Phenopackets

Offers a human and machine-readable way to structure clinical and phenotypic data about a patient or individual

Overview

Summary Benefits Target users Announcements

Healthcare systems capture vital clinical information, such as a patient’s disease symptoms, observable characteristics, and demographic data. Improving patient care and clinical outcomes rely on the ability to standardise and share this information, along with corresponding genomic data. Originating within the Monarch Initiative, and further developed within the GA4GH Clinical & Phenotypic Data Capture (Clin/Pheno) Work Stream, the Phenopackets standard provides a human and machine-readable way to structure phenotypic and clinical information about a patient or individual.

Video credit -

Phenopackets help researchers and clinicians exchange phenotypic data in a standard way to accelerate research and improve patient care.

Image summary -

A three-panel comic demonstrating how Phenopackets aims to enable the electronic sharing of phenotypic data

Benefits

Provides a format for creating computable representations of phenotypic and clinical data
Works with other GA4GH standards, such as the Variation Representation Standard, for representing genetic variation data
Works interoperably with community standards such as HL7 FHIR

Target users

Researchers, clinicians, clinical laboratories, and developers

Announcements

Date	Title
14 January 2025	GA4GH Phenopackets community meetings are back!

Title	Related Driver Projects and Organisations
CanDIG V2	Canadian Distributed Infrastructure for Genomics (CanDIG)
EJP-RD Virtual Platform	European Joint Programme on Rare Disease (EJP RD)
ELIXIR BioContainers
ELIXIR European Genome-phenome Archive (EGA)	European Genome-phenome Archive (EGA)
ELIXIR-Beacon	ELIXIR Beacon
EpiShare Platform	EpiShare
The Exomiser	Monarch Initiative

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Publications Documents

Publications

Title	Author(s)	Year
Towards a standard benchmark for phenotype-driven variant and gene prioritisation algorithms: PhEval - Phenotypic inference Evaluation framework	Bridges, Y. et al. Bridges, Y., de Souza, V., Cortes, K.G., Haendel, M., Harris, N.L., Korn, D.R., Marinakis, N.M., Matentzoglu, N., McLaughlin, J.A., Mungall, C.J., Odell, A., Robinson, P.N., Smedley, D., Jacobsen, J.O.B.	2025
The ICGC ARGO data dictionary for standardizing global cancer clinical data	Nahal-Bose, H.K. et al. Nahal-Bose, H.K., Lichter, P., Weber, U., Stein, L.D., Bajari, R., Xiang, L., Su, E., Eubank, J., Schütte, C., Yung, C.K., Courtot, M.	2025
GA4GH phenopacket-driven characterization of genotype-phenotype correlations in Mendelian disorders	Lauren Rekerle, L. et al. Lauren Rekerle, L., Danis, D., Rehburg, F., Graefe, A.S.L., Bily, V., Cacheiro, P., Chimirri, L., Chong, J.X., Connelly, E., de Vries, B.B.A., Dingemans, A.J.M., Duyzend, M.H., Freiberger, T., Gehle, P., Groza, T., Hansen, P., Jacobsen, J.O.B., Klocperk, A., Ladewig. M.S., Love, M.I., Mordhorst, A., Munoz-Torres, M.C., Reese, J., Schuetz, C., Smedley, D., Strauss, T., Vladyka, O., Zocche, D., Thun, S., Mungall, C.J., Haendel, M.A., Robinson, P.N.	2025
An ontology-based rare disease common data model harmonising international registries, FHIR, and Phenopackets	Graefe, A.S.L. et al. Graefe, A.S.L., Hübner, M.R., Rehburg, F., Sander, S., Alkarkoukly, S., Grönke, A., Weyersberg, A., Danis, D., Zschüntzsch, J., Nyoungui, E.F., Wiegand, S., Kühnen, P., Robinson, P.N., Beyan, O., Thun, S.	2025
Pheno-Ranker: a toolkit for comparison of phenotypic data stored in GA4GH standards and beyond	Leist, I.C. et al. Leist, I.C., Rivas-Torrubia, M., Barturen, G., Gut, I.G., Rueda, M.	2024
A corpus of GA4GH Phenopackets: case-level phenotyping for genomic diagnostics and discovery	Danis, D. et al. Danis, D., Bamshad M.J., Bridges, Y., Cacheiro, P., Carmody, L.C., Chong, J.X., Coleman, B., Dalgleish, R., Freeman, P.J., Graefe, A.S.L,, Groza, T., Jacobsen. J.O.B., Klocperk, A., Kusters, M., Ladewig, M.S., Marcello, A.J., Mattina, T., Mungall, C.J., Munoz-Torres, M.C., Reese, J.T., Rehburg, F., Reis, B.C.S., Schuetz, C., Smedley, D., Strauss, T., Sundaramurthi, J.C., Thun, S., Wissink, K., Wagstaff, J.F., Zocche, D., Haendel, M.A., Robinson, P.N.	2024
Phenopacket-tools: building and validating GA4GH Phenopackets	Danis, D et al. Danis, D, Jacobsen, JOB, Wagner, AH, Groza, T, Beckwith, MA, Rekerle, L, Carmody, LC, Reese, J, Hegde, H, Ladewig, MS, Seitz, B, Munoz-Torres, M, Harris, NL, Rambla, J, Baudis, M, Mungall, CJ, Haendel, MA, Robinson, PN.	2023
The GA4GH Phenopacket schema defines a computable representation of clinical data	Jacobsen, J. O. et al. Jacobsen, J. O., Baudis, M., Baynam, G. S., Beckmann, J. S., Beltran, S., Buske, O. J., Callahan, T. J., Chute, C. G., Courtot, M., Danis, D., Elemento, O., Essenwanger, A., Freimuth, R. R., Gargano, M. A., Groza, T., Hamosh, A., Harris, N. L., Kaliyaperumal, R., Lloyd, K. C., Robinson, P. N., Khalifa, Aly, Krawitz, Peter M., Köhler, Sebastian, Laraway, Brian J., Matalonga, Leslie, McMurry, Julie A., Ogishima, Soichi, Piscia, Davide, Pontikos, Nikolas, Roos, Marco, Sass, Julian, Schofield, Paul N., Seelow, Dominik, Siapos, Anastasios, Smedley, Damian, Smith, Lindsay D., Steinhaus, Robin, Swietlik, Emilia M., Thun, Sylvia, Wagner, Alex H., Warner, Jeremy L., Weiland, Claus, Haendel, Melissa A.	2022
GA4GH Phenopackets: a practical introduction	Ladewig, Markus S. et al. Ladewig, Markus S., Wagner, Alex H., Danis, Daniel, ElKassaby, Baha, Gargano, Michael, Groza, Tudor, Baudis, Michael, Steinhaus, Robin, Seelow, Dominik, Schofield, Paul N., Elemento, Olivier, Smith, Lindsay, McMurry, Julie A., Haendel, Melissa A., Robinson, Peter N.	2022

Documents

Date	Title
21 May 2025	GA4GH Implementation Forum (GIF) Ask Me Anything: Phenopackets
14 September 2023	Code of Ethics and Community Conduct (CECC)
30 March 2023	Phenopackets implementation resources
11 March 2023	Meeting minutes: Clin/Pheno (2023 to 2024)
27 May 2020	Meeting minutes: Clin/Pheno — Phenopackets Cancer Task Team

Contributors Driver Projects

Contributors

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Melissa HaendelPhenopackets LeadUNC School of Medicine
Jules JacobsenPhenopackets LeadQueen Mary University of London
Monica Munoz-TorresPhenopackets LeadUniversity of Colorado Anschutz Medical Campus, Aurora, California, USA
Peter RobinsonPhenopackets LeadThe Jackson Laboratory, Farmington
Michael BaudisUniversity of Zurich, Zurich
Jacqui BeckmannUniversité de Lausanne
Sergi BeltranCNAG CRG, Barcelona, Spain
David BujoldMcGill University / Université McGill, Montréal, Canada
Orion BuskePhenoTips, Toronto
Chritopher ChuteJohns Hopkins University School of Medicine, Maryland
Mélanie CourtotOntario Institute for Cancer Research (OICR), Toronto, Canada
Shahim EssaidUniversity of Colorado Anschutz Medical Campus, Aurora, California, USA
Mallory FreebergEMBL's European Bioinformatics Institute (EBI), Hinxton, UK
Robert FreimuthMayo Clinic, Rochester
Ian GreenSNOMED International, London
Tudor GrozaEMBL's European Bioinformatics Institute (EBI), Hinxton, UK
Allison HeathChildren's Hospital of Philadelphia, Philadelphia
Arthur HermannKaiser Permanente, Brentwood
Sebastian KoehlerAda Health
Adriana MalheiroNIH National Center for Biotechnology Information (NCBI)
Sabine OesterleSIB Swiss Institute of Bioinformatics, Lausanne
Soichi OgishimaTohoku University Tohoku, Medical Megabank Organization, Sendai
Helen ParkinsonEMBL's European Bioinformatics Institute (EBI), Hinxton, UK
Babita SinghCentre for Genomic Regulation, Barcelona
Dylan SpaldingCSC – IT CENTER FOR SCIENCE
Susheel VarmaInformation Commissioner's Office
Grant WoodMyGenomeTrust
Christina YungOntario Institute for Cancer Research (OICR), Toronto, Canada, Indoc Research, Toronto
Ksenia ZaytsevaCanadian Centre for Computational Genomics, McGill University / Université McGill, Montréal, Canada

Driver Projects

Title	Thematic Area
Canadian Distributed Infrastructure for Genomics (CanDIG)	Rare Disease Cancer Complex Traits Basic Biology
Monarch Initiative	Rare Disease Cancer Complex Traits Basic Biology
ELIXIR Beacon	Rare Disease Cancer Complex Traits Basic Biology
European Genome-phenome Archive (EGA)	Rare Disease Cancer Complex Traits Basic Biology
European Joint Programme on Rare Disease (EJP RD)	Rare Disease
EpiShare	Basic Biology