HiPub: translating PubMed and PMC texts to networks for knowledge discovery
Summary: 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.
Source: Bioinformatics - Category: Bioinformatics Authors: Lee, K., Shin, W., Kim, B., Lee, S., Choi, Y., Kim, S., Jeon, M., Tan, A. C., Kang, J. Tags: DATA AND TEXT MINING Source Type: research
More News: Bioinformatics | Databases & Libraries | Genetics | Learning | Universities & Medical Training