HiPub: translating PubMed and PMC texts to networks for knowledge discovery

作者：Lee Kyubum; Shin Wonho; Kim Byounggun; Lee Sunwon; Choi Yonghwa; Kim Sunkyu; Jeon Minji; Tan Aik Choon^*; Kang Jaewoo^*

来源：Bioinformatics, 2016, 32(18): 2886-2888.

DOI：10.1093/bioinformatics/btw511

We introduce HiPub, a seamless Chrome browser plug-in that automatically recognizes, annotates and translates biomedical entities from texts into networks for knowledge discovery. Using a combination of two different named-entity recognition resources, HiPub can recognize genes, proteins, diseases, drugs, mutations and cell lines in texts, and achieve high precision and recall. HiPub extracts biomedical entity-relationships from texts to construct context-specific networks, and integrates existing network data from external databases for knowledge discovery. It allows users to add additional entities from related articles, as well as user-defined entities for discovering new and unexpected entity-relationships. HiPub provides functional enrichment analysis on the biomedical entity network, and link-outs to external resources to assist users in learning new entities and relations.

• 出版日期2016-9-15