The GA4GH Phenopacket schema defines a computable representation of clinical data

GAGH Phenopacket Modeling Consortium

doi:10.1038/s41587-022-01357-4

The GA4GH Phenopacket schema defines a computable representation of clinical data

GAGH Phenopacket Modeling Consortium

Research output: Contribution to journal › Comment/Letter to the editor › Academic › peer-review

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Original language	English
Pages (from-to)	817-820
Number of pages	4
Journal	Nature Biotechnology
Volume	40
Issue number	6
DOIs	https://doi.org/10.1038/s41587-022-01357-4
Publication status	Published - 1 Jun 2022

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10.1038/s41587-022-01357-4

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@article{3b650c76b88245ab8028ad5076d9f384,

title = "The GA4GH Phenopacket schema defines a computable representation of clinical data",

author = "Jacobsen, \{Julius O.B.\} and Michael Baudis and Baynam, \{Gareth S.\} and Beckmann, \{Jacques S.\} and Sergi Beltran and Buske, \{Orion J.\} and Callahan, \{Tiffany J.\} and Chute, \{Christopher G.\} and M{\'e}lanie Courtot and Daniel Danis and Olivier Elemento and Andrea Essenwanger and Freimuth, \{Robert R.\} and Gargano, \{Michael A.\} and Tudor Groza and Ada Hamosh and Harris, \{Nomi L.\} and Rajaram Kaliyaperumal and Lloyd, \{Kevin C.Kent\} and Aly Khalifa and Krawitz, \{Peter M.\} and Sebastian K{\"o}hler and Laraway, \{Brian J.\} and Heikki Lehv{\"a}slaiho and Leslie Matalonga and McMurry, \{Julie A.\} and Alejandro Metke-Jimenez and Mungall, \{Christopher J.\} and Munoz-Torres, \{Monica C.\} and Soichi Ogishima and Anastasios Papakonstantinou and Davide Piscia and Nikolas Pontikos and N{\'u}ria Queralt-Rosinach and Marco Roos and Julian Sass and Schofield, \{Paul N.\} and Dominik Seelow and Anastasios Siapos and Damian Smedley and Smith, \{Lindsay D.\} and Robin Steinhaus and Sundaramurthi, \{Jagadish Chandrabose\} and Swietlik, \{Emilia M.\} and Sylvia Thun and Vasilevsky, \{Nicole A.\} and Wagner, \{Alex H.\} and Warner, \{Jeremy L.\} and Claus Weiland and Michel Dumontier and \{GAGH Phenopacket Modeling Consortium\}",

note = "Funding Information: The authors gratefully acknowledge insight and feedback from Marian H. Adly, Pier Luigi Buttigieg, Janine Lewis, Manuel Posada de la Paz and Maria Taboada. This work was supported by 7RM1HG010860-02 (NHGRI). Additional funding was as follows. P.N.R. was supported by NLM contract 75N97019P00280, NIH NHGRI RM1HG010860, NIH OD R24OD011883 and NIH NICHD 1R01HD103805-01. H.H. was supported by NIH OD R24OD011883. G.I.S. was supported by ELIXIR, the research infrastructure for life-science data. C.G.C. was supported by NIH NCATS U24TR002306. K.C.L. was supported by NIH OD 5UM1OD023221. M.B. was supported by the BioMedIT Network project of the Swiss Institute of Bioinformatics (SIB) and Swiss Personalized Health Network (SPHN). A.H.W. was supported by NIH NHGRI K99HG010157 and NIH NHGRI R00HG010157. C.J.M., M.A.H., M.C.M.-T., J.A.M. and D.D. were supported by NIH NHGRI RM1HG010860 and NIH OD R24OD011883. A.M.-J. was supported by Australian Genomics. Australian Genomics is supported by the National Health and Medical Research Council (GNT1113531). D. Smedley and J.O.B.J. were supported by NIH NHGRI RM1HG010860, NIH OD R24OD011883 and NIH NICHD 1R01HD103805-01. M.D. was supported by NIH NHGRI U54HG004028, NIH NHGRI 5U01HG008473-03 and NIH NCATS OT2TR003434-01S1U54HG008033-01. G.S.B. was supported by the Roy Hill Community Foundation, Angela Wright Bennett Foundation, McCusker Charitable Foundation, Borlaug Foundation and Stan Perron Charitable Foundation. L.B. was supported by NIH NHGRI U41HG006834 (Clinical Genome Resource). M.C. was supported by EMBL-EBI Core Funds and Wellcome Trust GA4GH award number 201535/Z/16/Z. A.H. was supported by NIH NHGRI 1U41HG006627, NIH NHGRI 1U54HG006542 and NIH NHGRI 1RM1HG010860. P.N.S. was supported by The Alan Turing Institute. N.L.H. was supported by NIH NHGRI RM1HG010860, NIH OD R24OD011883 and US Department of Energy Contract DE-AC02-05CH11231. N.P. was supported by Moorfields Eye Charity. N.Q.-R. was supported by EU Horizon 2020 research and innovation programme grant agreement 825575 (EJP-RD). O.E. was supported by NIH grants UL1TR002384, R01CA194547 and P01CA214274, LLS SCOR grants 180078-01 and 7021-20 and Starr Cancer Consortium grant I11-0027. H. Lochm{\"u}ller was supported by the CIHR Foundation Grant on Precision Health for Neuromuscular Diseases FDN-167281. R.T. was supported by CIHR postdoctoral fellowship award MFE-171275. L.D.S. was supported by Genome Canada and NIH NHGRI U24HG011025. S.O. was supported by AMED. D.P., L.M., A.P., S.B., M.R. and R.K. were supported by EU Horizon 2020 research and innovation programme grant agreements 779257 (Solve-RD) and 825575 (EJP-RD). R.R.F. was supported by NLM contract 75N97019P00280. Funding Information: The authors gratefully acknowledge insight and feedback from Marian H. Adly, Pier Luigi Buttigieg, Janine Lewis, Manuel Posada de la Paz and Maria Taboada. This work was supported by 7RM1HG010860-02 (NHGRI). Additional funding was as follows. P.N.R. was supported by NLM contract 75N97019P00280, NIH NHGRI RM1HG010860, NIH OD R24OD011883 and NIH NICHD 1R01HD103805-01. H.H. was supported by NIH OD R24OD011883. G.I.S. was supported by ELIXIR, the research infrastructure for life-science data. C.G.C. was supported by NIH NCATS U24TR002306. K.C.L. was supported by NIH OD 5UM1OD023221. M.B. was supported by the BioMedIT Network project of the Swiss Institute of Bioinformatics (SIB) and Swiss Personalized Health Network (SPHN). A.H.W. was supported by NIH NHGRI K99HG010157 and NIH NHGRI R00HG010157. C.J.M., M.A.H., M.C.M.-T., J.A.M. and D.D. were supported by NIH NHGRI RM1HG010860 and NIH OD R24OD011883. A.M.-J. was supported by Australian Genomics. Australian Genomics is supported by the National Health and Medical Research Council (GNT1113531). D. Smedley and J.O.B.J. were supported by NIH NHGRI RM1HG010860, NIH OD R24OD011883 and NIH NICHD 1R01HD103805-01. M.D. was supported by NIH NHGRI U54HG004028, NIH NHGRI 5U01HG008473-03 and NIH NCATS OT2TR003434-01S1U54HG008033-01. G.S.B. was supported by the Roy Hill Community Foundation, Angela Wright Bennett Foundation, McCusker Charitable Foundation, Borlaug Foundation and Stan Perron Charitable Foundation. L.B. was supported by NIH NHGRI U41HG006834 (Clinical Genome Resource). M.C. was supported by EMBL-EBI Core Funds and Wellcome Trust GA4GH award number 201535/Z/16/Z. A.H. was supported by NIH NHGRI 1U41HG006627, NIH NHGRI 1U54HG006542 and NIH NHGRI 1RM1HG010860. P.N.S. was supported by The Alan Turing Institute. N.L.H. was supported by NIH NHGRI RM1HG010860, NIH OD R24OD011883 and US Department of Energy Contract DE-AC02-05CH11231. N.P. was supported by Moorfields Eye Charity. N.Q.-R. was supported by EU Horizon 2020 research and innovation programme grant agreement 825575 (EJP-RD). O.E. was supported by NIH grants UL1TR002384, R01CA194547 and P01CA214274, LLS SCOR grants 180078-01 and 7021-20 and Starr Cancer Consortium grant I11-0027. H. Lochm{\"u}ller was supported by the CIHR Foundation Grant on Precision Health for Neuromuscular Diseases FDN-167281. R.T. was supported by CIHR postdoctoral fellowship award MFE-171275. L.D.S. was supported by Genome Canada and NIH NHGRI U24HG011025. S.O. was supported by AMED. D.P., L.M., A.P., S.B., M.R. and R.K. were supported by EU Horizon 2020 research and innovation programme grant agreements 779257 (Solve-RD) and 825575 (EJP-RD). R.R.F. was supported by NLM contract 75N97019P00280.",

year = "2022",

month = jun,

day = "1",

doi = "10.1038/s41587-022-01357-4",

language = "English",

volume = "40",

pages = "817--820",

journal = "Nature Biotechnology",

issn = "1087-0156",

publisher = "Nature Research",

number = "6",

}

TY - JOUR

T1 - The GA4GH Phenopacket schema defines a computable representation of clinical data

AU - Jacobsen, Julius O.B.

AU - Baudis, Michael

AU - Baynam, Gareth S.

AU - Beckmann, Jacques S.

AU - Beltran, Sergi

AU - Buske, Orion J.

AU - Callahan, Tiffany J.

AU - Chute, Christopher G.

AU - Courtot, Mélanie

AU - Danis, Daniel

AU - Elemento, Olivier

AU - Essenwanger, Andrea

AU - Freimuth, Robert R.

AU - Gargano, Michael A.

AU - Groza, Tudor

AU - Hamosh, Ada

AU - Harris, Nomi L.

AU - Kaliyaperumal, Rajaram

AU - Lloyd, Kevin C.Kent

AU - Khalifa, Aly

AU - Krawitz, Peter M.

AU - Köhler, Sebastian

AU - Laraway, Brian J.

AU - Lehväslaiho, Heikki

AU - Matalonga, Leslie

AU - McMurry, Julie A.

AU - Metke-Jimenez, Alejandro

AU - Mungall, Christopher J.

AU - Munoz-Torres, Monica C.

AU - Ogishima, Soichi

AU - Papakonstantinou, Anastasios

AU - Piscia, Davide

AU - Pontikos, Nikolas

AU - Queralt-Rosinach, Núria

AU - Roos, Marco

AU - Sass, Julian

AU - Schofield, Paul N.

AU - Seelow, Dominik

AU - Siapos, Anastasios

AU - Smedley, Damian

AU - Smith, Lindsay D.

AU - Steinhaus, Robin

AU - Sundaramurthi, Jagadish Chandrabose

AU - Swietlik, Emilia M.

AU - Thun, Sylvia

AU - Vasilevsky, Nicole A.

AU - Wagner, Alex H.

AU - Warner, Jeremy L.

AU - Weiland, Claus

AU - Dumontier, Michel

AU - GAGH Phenopacket Modeling Consortium

N1 - Funding Information: The authors gratefully acknowledge insight and feedback from Marian H. Adly, Pier Luigi Buttigieg, Janine Lewis, Manuel Posada de la Paz and Maria Taboada. This work was supported by 7RM1HG010860-02 (NHGRI). Additional funding was as follows. P.N.R. was supported by NLM contract 75N97019P00280, NIH NHGRI RM1HG010860, NIH OD R24OD011883 and NIH NICHD 1R01HD103805-01. H.H. was supported by NIH OD R24OD011883. G.I.S. was supported by ELIXIR, the research infrastructure for life-science data. C.G.C. was supported by NIH NCATS U24TR002306. K.C.L. was supported by NIH OD 5UM1OD023221. M.B. was supported by the BioMedIT Network project of the Swiss Institute of Bioinformatics (SIB) and Swiss Personalized Health Network (SPHN). A.H.W. was supported by NIH NHGRI K99HG010157 and NIH NHGRI R00HG010157. C.J.M., M.A.H., M.C.M.-T., J.A.M. and D.D. were supported by NIH NHGRI RM1HG010860 and NIH OD R24OD011883. A.M.-J. was supported by Australian Genomics. Australian Genomics is supported by the National Health and Medical Research Council (GNT1113531). D. Smedley and J.O.B.J. were supported by NIH NHGRI RM1HG010860, NIH OD R24OD011883 and NIH NICHD 1R01HD103805-01. M.D. was supported by NIH NHGRI U54HG004028, NIH NHGRI 5U01HG008473-03 and NIH NCATS OT2TR003434-01S1U54HG008033-01. G.S.B. was supported by the Roy Hill Community Foundation, Angela Wright Bennett Foundation, McCusker Charitable Foundation, Borlaug Foundation and Stan Perron Charitable Foundation. L.B. was supported by NIH NHGRI U41HG006834 (Clinical Genome Resource). M.C. was supported by EMBL-EBI Core Funds and Wellcome Trust GA4GH award number 201535/Z/16/Z. A.H. was supported by NIH NHGRI 1U41HG006627, NIH NHGRI 1U54HG006542 and NIH NHGRI 1RM1HG010860. P.N.S. was supported by The Alan Turing Institute. N.L.H. was supported by NIH NHGRI RM1HG010860, NIH OD R24OD011883 and US Department of Energy Contract DE-AC02-05CH11231. N.P. was supported by Moorfields Eye Charity. N.Q.-R. was supported by EU Horizon 2020 research and innovation programme grant agreement 825575 (EJP-RD). O.E. was supported by NIH grants UL1TR002384, R01CA194547 and P01CA214274, LLS SCOR grants 180078-01 and 7021-20 and Starr Cancer Consortium grant I11-0027. H. Lochmüller was supported by the CIHR Foundation Grant on Precision Health for Neuromuscular Diseases FDN-167281. R.T. was supported by CIHR postdoctoral fellowship award MFE-171275. L.D.S. was supported by Genome Canada and NIH NHGRI U24HG011025. S.O. was supported by AMED. D.P., L.M., A.P., S.B., M.R. and R.K. were supported by EU Horizon 2020 research and innovation programme grant agreements 779257 (Solve-RD) and 825575 (EJP-RD). R.R.F. was supported by NLM contract 75N97019P00280. Funding Information: The authors gratefully acknowledge insight and feedback from Marian H. Adly, Pier Luigi Buttigieg, Janine Lewis, Manuel Posada de la Paz and Maria Taboada. This work was supported by 7RM1HG010860-02 (NHGRI). Additional funding was as follows. P.N.R. was supported by NLM contract 75N97019P00280, NIH NHGRI RM1HG010860, NIH OD R24OD011883 and NIH NICHD 1R01HD103805-01. H.H. was supported by NIH OD R24OD011883. G.I.S. was supported by ELIXIR, the research infrastructure for life-science data. C.G.C. was supported by NIH NCATS U24TR002306. K.C.L. was supported by NIH OD 5UM1OD023221. M.B. was supported by the BioMedIT Network project of the Swiss Institute of Bioinformatics (SIB) and Swiss Personalized Health Network (SPHN). A.H.W. was supported by NIH NHGRI K99HG010157 and NIH NHGRI R00HG010157. C.J.M., M.A.H., M.C.M.-T., J.A.M. and D.D. were supported by NIH NHGRI RM1HG010860 and NIH OD R24OD011883. A.M.-J. was supported by Australian Genomics. Australian Genomics is supported by the National Health and Medical Research Council (GNT1113531). D. Smedley and J.O.B.J. were supported by NIH NHGRI RM1HG010860, NIH OD R24OD011883 and NIH NICHD 1R01HD103805-01. M.D. was supported by NIH NHGRI U54HG004028, NIH NHGRI 5U01HG008473-03 and NIH NCATS OT2TR003434-01S1U54HG008033-01. G.S.B. was supported by the Roy Hill Community Foundation, Angela Wright Bennett Foundation, McCusker Charitable Foundation, Borlaug Foundation and Stan Perron Charitable Foundation. L.B. was supported by NIH NHGRI U41HG006834 (Clinical Genome Resource). M.C. was supported by EMBL-EBI Core Funds and Wellcome Trust GA4GH award number 201535/Z/16/Z. A.H. was supported by NIH NHGRI 1U41HG006627, NIH NHGRI 1U54HG006542 and NIH NHGRI 1RM1HG010860. P.N.S. was supported by The Alan Turing Institute. N.L.H. was supported by NIH NHGRI RM1HG010860, NIH OD R24OD011883 and US Department of Energy Contract DE-AC02-05CH11231. N.P. was supported by Moorfields Eye Charity. N.Q.-R. was supported by EU Horizon 2020 research and innovation programme grant agreement 825575 (EJP-RD). O.E. was supported by NIH grants UL1TR002384, R01CA194547 and P01CA214274, LLS SCOR grants 180078-01 and 7021-20 and Starr Cancer Consortium grant I11-0027. H. Lochmüller was supported by the CIHR Foundation Grant on Precision Health for Neuromuscular Diseases FDN-167281. R.T. was supported by CIHR postdoctoral fellowship award MFE-171275. L.D.S. was supported by Genome Canada and NIH NHGRI U24HG011025. S.O. was supported by AMED. D.P., L.M., A.P., S.B., M.R. and R.K. were supported by EU Horizon 2020 research and innovation programme grant agreements 779257 (Solve-RD) and 825575 (EJP-RD). R.R.F. was supported by NLM contract 75N97019P00280.

PY - 2022/6/1

Y1 - 2022/6/1

UR - https://www.scopus.com/pages/publications/85132078778

U2 - 10.1038/s41587-022-01357-4

DO - 10.1038/s41587-022-01357-4

M3 - Comment/Letter to the editor

C2 - 35705716

SN - 1087-0156

VL - 40

SP - 817

EP - 820

JO - Nature Biotechnology

JF - Nature Biotechnology

IS - 6

ER -

The GA4GH Phenopacket schema defines a computable representation of clinical data

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