LinkML – A Linked Open Data Modeling Language

Lecture

Speaker(s)

Chris Mungall

Staff Scientist and Head of the Biosystems Data Science Department, Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, BIDS Research Affiliate

Chris Mungall is a Staff Scientist in the Environmental Genomics and Systems Biology Division at LBNL, where he heads the Biosystems Data Science department. He is a PI on the Gene Ontology (GO) project, and the Monarch Initiative, and metadata lead for the National Microbiome Data Collaborative (NMDC). His research focuses on combining knowledge-based methods and AI to investigate molecular mechanisms underpinning the health of humans and the health of the planet. In 2017 he received the International Society for Biocuration Exceptional Contributions to Biocuration Award.

Harold Solbrig

Assistant Professor, Johns Hopkins University

Harold Solbrig is an active contributor to healthcare information modeling, semantics and standards-based information exchange for 40+ years. He has served in multiple roles in the ISO, W3C, HL7 and other standards communities. He has a master’s degree in Software Engineering from Oxford University and is an assistant professor at Johns Hopkins University.

Wednesday, April 14, 2021

Harold Solbrig, an assistant professor at Johns Hopkins University, and BIDS Research Affiliate Chris Mungall, a staff scientist and the head of the Biosystems Data Science Department in the Environmental Genomics and Systems Biology Division of Lawrence Berkeley National Laboratory, presented this short introduction to the LinkML modeling language and tools as part of the Yosemite Project Webinar Series on Wednesday April. 14, 2021. Download slides

Abstract: LinkML is a modeling language and collection of tools that joins the data processing world with the semantic, making it possible for developers to continue to employ tools such as JSON, YAML, SQL, spreadsheets, etc., while _directly_ working with RDF and ontology based semantics. LinkML leverages and integrates technologies such as JSON-LD, Knowledge Graphs, RDF and Shape Expressions (ShEx), and provides an environment where semantics and data are seamlessly integrated and structural and representational transformations between communities can be based on the combination of RDF and ontology.

Why LinkML? Twenty years ago, Tim Berners-Lee coined the term “The Semantic Web” in a seminal article in Scientific American. While it is heartening to see how much of his vision has been realized, gaps still remain. Berners-Lee’s vision included the notion that the “Semantic Web is not a separate Web but an _extension_ of the current one, in which information is given well-defined meaning…”. While progress has been made in some areas (e.g. schema.org), the world of data and the world of semantics still exist in separate spaces. While tools and techniques exist to _transform_ (lift) data into the RDF space, to date these environments have been separate. LinkML helps to bridge this gap.

This webinar provides a short introduction to the LinkML modeling language and tools: how it came to be, what it can be used for today, how it is being used in biomedical research, and where the developers intend to take it in the future.

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