Cross-linking BioThings APIs through JSON-LD to facilitate knowledge exploration
Related Experiment Video
Updated: Feb 15, 2026

Evidence-based Knowledge Synthesis and Hypothesis Validation: Navigating Biomedical Knowledge Bases via Explainable AI and Agentic Systems
Published on: June 13, 2025
Jiwen Xin1, Cyrus Afrasiabi1, Sebastien Lelong1
1Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA.
Background:
Application Programming Interfaces (APIs) are now widely used to distribute biological data. And many popular biological APIs developed by many different research teams have adopted Javascript Object Notation (JSON) as their primary data format. While usage of a common data format offers significant advantages, that alone is not sufficient for rich integrative queries across APIs.
Results:
Here, we have implemented JSON for Linking Data (JSON-LD) technology on the BioThings APIs that we have developed, MyGene.info , MyVariant.info and MyChem.info . JSON-LD provides a standard way to add semantic context to the existing JSON data structure, for the purpose of enhancing the interoperability between APIs. We demonstrated several use cases that were facilitated by semantic annotations using JSON-LD, including simpler and more precise query capabilities as well as API cross-linking.
Conclusions:
We believe that this pattern offers a generalizable solution for interoperability of APIs in the life sciences.
Related Concept Videos
Crossing Over
The homologous pairs of sister chromosomes—one from the maternal and one from the paternal genome—then begin to align alongside each other lengthwise, matching corresponding DNA positions in a process...
Facilitated Transport
Facilitated Transport
Social Facilitation
Cross-Sectional Research
Facilitated Diffusion
In this process, substrates such as organic compounds and ions interact with a transporter on one side, triggering conformational changes in proteins that enable...

