RESTful API for integrative literature information and knowledge service
Date
2017
Authors
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Journal ISSN
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Publisher
University of Delaware
Abstract
Biocuration needs efficient and high-quality data sources as well as automatic literature curation as the result of dramatically increasing the volume of literature in life science and biology fields. API is a stable and scalable mechanism to deliver programmable data, which can become the data source for biocuration and data presentation. RESTful API for Integrative Literature Information and Knowledge Service (abbreviated to iLINKS) is designed to expose the text-mining data gained from analyzing PubMed articles to support potential application development. The iLINKS system integrated three text-mining tools, RLIMS-P, miRTex and PubTator to capture phosphorylation relation, gene-miRNA relation and biological relation in general. With the data generated by those text-mining tools, three different types of APIs are built to deliver PubMed article full information, relation-specific information, and across-article entity information. Following the best practice of API design principle as well as the business rules in iLINKS system, the APIs are used to deliver text-mining results along with PubMed article abstract/full text. API documentation website is set to help developers to develop applications using the APIs. An example PubMed ID based search web page can help biocurators quickly searching for biological entities and relations for a given PubMed article. The RESTful APIs will be widely used for developing other iLINKS applications, which include Cytoscape knowledge network visualization, and BRAT literature annotation.