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HiPub: translating PubMed and PMC texts to networks for knowledge discovery
Kyubum Lee1, Wonho Shin2, Byounggun Kim2
1Department of Computer Science and Engineering, Korea University, Seoul, Korea.
Unlabelled:
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.
Availability And Implementation:
HiPub and detailed user guide are available at http://hipub.korea.ac.kr
Contact:
kangj@korea.ac.kr, aikchoon.tan@ucdenver.edu
Supplementary Information:
Supplementary data are available at Bioinformatics online.
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