The Monarch Initiative in 2024:ãnãnalytic platform integrating phenotypes, g enesãnd diseasesãcross species

Tim E. Putman; Kevin Schaper; Nicolas Matentzoglu; Vincent P. Rubinetti; Faisal S. Alquaddoomi; Corey Cox; J. Harry Caufield; Glass Elsarboukh; Sarah Gehrke; Harshad Hegde; Justin T. Reese; Ian Braun; Richard M. Bruskiewich; Luca Cappelletti; Seth Carbon; Anita R. Caron; Lauren E. Chan; Christopher G. Chute; Katherina G. Cortes; Vinícius De Souza; Tommaso Fontana; Nomi L. Harris; Emily L. Hartley; Eric Hurwitz; Julius O.B. Jacobsen; Madan Krishnamurthy; Bryan J. Laraway; James A. McLaughlin; Julie A. McMurry; Sierra A.T. Moxon; Kathleen R. Mullen; Shawn T. O'Neil; Kent A. Shefchek; Ray Stefancsik; Sabrina Toro; Nicole A. Vasilevsky; Ramona L. Walls; Patricia L. Whetzel; David Osumi-Sutherland; Damian Smedley; Peter N. Robinson; Christopher J. Mungall; Melissa A. Haendel; Monica C. Munoz-Torres

doi:10.1093/nar/gkad1082

The Monarch Initiative in 2024:ãnãnalytic platform integrating phenotypes, g enesãnd diseasesãcross species

Tim E. Putman, Kevin Schaper, Nicolas Matentzoglu, Vincent P. Rubinetti, Faisal S. Alquaddoomi, Corey Cox, J. Harry Caufield, Glass Elsarboukh, Sarah Gehrke, Harshad Hegde, Justin T. Reese, Ian Braun, Richard M. Bruskiewich, Luca Cappelletti, Seth Carbon, Anita R. Caron, Lauren E. Chan, Christopher G. Chute, Katherina G. Cortes, Vinícius De SouzaTommaso Fontana, Nomi L. Harris, Emily L. Hartley, Eric Hurwitz, Julius O.B. Jacobsen, Madan Krishnamurthy, Bryan J. Laraway, James A. McLaughlin, Julie A. McMurry, Sierra A.T. Moxon, Kathleen R. Mullen, Shawn T. O'Neil, Kent A. Shefchek, Ray Stefancsik, Sabrina Toro, Nicole A. Vasilevsky, Ramona L. Walls, Patricia L. Whetzel, David Osumi-Sutherland, Damian Smedley, Peter N. Robinson, Christopher J. Mungall, Melissa A. Haendel, Monica C. Munoz-Torres

Software Engineering

Research output: Contribution to journal › Article › peer-review

16 Scopus citations

Abstract

Bridging the gap between genetic vãriations, en vironmentãl determinants,ãnd phenot ypic outcomes is critical for supporting clinical diagnosisãnd understanding mechanisms of diseases. It requires integrating open dataãtã global scale. The Monarch Initiativeãdvances these goals b y de v eloping open ontologies, semantic data models,ãnd kno wledge graphs f or translational research. T he Monarch App isãn integrated platform combining dataãbout genes, phenotypes,ãnd diseasesãcross species. Monarch's APIs enableãccess to carefully curated datasetsãndãdvãncedãnaly sis tools that support the understandingãnd diagnosis of disease for diverseãpplications suchãs variant prioritization, deep phenot yping ,ãnd patient profile-matching . We ha v e migrated our sy stem intoã scalable, cloud-based infrastr uct ure; simplified Monarch's data ingestionãnd knowledge graph integration systems; enhanced data mappingãnd integration standards;ãnd de v elopedã ne w user interfãce with no v el searchãnd graph navigation features. Furthermore, weãdvanced Monarch'sãnalytic tools by developingã customized plugin for OpenAI's ChatGPT to increase the reliability of its responsesãbout phenot ypic datã,ãllowing us to interrogate the knowledge in the Monarch graph using state-of-the-art Large Language Models. The resources of the Monarch Initiative can be foundãt monarchinitiative.orgãnd its corresponding code repositoryãt github.com / monarc h-initiative / monarc h-app.

Original language	English
Pages (from-to)	D938-D949
Journal	Nucleic Acids Research
Volume	52
Issue number	D1
DOIs	https://doi.org/10.1093/nar/gkad1082
State	Published - Jan 5 2024

Funding

Office of the Director National Institute of Health [5R24OD011883-12, 3R24OD011883-11S1]; NIH National Human Genome Research Institute [5RM1HG010860-04, 3RM1HG010860-03S1, 5U24HG011449-03]; NIH National Library of Medicine [T15LM009451]; J.R., S.C., S.M., H.H., N.L.H., C.J.M. and J.H.C. were partly supported by the Director, Office of Science, Office of Basic Energy Sciences, of the U.S. Department of Energy [DE-AC02-05CH11231]; Critical Path Institute is supported by the Food and Drug Administration (FDA) of the U.S. Department of Health and Human Services (HHS) and FDA/HHS (56.5%), totaling $16749891, and by non-government sources (43.5%), totaling $12895366. Funding for open access charge: NIH [5R24OD011883-12].

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10.1093/nar/gkad1082

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Putman, T. E., Schaper, K., Matentzoglu, N., Rubinetti, V. P., Alquaddoomi, F. S., Cox, C., Caufield, J. H., Elsarboukh, G., Gehrke, S., Hegde, H., Reese, J. T., Braun, I., Bruskiewich, R. M., Cappelletti, L., Carbon, S., Caron, A. R., Chan, L. E., Chute, C. G., Cortes, K. G., ... Munoz-Torres, M. C. (2024). The Monarch Initiative in 2024:ãnãnalytic platform integrating phenotypes, g enesãnd diseasesãcross species. Nucleic Acids Research, 52(D1), D938-D949. https://doi.org/10.1093/nar/gkad1082

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title = "The Monarch Initiative in 2024:{\~a}n{\~a}nalytic platform integrating phenotypes, g enes{\~a}nd diseases{\~a}cross species",

abstract = "Bridging the gap between genetic v{\~a}riations, en vironment{\~a}l determinants,{\~a}nd phenot ypic outcomes is critical for supporting clinical diagnosis{\~a}nd understanding mechanisms of diseases. It requires integrating open data{\~a}t{\~a} global scale. The Monarch Initiative{\~a}dvances these goals b y de v eloping open ontologies, semantic data models,{\~a}nd kno wledge graphs f or translational research. T he Monarch App is{\~a}n integrated platform combining data{\~a}bout genes, phenotypes,{\~a}nd diseases{\~a}cross species. Monarch's APIs enable{\~a}ccess to carefully curated datasets{\~a}nd{\~a}dv{\~a}nced{\~a}naly sis tools that support the understanding{\~a}nd diagnosis of disease for diverse{\~a}pplications such{\~a}s variant prioritization, deep phenot yping ,{\~a}nd patient profile-matching . We ha v e migrated our sy stem into{\~a} scalable, cloud-based infrastr uct ure; simplified Monarch's data ingestion{\~a}nd knowledge graph integration systems; enhanced data mapping{\~a}nd integration standards;{\~a}nd de v eloped{\~a} ne w user interf{\~a}ce with no v el search{\~a}nd graph navigation features. Furthermore, we{\~a}dvanced Monarch's{\~a}nalytic tools by developing{\~a} customized plugin for OpenAI's ChatGPT to increase the reliability of its responses{\~a}bout phenot ypic dat{\~a},{\~a}llowing us to interrogate the knowledge in the Monarch graph using state-of-the-art Large Language Models. The resources of the Monarch Initiative can be found{\~a}t monarchinitiative.org{\~a}nd its corresponding code repository{\~a}t github.com / monarc h-initiative / monarc h-app.",

author = "Putman, {Tim E.} and Kevin Schaper and Nicolas Matentzoglu and Rubinetti, {Vincent P.} and Alquaddoomi, {Faisal S.} and Corey Cox and Caufield, {J. Harry} and Glass Elsarboukh and Sarah Gehrke and Harshad Hegde and Reese, {Justin T.} and Ian Braun and Bruskiewich, {Richard M.} and Luca Cappelletti and Seth Carbon and Caron, {Anita R.} and Chan, {Lauren E.} and Chute, {Christopher G.} and Cortes, {Katherina G.} and {De Souza}, Vin{\'i}cius and Tommaso Fontana and Harris, {Nomi L.} and Hartley, {Emily L.} and Eric Hurwitz and Jacobsen, {Julius O.B.} and Madan Krishnamurthy and Laraway, {Bryan J.} and McLaughlin, {James A.} and McMurry, {Julie A.} and Moxon, {Sierra A.T.} and Mullen, {Kathleen R.} and O'Neil, {Shawn T.} and Shefchek, {Kent A.} and Ray Stefancsik and Sabrina Toro and Vasilevsky, {Nicole A.} and Walls, {Ramona L.} and Whetzel, {Patricia L.} and David Osumi-Sutherland and Damian Smedley and Robinson, {Peter N.} and Mungall, {Christopher J.} and Haendel, {Melissa A.} and Munoz-Torres, {Monica C.}",

note = "Publisher Copyright: {\textcopyright} The Author ( s ) 2023.",

year = "2024",

month = jan,

day = "5",

doi = "10.1093/nar/gkad1082",

language = "English",

volume = "52",

pages = "D938--D949",

journal = "Nucleic Acids Research",

issn = "0305-1048",

publisher = "Oxford University Press",

number = "D1",

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Putman, TE, Schaper, K, Matentzoglu, N, Rubinetti, VP, Alquaddoomi, FS, Cox, C, Caufield, JH, Elsarboukh, G, Gehrke, S, Hegde, H, Reese, JT, Braun, I, Bruskiewich, RM, Cappelletti, L, Carbon, S, Caron, AR, Chan, LE, Chute, CG, Cortes, KG, De Souza, V, Fontana, T, Harris, NL, Hartley, EL, Hurwitz, E, Jacobsen, JOB, Krishnamurthy, M, Laraway, BJ, McLaughlin, JA, McMurry, JA, Moxon, SAT, Mullen, KR, O'Neil, ST, Shefchek, KA, Stefancsik, R, Toro, S, Vasilevsky, NA, Walls, RL, Whetzel, PL, Osumi-Sutherland, D, Smedley, D, Robinson, PN, Mungall, CJ, Haendel, MA & Munoz-Torres, MC 2024, 'The Monarch Initiative in 2024:ãnãnalytic platform integrating phenotypes, g enesãnd diseasesãcross species', Nucleic Acids Research, vol. 52, no. D1, pp. D938-D949. https://doi.org/10.1093/nar/gkad1082

TY - JOUR

T1 - The Monarch Initiative in 2024:ãnãnalytic platform integrating phenotypes, g enesãnd diseasesãcross species

AU - Putman, Tim E.

AU - Schaper, Kevin

AU - Matentzoglu, Nicolas

AU - Rubinetti, Vincent P.

AU - Alquaddoomi, Faisal S.

AU - Cox, Corey

AU - Caufield, J. Harry

AU - Elsarboukh, Glass

AU - Gehrke, Sarah

AU - Hegde, Harshad

AU - Reese, Justin T.

AU - Braun, Ian

AU - Bruskiewich, Richard M.

AU - Cappelletti, Luca

AU - Carbon, Seth

AU - Caron, Anita R.

AU - Chan, Lauren E.

AU - Chute, Christopher G.

AU - Cortes, Katherina G.

AU - De Souza, Vinícius

AU - Fontana, Tommaso

AU - Harris, Nomi L.

AU - Hartley, Emily L.

AU - Hurwitz, Eric

AU - Jacobsen, Julius O.B.

AU - Krishnamurthy, Madan

AU - Laraway, Bryan J.

AU - McLaughlin, James A.

AU - McMurry, Julie A.

AU - Moxon, Sierra A.T.

AU - Mullen, Kathleen R.

AU - O'Neil, Shawn T.

AU - Shefchek, Kent A.

AU - Stefancsik, Ray

AU - Toro, Sabrina

AU - Vasilevsky, Nicole A.

AU - Walls, Ramona L.

AU - Whetzel, Patricia L.

AU - Osumi-Sutherland, David

AU - Smedley, Damian

AU - Robinson, Peter N.

AU - Mungall, Christopher J.

AU - Haendel, Melissa A.

AU - Munoz-Torres, Monica C.

PY - 2024/1/5

Y1 - 2024/1/5

N2 - Bridging the gap between genetic vãriations, en vironmentãl determinants,ãnd phenot ypic outcomes is critical for supporting clinical diagnosisãnd understanding mechanisms of diseases. It requires integrating open dataãtã global scale. The Monarch Initiativeãdvances these goals b y de v eloping open ontologies, semantic data models,ãnd kno wledge graphs f or translational research. T he Monarch App isãn integrated platform combining dataãbout genes, phenotypes,ãnd diseasesãcross species. Monarch's APIs enableãccess to carefully curated datasetsãndãdvãncedãnaly sis tools that support the understandingãnd diagnosis of disease for diverseãpplications suchãs variant prioritization, deep phenot yping ,ãnd patient profile-matching . We ha v e migrated our sy stem intoã scalable, cloud-based infrastr uct ure; simplified Monarch's data ingestionãnd knowledge graph integration systems; enhanced data mappingãnd integration standards;ãnd de v elopedã ne w user interfãce with no v el searchãnd graph navigation features. Furthermore, weãdvanced Monarch'sãnalytic tools by developingã customized plugin for OpenAI's ChatGPT to increase the reliability of its responsesãbout phenot ypic datã,ãllowing us to interrogate the knowledge in the Monarch graph using state-of-the-art Large Language Models. The resources of the Monarch Initiative can be foundãt monarchinitiative.orgãnd its corresponding code repositoryãt github.com / monarc h-initiative / monarc h-app.

AB - Bridging the gap between genetic vãriations, en vironmentãl determinants,ãnd phenot ypic outcomes is critical for supporting clinical diagnosisãnd understanding mechanisms of diseases. It requires integrating open dataãtã global scale. The Monarch Initiativeãdvances these goals b y de v eloping open ontologies, semantic data models,ãnd kno wledge graphs f or translational research. T he Monarch App isãn integrated platform combining dataãbout genes, phenotypes,ãnd diseasesãcross species. Monarch's APIs enableãccess to carefully curated datasetsãndãdvãncedãnaly sis tools that support the understandingãnd diagnosis of disease for diverseãpplications suchãs variant prioritization, deep phenot yping ,ãnd patient profile-matching . We ha v e migrated our sy stem intoã scalable, cloud-based infrastr uct ure; simplified Monarch's data ingestionãnd knowledge graph integration systems; enhanced data mappingãnd integration standards;ãnd de v elopedã ne w user interfãce with no v el searchãnd graph navigation features. Furthermore, weãdvanced Monarch'sãnalytic tools by developingã customized plugin for OpenAI's ChatGPT to increase the reliability of its responsesãbout phenot ypic datã,ãllowing us to interrogate the knowledge in the Monarch graph using state-of-the-art Large Language Models. The resources of the Monarch Initiative can be foundãt monarchinitiative.orgãnd its corresponding code repositoryãt github.com / monarc h-initiative / monarc h-app.

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U2 - 10.1093/nar/gkad1082

DO - 10.1093/nar/gkad1082

M3 - Article

C2 - 38000386

AN - SCOPUS:85181766041

SN - 0305-1048

VL - 52

SP - D938-D949

JO - Nucleic Acids Research

JF - Nucleic Acids Research

IS - D1

ER -

The Monarch Initiative in 2024:ãnãnalytic platform integrating phenotypes, g enesãnd diseasesãcross species

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