دورية أكاديمية
Biolink Model: A universal schema for knowledge graphs in clinical, biomedical, and translational science.
| العنوان: | Biolink Model: A universal schema for knowledge graphs in clinical, biomedical, and translational science. |
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| المؤلفون: | Unni DR; Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.; Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, California, USA., Moxon SAT; Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, California, USA., Bada M; Center for Health AI, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA., Brush M; Center for Health AI, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA., Bruskiewich R; Star Informatics, Sooke, British Columbia, Canada., Caufield JH; Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, California, USA., Clemons PA; Chemical Biology and Therapeutics Science Program, Broad Institute, Cambridge, Massachusetts, USA., Dancik V; Chemical Biology and Therapeutics Science Program, Broad Institute, Cambridge, Massachusetts, USA., Dumontier M; Institute of Data Science, Maastricht University, Maastricht, The Netherlands., Fecho K; Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA., Glusman G; Institute for Systems Biology, Seattle, Washington, USA., Hadlock JJ; Institute for Systems Biology, Seattle, Washington, USA., Harris NL; Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, California, USA., Joshi A; Institute for Systems Biology, Seattle, Washington, USA., Putman T; Center for Health AI, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA., Qin G; Institute for Systems Biology, Seattle, Washington, USA., Ramsey SA; Department of Biomedical Sciences, Oregon State University, Corvallis, Oregon, USA., Shefchek KA; Center for Health AI, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA., Solbrig H; Johns Hopkins University, Baltimore, Maryland, USA., Soman K; Department of Neurology, University of California San Francisco, San Francisco, California, USA., Thessen AE; Center for Health AI, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA., Haendel MA; Center for Health AI, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA., Bizon C; Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA., Mungall CJ; Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, California, USA. |
| مؤلفون مشاركون: | Biomedical Data Translator Consortium |
| المصدر: | Clinical and translational science [Clin Transl Sci] 2022 Aug; Vol. 15 (8), pp. 1848-1855. Date of Electronic Publication: 2022 Jun 06. |
| نوع المنشور: | Journal Article; Review; Research Support, U.S. Gov't, Non-P.H.S.; Research Support, N.I.H., Extramural |
| اللغة: | English |
| بيانات الدورية: | Publisher: WileyBlackwell Pub Country of Publication: United States NLM ID: 101474067 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1752-8062 (Electronic) Linking ISSN: 17528054 NLM ISO Abbreviation: Clin Transl Sci Subsets: MEDLINE |
| أسماء مطبوعة: | Original Publication: Malden, MA : WileyBlackwell Pub., 2008- |
| مواضيع طبية MeSH: | Pattern Recognition, Automated* , Translational Science, Biomedical*, Knowledge |
| مستخلص: | Within clinical, biomedical, and translational science, an increasing number of projects are adopting graphs for knowledge representation. Graph-based data models elucidate the interconnectedness among core biomedical concepts, enable data structures to be easily updated, and support intuitive queries, visualizations, and inference algorithms. However, knowledge discovery across these "knowledge graphs" (KGs) has remained difficult. Data set heterogeneity and complexity; the proliferation of ad hoc data formats; poor compliance with guidelines on findability, accessibility, interoperability, and reusability; and, in particular, the lack of a universally accepted, open-access model for standardization across biomedical KGs has left the task of reconciling data sources to downstream consumers. Biolink Model is an open-source data model that can be used to formalize the relationships between data structures in translational science. It incorporates object-oriented classification and graph-oriented features. The core of the model is a set of hierarchical, interconnected classes (or categories) and relationships between them (or predicates) representing biomedical entities such as gene, disease, chemical, anatomic structure, and phenotype. The model provides class and edge attributes and associations that guide how entities should relate to one another. Here, we highlight the need for a standardized data model for KGs, describe Biolink Model, and compare it with other models. We demonstrate the utility of Biolink Model in various initiatives, including the Biomedical Data Translator Consortium and the Monarch Initiative, and show how it has supported easier integration and interoperability of biomedical KGs, bringing together knowledge from multiple sources and helping to realize the goals of translational science. (© 2022 The Authors. Clinical and Translational Science published by Wiley Periodicals LLC on behalf of American Society for Clinical Pharmacology and Therapeutics.) |
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| معلومات مُعتمدة: | OT3TR002019 National Center for Advancing Translational Sciences, Biomedical Data Translator Program; OT2TR003445 National Center for Advancing Translational Sciences, Biomedical Data Translator Program; OT2TR003449 National Center for Advancing Translational Sciences, Biomedical Data Translator Program; OT2TR002515 National Center for Advancing Translational Sciences, Biomedical Data Translator Program; OT2TR002584 National Center for Advancing Translational Sciences, Biomedical Data Translator Program; OT2TR003434 National Center for Advancing Translational Sciences, Biomedical Data Translator Program; RM1 HG010860 United States HG NHGRI NIH HHS; OT2TR003433 National Center for Advancing Translational Sciences, Biomedical Data Translator Program; OT2TR003435 National Center for Advancing Translational Sciences, Biomedical Data Translator Program; OT2TR002517 National Center for Advancing Translational Sciences, Biomedical Data Translator Program; OT3TR002027 National Center for Advancing Translational Sciences, Biomedical Data Translator Program; OT2TR003422 National Center for Advancing Translational Sciences, Biomedical Data Translator Program; OT2TR003441 National Center for Advancing Translational Sciences, Biomedical Data Translator Program; OT3TR002020 National Center for Advancing Translational Sciences, Biomedical Data Translator Program; OT3 TR002019 United States TR NCATS NIH HHS; OT2TR003448 National Center for Advancing Translational Sciences, Biomedical Data Translator Program; OT2TR003428 National Center for Advancing Translational Sciences, Biomedical Data Translator Program; OT2TR002520 National Center for Advancing Translational Sciences, Biomedical Data Translator Program; OT2TR003427 National Center for Advancing Translational Sciences, Biomedical Data Translator Program; OT2TR003436 National Center for Advancing Translational Sciences, Biomedical Data Translator Program; OT2TR002514 National Center for Advancing Translational Sciences, Biomedical Data Translator Program; R24 OD011883 United States OD NIH HHS; OT2TR003443 National Center for Advancing Translational Sciences, Biomedical Data Translator Program; OT3TR002025 National Center for Advancing Translational Sciences, Biomedical Data Translator Program; OT2 TR003428 United States TR NCATS NIH HHS; OT2TR003437 National Center for Advancing Translational Sciences, Biomedical Data Translator Program; OT2TR003450 National Center for Advancing Translational Sciences, Biomedical Data Translator Program; OT3TR002026 National Center for Advancing Translational Sciences, Biomedical Data Translator Program; OT2TR003430 National Center for Advancing Translational Sciences, Biomedical Data Translator Program |
| فهرسة مساهمة: | Investigator: L Acevedo; SC Ahalt; J Alden; A Alkanaq; N Amin; R Avila; J Balhoff; SE Baranzini; A Baumgartner; W Baumgartner; B Belhu; M Brandes; N Brandon; N Burtt; W Byrd; J Callaghan; MA Cano; S Carrell; R Celebi; J Champion; Z Chen; MJ Chen; L Chung; K Cohen; T Conlin; D Corkill; M Costanzo; S Cox; A Crouse; C Crowder; ME Crumbley; C Dai; V Dančík; R De Miranda Azevedo; E Deutsch; J Dougherty; MP Duby; V Duvvuri; S Edwards; V Emonet; N Fehrmann; J Flannick; AM Foksinska; V Gardner; E Gatica; A Glen; P Goel; J Gormley; A Greyber; P Haaland; K Hanspers; K He; K He; J Henrickson; EW Hinderer; M Hoatlin; A Hoffman; S Huang; C Huang; R Hubal; K Huellas-Bruskiewicz; FB Huls; L Hunter; G Hyde; T Issabekova; M Jarrell; L Jenkins; A Johs; J Kang; R Kanwar; Y Kebede; KJ Kim; A Kluge; M Knowles; R Koesterer; D Korn; D Koslicki; A Krishnamurthy; L Kvarfordt; J Lee; M Leigh; J Lin; Z Liu; S Liu; C Ma; A Magis; T Mamidi; M Mandal; M Mantilla; J Massung; D Mauldin; J McClelland; J McMurry; P Mease; L Mendoza; M Mersmann; A Mesbah; M Might; K Morton; S Muller; AT Muluka; J Osborne; P Owen; M Patton; DB Peden; RC Peene; B Persaud; E Pfaff; A Pico; E Pollard; G Price; S Raj; J Reilly; A Riutta; J Roach; RT Roper; G Rosenblatt; I Rubin; S Rucka; N Rudavsky-Brody; R Sakaguchi; E Santos; K Schaper; CP Schmitt; S Schurman; E Scott; S Seitanakis; P Sharma; I Shmulevich; M Shrestha; S Shrivastava; M Sinha; B Smith; N Southall; N Southern; L Stillwell; MM Strasser; AI Su; C Ta; AE Thessen; J Tinglin; L Tonstad; T Tran-Nguyen; A Tropsha; G Vaidya; L Veenhuis; A Viola; M von Grotthuss; M Wang; P Wang; PB Watkins; R Weber; Q Wei; C Weng; J Whitlock; MD Williams; A Williams; F Womack; E Wood; C Wu; JK Xin; H Xu; C Xu; C Yakaboski; Y Yao; H Yi; A Yilmaz; M Zheng; X Zhou; E Zhou; Q Zhu; T Zisk |
| تواريخ الأحداث: | Date Created: 20220920 Date Completed: 20220922 Latest Revision: 20230411 |
| رمز التحديث: | 20240628 |
| مُعرف محوري في PubMed: | PMC9372416 |
| DOI: | 10.1111/cts.13302 |
| PMID: | 36125173 |
| قاعدة البيانات: | MEDLINE |
Full Text Finder | تدمد: | 1752-8062 |
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| DOI: | 10.1111/cts.13302 |