants and disease, and assays to measure them change daily, it is necessary to create a standard framework for community-driven terminological content development. Such a framework will allow granular representation and exchange of text definitions, synonyms, provenance, and attribution so as to ensure accurate application of the terms for use in variant interpretation. This common framework will support distributed authoring, community vetting, and delivery to EHRs, registries, databases, and other systems to maximize interoperability and advancement of terminologies for genomic medicine. Ongoing work will also provide standards for ontology mapping and clinically specific value sets for use in the capture of clinical data for genomic medicine.
We have bi-weekly/fortnightly call on Wednesday at 12pm PST/3pm EST/8pm BST/9pm CEST/5am (Thursday) AEST, etc. (19:00 UTC). Please email Lindsay Smith for meeting invitations.