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Journal article
Biolink Model: A universal schema for knowledge graphs in clinical, biomedical, and translational science
Clinical and Translational Science, v 15(8), pp 1848-1855
01 Aug 2022
Featured in Collection : UN Sustainable Development Goals @ Drexel
Abstract
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.
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52 citations in Scopus
Details
- Title
- Biolink Model: A universal schema for knowledge graphs in clinical, biomedical, and translational science
- Creators
- Deepak R UnniSierra AT MoxonMichael BadaMatthew Brush - University of North Carolina at Chapel HillRichard BruskiewichJ Harry CaufieldPaul A Clemons - Agency for Science, Technology and ResearchMichel Dumontier - Maastricht UniversityKaramarie Fecho - University of North Carolina at Chapel HillGustavo GlusmanJennifer J Hadlock - Institute for Systems BiologyNomi L HarrisArpita JoshiTim PutmanGuangrong Qin - Institute for Systems BiologyStephen A Ramsey - Oregon State UniversityKent A ShefchekHarold SolbrigKarthik Soman - University of California, San FranciscoAnne E ThessenMelissa A Haendel - Oregon Health & Science UniversityChris Bizon - Renaissance Computing InstituteChristopher J Mungall - Lawrence Berkeley National LaboratoryThe Biomedical Data Translator ConsortiumLiliana AcevedoStanley C AhaltJohn AldenAhmed AlkanaqNada AminRicardo AvilaJim BalhoffSergio E Baranzini - University of California, San FranciscoAndrew BaumgartnerWilliam BaumgartnerBasazin BelhuMacKenzie BrandesNamdi BrandonNoel BurttWilliam Byrd - University of Alabama at BirminghamJackson CallaghanMarco Alvarado CanoSteven CarrellRemzi CelebiJames ChampionZhehuan ChenMei‐Jan ChenLawrence Chung - Columbia UniversityKevin CohenTom ConlinDan CorkillMaria Costanzo - National Heart Foundation of AustraliaSteven CoxAndrew Crouse - University of Alabama at BirminghamCamerron CrowderMary E CrumbleyCheng DaiVlado DančíkRicardo De Miranda AzevedoEric Deutsch - Institute for Systems BiologyJennifer DoughertyMarc P DubyVenkata DuvvuriStephen EdwardsVincent EmonetNathaniel FehrmannJason FlannickAleksandra M Foksinska - University of Alabama at BirminghamVicki GardnerEdgar GaticaAmy GlenPrateek Goel - Drexel University, Information Science (Informatics)Joseph GormleyAlon GreyberPerry HaalandKristina HanspersKaiwen He - University of Alabama at BirminghamJeff HenricksonEugene W HindererMaureen HoatlinAndrew HoffmanSui Huang - Institute for Systems BiologyConrad HuangRobert Hubal - University of North Carolina at Chapel HillKenneth Huellas-BruskiewiczForest B HulsLawrence HunterGreg HydeTursynay IssabekovaMatthew JarrellLindsay JenkinsAdam JohsJimin KangRicha KanwarYaphet KebedeKeum Joo KimAlexandria KlugeMichael KnowlesRyan Koesterer
- Publication Details
- Clinical and Translational Science, v 15(8), pp 1848-1855
- Publisher
- eScholarship, University of California
- Number of pages
- 1848 - 1855
- Resource Type
- Journal article
- Language
- English
- Academic Unit
- Information Science (Informatics); Computer Science (Computing)
- Other Identifier
- 991019238527704721
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- Collaboration types
- Domestic collaboration
- International collaboration
- Web of Science research areas
- Medicine, Research & Experimental