Clinical & Phenotypic Data Capture (Clin/Pheno) Work Stream

Helps clinicians and researchers store, describe, and send data about observable traits (phenotypes) and clinical care.

Overview

Advances like electronic health records, deep phenotyping methods, and genetic testing offer the opportunity to build genomics into our digital health infrastructure. Patient care would improve if clinicians could quickly share genomic test results or link patient symptoms to genetic variants. The Clinical & Phenotypic Data Capture (Clin/Pheno) Work Stream accelerates the use of genomics in medicine by standardising how we describe clinical data, with a particular focus on observable traits (phenotypes) and family health history information. Clin/Pheno produces information models and standards that help clinicians and researchers capture, describe, and exchange clinical and phenotypic data.

Announcements

Date	Title
30 January 2025	GA4GH welcomes new Co-Leads for four Work Streams
14 January 2025	GA4GH Phenopackets community meetings are back!
5 June 2023	Interested in pharmacogenomics? Join our Study Group on 5 June 2023 at 15:00 UTC!
12 May 2023	Welcome to the new GA4GH website!

Publications Documents Videos

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
Characterizing pharmacogenetic programs using the consolidated framework for implementation research: A structured scoping review	McDermott J.H. et al. McDermott J.H., Wright S., Sharma V., Newman W.G., Payne K., Wilson P.	2022
Review and comparison of electronic patient-facing family health history tools	Welch, B.M. et al. Welch, B.M., Wiley, K., Pflieger, L., Achiangia, R., Baker, K., Hughes-Halbert, C., Morrison, H., Schiffman, J., Doerr, M.	2018
Facilitating a Culture of Responsible and Effective Sharing of Cancer Genome Data	Siu, L.L. et al. Siu, L.L., Lawler, M., Haussler, D., Knoppers, B.M., Lewin, J.H., Vis, D.J., Liao, R.G.	2016
All the World’s a Stage: Facilitating Discovery Science and Improved Cancer Care through the Global Alliance for Genomics and Health	Lawler, M. et al. Lawler, M., Siu, L.L., Rehm, H.L., Chanock, S.J., Alterovitz, G., Burn, J., Calvo, F.	2015

Documents

Date	Title
21 May 2025	GA4GH Implementation Forum (GIF) Ask Me Anything: Phenopackets
27 August 2024	GA4GH Updates Report — August 2024
24 May 2024	Meeting report: April Connect 2024
22 February 2024	Federated Cohort Building meeting minutes
7 November 2023	Meeting Report: September Connect 2023
19 September 2023	GA4GH Product Development and Approval Process
14 September 2023	Code of Ethics and Community Conduct (CECC)
14 September 2023	Guidelines for respectful engagement
14 September 2023	Procedures for reviewing reported violations of the Code of Ethics and Community Conduct
5 May 2023	Agendas and meeting minutes: Pharmacogenomics Data Standardisation & Storage
5 May 2023	Landscape analysis: PGx data standardisation
28 April 2023	Family history tools inventory (v2.0)
5 April 2023	Informational packet: getting involved with GA4GH
30 March 2023	Phenopackets implementation resources
11 March 2023	Meeting minutes: Clin/Pheno (2023 to 2024)
28 April 2022	Working document: Computable Cohort Hackathon 2022
22 February 2022	Road map: Clin/Pheno (2022 to 2023)
16 February 2022	Working document: Pedigree road map planning (2022 to 2023)
8 December 2021	Working document: common dataset for family health history
27 July 2021	Working document: Computable Cohort Representation — scope
27 May 2021	Working document: Cohort Representation landscape analysis
11 May 2021	Meeting minutes and agendas: Computable Cohort Representation
27 May 2020	Meeting minutes: Clin/Pheno — Phenopackets Cancer Task Team
29 August 2019	Meeting recordings: Clin/Pheno
8 July 2019	Working document: Pedigree data — use case/requirements
4 July 2019	Working document: Pedigree questionnaire results
7 February 2016	Enabling family history use in clinical practice: a review of current practice and policy considerations
7 February 2016	Family history tools inventory (v1.0)

Videos

	Date	Title
	24 September 2020	GA4GH 8th Plenary: Clinical & Phenotypic Data Capture (Clin/Pheno) Work Stream 2020 Update
	9 June 2015	GA4GH 3rd Plenary: emerging projects — clinical cancer genomes
	9 June 2015	GA4GH 3rd Plenary: emerging projects — eHealth