The Monarch Initiative in 2024: an analytic platform integrating phenotypes, genes and diseases across species.

التفاصيل البيبلوغرافية
العنوان:	The Monarch Initiative in 2024: an analytic platform integrating phenotypes, genes and diseases across species.
المؤلفون:	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.
المصدر:	Nucleic acids research [Nucleic Acids Res] 2024 Jan 05; Vol. 52 (D1), pp. D938-D949.
نوع المنشور:	Journal Article
اللغة:	English
بيانات الدورية:	Publisher: Oxford University Press Country of Publication: England NLM ID: 0411011 Publication Model: Print Cited Medium: Internet ISSN: 1362-4962 (Electronic) Linking ISSN: 03051048 NLM ISO Abbreviation: Nucleic Acids Res Subsets: MEDLINE
أسماء مطبوعة:	Publication: 1992- : Oxford : Oxford University Press Original Publication: London, Information Retrieval ltd.
مواضيع طبية MeSH:	Phenotype* , Databases, Factual/standards , Genes/genetics , Disease*/genetics, Humans ; Internet ; Software
مستخلص:	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. (© The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research.)
References:	Am J Hum Genet. 2009 Apr;84(4):524-33. (PMID: 19344873) J Biomed Inform. 2009 Jun;42(3):530-9. (PMID: 19475726) J Transl Med. 2023 Feb 25;21(1):148. (PMID: 36829165) Clin Transl Sci. 2022 May 25;:. (PMID: 35611543) Nat Biotechnol. 2022 Jun;40(6):817-820. (PMID: 35705716) BioData Min. 2023 Jul 13;16(1):20. (PMID: 37443040) BMC Bioinformatics. 2013 Jun 21;14:203. (PMID: 23800157) Nucleic Acids Res. 2012 Jan;40(Database issue):D700-5. (PMID: 22110037) Methods Mol Biol. 2013;983:59-92. (PMID: 23494302) Nucleic Acids Res. 2019 Jan 8;47(D1):D607-D613. (PMID: 30476243) Nucleic Acids Res. 2021 Jan 8;49(D1):D1207-D1217. (PMID: 33264411) Genetics. 2023 May 4;224(1):. (PMID: 36755307) Nucleic Acids Res. 2022 Jan 7;50(D1):D988-D995. (PMID: 34791404) Nucleic Acids Res. 2019 Jan 8;47(D1):D1186-D1194. (PMID: 30407590) Nucleic Acids Res. 2020 Jan 8;48(D1):D704-D715. (PMID: 31701156) Protein Sci. 2022 Jan;31(1):8-22. (PMID: 34717010) Genetics. 2022 Apr 4;220(4):. (PMID: 35166825) Proc Natl Acad Sci U S A. 2010 Apr 6;107(14):6544-9. (PMID: 20308572) Nucleic Acids Res. 2022 Jan 7;50(D1):D687-D692. (PMID: 34788843) Nucleic Acids Res. 2021 Jan 8;49(D1):D981-D987. (PMID: 33231642) Nat Comput Sci. 2023 Jun;3(6):552-568. (PMID: 38177435) Bioinformatics. 2023 Jul 1;39(7):. (PMID: 37389415) Database (Oxford). 2022 May 25;2022:. (PMID: 35616100) Nucleic Acids Res. 2023 Jan 6;51(D1):D1003-D1009. (PMID: 36243972) Genes (Basel). 2020 Apr 23;11(4):. (PMID: 32340307) Genetics. 2022 Apr 4;220(4):. (PMID: 35380658) Nucleic Acids Res. 2005 Jan 1;33(Database issue):D514-7. (PMID: 15608251) Genome Biol. 2012 Jan 31;13(1):R5. (PMID: 22293552) Genetics. 2022 Apr 4;220(4):. (PMID: 35266522) Database (Oxford). 2022 Oct 8;2022:. (PMID: 36208225) Genetics. 2023 May 4;224(1):. (PMID: 36866529) Nat Protoc. 2015 Dec;10(12):2004-15. (PMID: 26562621) Mamm Genome. 2023 Sep;34(3):364-378. (PMID: 37076585) Nucleic Acids Res. 2017 Jan 4;45(D1):D712-D722. (PMID: 27899636) Clin Transl Sci. 2022 Aug;15(8):1848-1855. (PMID: 36125173) Genetics. 2022 Apr 4;220(4):. (PMID: 35100366) Nucleic Acids Res. 2021 Jan 8;49(D1):D831-D847. (PMID: 33037820) Genetics. 2022 Apr 4;220(4):. (PMID: 35134929) F1000Res. 2013 Feb 01;2:30. (PMID: 24358873)
معلومات مُعتمدة:	T15 LM009451 United States LM NLM NIH HHS; 5RM1HG010860-04 United States HG NHGRI NIH HHS; R24 OD011883 United States OD NIH HHS; U24 HG011449 United States HG NHGRI NIH HHS; RM1 HG010860 United States HG NHGRI NIH HHS; T15LM009451 United States LM NLM NIH HHS
تواريخ الأحداث:	Date Created: 20231124 Date Completed: 20240111 Latest Revision: 20240331
رمز التحديث:	20240331
مُعرف محوري في PubMed:	PMC10767791
DOI:	10.1093/nar/gkad1082
PMID:	38000386
قاعدة البيانات:	MEDLINE

Full Text Finder

الوصف
تدمد:	1362-4962
DOI:	10.1093/nar/gkad1082