HiPub: Highlighter for PubMed

  HiPub :   Translating PubMed and PMC Texts to Networks for Knowledge Discovery

We introduce HiPub, a seamless Chrome browser plug-in that automatically recognizes, annotates and translates biomedical entities from texts into networks for discovering knowledge. 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. HiPub 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.

You can install HiPub in Chrome Web Store

1. Program availability and requirements

2. Installation and Usage

3. Documentation

User Manual : HiPub User Manual

4. Citation

Kyubum Lee, Wonho Shin, Byounggun Kim, Sunwon Lee, Yonghwa Choi, Sunkyu Kim, Minji Jeon, Aik Choon Tan*, and Jaewoo Kang*
HiPub: translating PubMed and PMC texts to networks for knowledge discovery
Bioinformatics (2016) 32 (18): 2886-2888 first published online August 2, 2016 doi:10.1093/bioinformatics/btw511 [Link] [PDF] [PMID: 27485446]

5. License

HiPub is licensed under the GNU General Public License and is 100% freely available to both commercial and academic users. See the file LICENSE.txt in the BEReX distribution package or this URL for the full text of the license: http://www.gnu.org/licenses/gpl.html https://sites.google.com/site/kyubumlee/

6. Contact - for bugs, comments and questions

Kyubum Lee: kyubumlee_at_gmail_dot_com
Aik-Choon Tan: aikchoon.tan_at_ucdenver_dot_edu
Jaewoo Kang: kangj_at_korea_dot_ac_dot_kr

Last updated on December 23, 2016