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BMC Bioinformatics. 2018 Feb 1;19(1):30. doi: 10.1186/s12859-018-2041-5.

Cross-linking BioThings APIs through JSON-LD to facilitate knowledge exploration.

Author information

1
Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA.
2
Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA. cwu@scripps.edu.

Abstract

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.

KEYWORDS:

API; API interoperability; JSON-LD; Knowledge discovery; Linking APIs; Semantic web

PMID:
29390967
PMCID:
PMC5796402
DOI:
10.1186/s12859-018-2041-5
[Indexed for MEDLINE]
Free PMC Article

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