ISCBacademy webinar Oct 3
Sierra Moxon to speak about “LinkML: an open data modeling framework, grounded with ontologies”
[If you missed the webinar, the video is here and the slides are here.]
ISCBacademy is a series of free webinars sponsored by the International Society for Computational Biology. They are open to all, including those who are not ISCB members. ISCB members can access the webinars via the ISCB Nucleus platform: https://iscb.junolive.co/. Non-members need to register for Nucleus: https://iscb.swoogo.com/ISCBnucleus-registration
BOSC and Bio-Ontologies are pleased to co-host an ISCBacademy talk on October 3, 2023, at 8am Pacific Daylight Time (15:00 UTC). Sierra Moxon (see bio below) will speak about “LinkML: an open data modeling framework, grounded with ontologies”.
Abstract
The Linked data Modeling Language (LinkML, https://linkml.io) is an open, extensible modeling framework that allows computers and people to work cooperatively to document, validate, and distribute data that is reusable and interoperable. It provides a flexible yet expressive standard for describing many kinds of data models from value sets and flat, checklist-style standards to complex normalized data structures that use polymorphism and inheritance. LinkML enables even non-developers to create data models. It is designed to allow software engineers and subject matter experts to communicate effectively in the same language, while also providing the semantic underpinnings to make data easier to validate, understand and reuse computationally. LinkML has an active and growing user community, and has seen uptake by projects including cancer data harmonization, environmental genomics, microbiome data, knowledge graph integration, ontology mappings and language profiles.
In this talk, which expands on the short talk I gave at BOSC 2023, I will describe the LinkML framework and give examples demonstrating how to use it for biological data modeling, ontology-supported validation, conversion, and serialization. I will discuss how LinkML was used to create the Biolink Model, a unifying data model that brings together heterogeneous datasets to answer novel biomedical questions. I’ll also introduce the role the Biolink Model plays in the NCATS Biomedical Data Translator project.
About the speaker
Sierra Moxon is a software developer in the Biosystems Data Science group at the Lawrence Berkeley National Laboratory. Sierra’s work focuses on designing and developing reusable software to harmonize diverse scientific research data into findable, accessible, interoperable and reproducible (FAIR) formats, with applications ranging from biomedicine to the environment.
Sierra leads the Data Modeling Committee for the NCATS Biomedical Data Translator project, which aims to accelerate the path from biomedical research to clinical trials. She is a lead developer of the LinkML data modeling framework and the LinkML-based knowledge graph standard called Biolink Model, which forms a core part of the Translator infrastructure. Additionally, she is the Data Harmonization Lead for the Alliance of Genome Resources project, and she writes software used by the Gene Ontology, one of the most widely used ontologies in biology.