دورية أكاديمية
أعرض في EDS

KG-Hub-building and exchanging biological knowledge graphs.

التفاصيل البيبلوغرافية
العنوان: KG-Hub-building and exchanging biological knowledge graphs.
المؤلفون: Caufield JH; Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States., Putman T; Anschutz Medical Campus, University of Colorado, Aurora, CO 80045, United States., Schaper K; Anschutz Medical Campus, University of Colorado, Aurora, CO 80045, United States., Unni DR; SIB Swiss Institute of Bioinformatics, Basel 1015, Switzerland., Hegde H; Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States., Callahan TJ; Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY 10032, United States., Cappelletti L; Department of Computer Science, University of Milano, Milan 20126, Italy., Moxon SAT; Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States., Ravanmehr V; Department of Lymphoma-Myeloma, MD Anderson Cancer Center, Houston, TX 77030, United States., Carbon S; Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States., Chan LE; College of Public Health and Human Sciences, Oregon State University, Corvallis, OR 97331, United States., Cortes K; Anschutz Medical Campus, University of Colorado, Aurora, CO 80045, United States., Shefchek KA; Anschutz Medical Campus, University of Colorado, Aurora, CO 80045, United States., Elsarboukh G; Anschutz Medical Campus, University of Colorado, Aurora, CO 80045, United States., Balhoff J; Renaissance Computing Institute, University of North Carolina, Chapel Hill, NC 27517, United States., Fontana T; Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Milan 20133, Italy., Matentzoglu N; Semanticly, Athens, Greece., Bruskiewich RM; STAR Informatics, Delphinai Corporation, Sooke, BC V9Z 0M3, Canada., Thessen AE; Anschutz Medical Campus, University of Colorado, Aurora, CO 80045, United States., Harris NL; Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States., Munoz-Torres MC; Anschutz Medical Campus, University of Colorado, Aurora, CO 80045, United States., Haendel MA; Anschutz Medical Campus, University of Colorado, Aurora, CO 80045, United States., Robinson PN; The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, United States., Joachimiak MP; Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States., Mungall CJ; Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States., Reese JT; Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States.
المصدر: Bioinformatics (Oxford, England) [Bioinformatics] 2023 Jul 01; Vol. 39 (7).
نوع المنشور: Journal Article; Research Support, N.I.H., Extramural; Research Support, U.S. Gov't, Non-P.H.S.
اللغة: English
بيانات الدورية: Publisher: Oxford University Press Country of Publication: England NLM ID: 9808944 Publication Model: Print Cited Medium: Internet ISSN: 1367-4811 (Electronic) Linking ISSN: 13674803 NLM ISO Abbreviation: Bioinformatics Subsets: MEDLINE
أسماء مطبوعة: Original Publication: Oxford : Oxford University Press, c1998-
مواضيع طبية MeSH: COVID-19* , Biological Ontologies*, Humans ; Pattern Recognition, Automated ; Rare Diseases ; Machine Learning
مستخلص: Motivation: Knowledge graphs (KGs) are a powerful approach for integrating heterogeneous data and making inferences in biology and many other domains, but a coherent solution for constructing, exchanging, and facilitating the downstream use of KGs is lacking.
Results: Here we present KG-Hub, a platform that enables standardized construction, exchange, and reuse of KGs. Features include a simple, modular extract-transform-load pattern for producing graphs compliant with Biolink Model (a high-level data model for standardizing biological data), easy integration of any OBO (Open Biological and Biomedical Ontologies) ontology, cached downloads of upstream data sources, versioned and automatically updated builds with stable URLs, web-browsable storage of KG artifacts on cloud infrastructure, and easy reuse of transformed subgraphs across projects. Current KG-Hub projects span use cases including COVID-19 research, drug repurposing, microbial-environmental interactions, and rare disease research. KG-Hub is equipped with tooling to easily analyze and manipulate KGs. KG-Hub is also tightly integrated with graph machine learning (ML) tools which allow automated graph ML, including node embeddings and training of models for link prediction and node classification.
Availability and Implementation: https://kghub.org.
(© The Author(s) 2023. Published by Oxford University Press.)
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معلومات مُعتمدة: #1RM1HG010860-01 United States HG NHGRI NIH HHS; U24 GM143402 United States GM NIGMS NIH HHS; OT2 TR003449 United States TR NCATS NIH HHS; R24 OD011883 United States OD NIH HHS; U24 HG011449 United States HG NHGRI NIH HHS; U01 CA239108 United States CA NCI NIH HHS; RM1 HG010860 United States HG NHGRI NIH HHS
تواريخ الأحداث: Date Created: 20230630 Date Completed: 20230713 Latest Revision: 20240425
رمز التحديث: 20240425
مُعرف محوري في PubMed: PMC10336030
DOI: 10.1093/bioinformatics/btad418
PMID: 37389415
قاعدة البيانات: MEDLINE
الوصف
تدمد:1367-4811
DOI:10.1093/bioinformatics/btad418