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The Monarch Initiative in 2024: an analytic platform integrating phenotypes, genes and diseases across species.
Putman, Tim E; Schaper, Kevin; Matentzoglu, Nicolas; Rubinetti, Vincent P; Alquaddoomi, Faisal S; Cox, Corey; Caufield, J Harry; Elsarboukh, Glass; Gehrke, Sarah; Hegde, Harshad; Reese, Justin T; Braun, Ian; Bruskiewich, Richard M; Cappelletti, Luca; Carbon, Seth; Caron, Anita R; Chan, Lauren E; Chute, Christopher G; Cortes, Katherina G; De Souza, Vinícius; Fontana, Tommaso; Harris, Nomi L; Hartley, Emily L; Hurwitz, Eric; Jacobsen, Julius O B; Krishnamurthy, Madan; Laraway, Bryan J; McLaughlin, James A; McMurry, Julie A; Moxon, Sierra A T; Mullen, Kathleen R; O'Neil, Shawn T; Shefchek, Kent A; Stefancsik, Ray; Toro, Sabrina; Vasilevsky, Nicole A; Walls, Ramona L; Whetzel, Patricia L; Osumi-Sutherland, David; Smedley, Damian; Robinson, Peter N; Mungall, Christopher J; Haendel, Melissa A; Munoz-Torres, Monica C.
Afiliación
  • Putman TE; Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.
  • Schaper K; Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.
  • Matentzoglu N; Independent Consultant, Semanticly, Athens, Greece.
  • Rubinetti VP; Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.
  • Alquaddoomi FS; Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.
  • Cox C; Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.
  • Caufield JH; Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
  • Elsarboukh G; Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.
  • Gehrke S; Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.
  • Hegde H; Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
  • Reese JT; Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
  • Braun I; Data Collaboration Center, Critical Path Institute, Tucson, AZ 85718, USA.
  • Bruskiewich RM; STAR Informatics, Delphinai Corporation, Sooke, BC V9Z 0M3, Canada.
  • Cappelletti L; Biology, University of Fribourg, Fribourg, Switzerland.
  • Carbon S; Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
  • Caron AR; European Bioinformatics Institute (EMBL-EBI), Hinxton CB10 1SD, UK.
  • Chan LE; College of Public Health and Human Sciences, Oregon State University, Corvallis, OR 97331, USA.
  • Chute CG; Schools of Medicine, Public Health, and Nursing, Johns Hopkins University, Baltimore, MD 21205, USA.
  • Cortes KG; Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.
  • De Souza V; European Bioinformatics Institute (EMBL-EBI), Hinxton CB10 1SD, UK.
  • Fontana T; Dipartimento di Informatica, Università degli Studi di Milano Statale, Milano, Italy.
  • Harris NL; Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
  • Hartley EL; Data Collaboration Center, Critical Path Institute, Tucson, AZ 85718, USA.
  • Hurwitz E; Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.
  • Jacobsen JOB; William Harvey Research Institute, Queen Mary University of London, London EC1M 6BQ, UK.
  • Krishnamurthy M; Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.
  • Laraway BJ; Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.
  • McLaughlin JA; European Bioinformatics Institute (EMBL-EBI), Hinxton CB10 1SD, UK.
  • McMurry JA; Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.
  • Moxon SAT; Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
  • Mullen KR; Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.
  • O'Neil ST; Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.
  • Shefchek KA; Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.
  • Stefancsik R; European Bioinformatics Institute (EMBL-EBI), Hinxton CB10 1SD, UK.
  • Toro S; Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.
  • Vasilevsky NA; Data Collaboration Center, Critical Path Institute, Tucson, AZ 85718, USA.
  • Walls RL; Data Collaboration Center, Critical Path Institute, Tucson, AZ 85718, USA.
  • Whetzel PL; Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.
  • Osumi-Sutherland D; European Bioinformatics Institute (EMBL-EBI), Hinxton CB10 1SD, UK.
  • Smedley D; William Harvey Research Institute, Queen Mary University of London, London EC1M 6BQ, UK.
  • Robinson PN; The Jackson Laboratory for Genomic Medicine, Farmington, CT 6032, USA.
  • Mungall CJ; Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
  • Haendel MA; Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.
  • Munoz-Torres MC; Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.
Nucleic Acids Res ; 52(D1): D938-D949, 2024 Jan 05.
Article en En | MEDLINE | ID: mdl-38000386
ABSTRACT
Bridging the gap between genetic variations, environmental determinants, and phenotypic outcomes is critical for supporting clinical diagnosis and understanding mechanisms of diseases. It requires integrating open data at a global scale. The Monarch Initiative advances these goals by developing open ontologies, semantic data models, and knowledge graphs for translational research. The Monarch App is an integrated platform combining data about genes, phenotypes, and diseases across species. Monarch's APIs enable access to carefully curated datasets and advanced analysis tools that support the understanding and diagnosis of disease for diverse applications such as variant prioritization, deep phenotyping, and patient profile-matching. We have migrated our system into a scalable, cloud-based infrastructure; simplified Monarch's data ingestion and knowledge graph integration systems; enhanced data mapping and integration standards; and developed a new user interface with novel search and graph navigation features. Furthermore, we advanced Monarch's analytic tools by developing a customized plugin for OpenAI's ChatGPT to increase the reliability of its responses about phenotypic data, allowing 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 at monarchinitiative.org and its corresponding code repository at github.com/monarch-initiative/monarch-app.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Contexto en salud: 1_ASSA2030 Problema de salud: 1_geracao_evidencia_conhecimento Asunto principal: Fenotipo / Enfermedad / Bases de Datos Factuales / Genes Límite: Humans Idioma: En Revista: Nucleic Acids Res Año: 2024 Tipo del documento: Article País de afiliación: Estados Unidos
Texto completo
Añadir a Mi BVS
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XML
PubMed Links
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Contexto en salud: 1_ASSA2030 Problema de salud: 1_geracao_evidencia_conhecimento Asunto principal: Fenotipo / Enfermedad / Bases de Datos Factuales / Genes Límite: Humans Idioma: En Revista: Nucleic Acids Res Año: 2024 Tipo del documento: Article País de afiliación: Estados Unidos