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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Vydané v:BMC bioinformatics Ročník 19; číslo 1; s. 30 - 7
Hlavní autori: Xin, Jiwen, Afrasiabi, Cyrus, Lelong, Sebastien, Adesara, Julee, Tsueng, Ginger, Su, Andrew I., Wu, Chunlei
Médium: Journal Article
Jazyk:English
Vydavateľské údaje: London BioMed Central 01.02.2018
BioMed Central Ltd
BMC
Predmet:
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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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.
AbstractList 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, JSON-LD, API interoperability, Knowledge discovery, Semantic web, Linking APIs
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.
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. 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. We believe that this pattern offers a generalizable solution for interoperability of APIs in the life sciences.
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. 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. We believe that this pattern offers a generalizable solution for interoperability of APIs in the life sciences.
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.
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.BACKGROUNDApplication 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.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.RESULTSHere, 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.We believe that this pattern offers a generalizable solution for interoperability of APIs in the life sciences.CONCLUSIONSWe believe that this pattern offers a generalizable solution for interoperability of APIs in the life sciences.
ArticleNumber 30
Audience Academic
Author Wu, Chunlei
Xin, Jiwen
Lelong, Sebastien
Su, Andrew I.
Tsueng, Ginger
Afrasiabi, Cyrus
Adesara, Julee
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Issue 1
Keywords Semantic web
Linking APIs
JSON-LD
Knowledge discovery
API
API interoperability
Language English
License Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
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Snippet Background Application Programming Interfaces (APIs) are now widely used to distribute biological data. And many popular biological APIs developed by many...
Application Programming Interfaces (APIs) are now widely used to distribute biological data. And many popular biological APIs developed by many different...
Background Application Programming Interfaces (APIs) are now widely used to distribute biological data. And many popular biological APIs developed by many...
Abstract Background Application Programming Interfaces (APIs) are now widely used to distribute biological data. And many popular biological APIs developed by...
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SubjectTerms 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
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Title Cross-linking BioThings APIs through JSON-LD to facilitate knowledge exploration
URI https://link.springer.com/article/10.1186/s12859-018-2041-5
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