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

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...

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Vydáno v:BMC bioinformatics Ročník 19; číslo 1; s. 30 - 7
Hlavní autoři: Xin, Jiwen, Afrasiabi, Cyrus, Lelong, Sebastien, Adesara, Julee, Tsueng, Ginger, Su, Andrew I., Wu, Chunlei
Médium: Journal Article
Jazyk:angličtina
Vydáno: London BioMed Central 01.02.2018
BioMed Central Ltd
BMC
Témata:
Algorithms
Analysis
API
API (Computer programming)
API interoperability
Bioinformatics
Biomedical and Life Sciences
Computational biology
Computational Biology/Bioinformatics
Computer Appl. in Life Sciences
JSON-LD
Knowledge discovery
Knowledge-based analysis
Life Sciences
Linking APIs
Microarrays
Research Article
Semantic web
Semantic web
Linking APIs
JSON-LD
Knowledge discovery
API
API interoperability
ISSN:1471-2105, 1471-2105
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Shrnutí: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.
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ISSN:1471-2105
1471-2105
DOI:10.1186/s12859-018-2041-5