Title |
Cross-linking BioThings APIs through JSON-LD to facilitate knowledge exploration
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Published in |
BMC Bioinformatics, February 2018
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DOI | 10.1186/s12859-018-2041-5 |
Pubmed ID | |
Authors |
Jiwen Xin, Cyrus Afrasiabi, Sebastien Lelong, Julee Adesara, Ginger Tsueng, Andrew I. Su, Chunlei Wu |
Abstract |
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. |
X Demographics
Geographical breakdown
Country | Count | As % |
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United States | 9 | 38% |
Spain | 1 | 4% |
France | 1 | 4% |
India | 1 | 4% |
Italy | 1 | 4% |
Unknown | 11 | 46% |
Demographic breakdown
Type | Count | As % |
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Members of the public | 17 | 71% |
Scientists | 7 | 29% |
Mendeley readers
Geographical breakdown
Country | Count | As % |
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Unknown | 41 | 100% |
Demographic breakdown
Readers by professional status | Count | As % |
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Researcher | 7 | 17% |
Student > Master | 6 | 15% |
Student > Ph. D. Student | 5 | 12% |
Student > Doctoral Student | 4 | 10% |
Student > Bachelor | 3 | 7% |
Other | 8 | 20% |
Unknown | 8 | 20% |
Readers by discipline | Count | As % |
---|---|---|
Computer Science | 10 | 24% |
Agricultural and Biological Sciences | 8 | 20% |
Biochemistry, Genetics and Molecular Biology | 6 | 15% |
Engineering | 4 | 10% |
Pharmacology, Toxicology and Pharmaceutical Science | 1 | 2% |
Other | 2 | 5% |
Unknown | 10 | 24% |