Proposal for Text Mining PubAg
- 1. Text mining PubAg Jake Lever & Ben Busby National Center for Biotechnology Information National Library of Medicine jake.lever@nih.gov, ben.busby@nih.gov
- 2. Why text mine? Reading papers takes time and effort https://commons.wikimedia.org/wiki/File:FileStack_retouched.jpg https://commons.wikimedia.org/wiki/File:Cup-o-coffee-simple.svg https://commons.wikimedia.org/wiki/File:Modern_clock_chris_kemps_01.svg https://commons.wikimedia.org/wiki/File:Mad_scientist_transparent_background.svg
- 3. What can text mining do? Help build navigable biological databases https://www.civicdb.org https://www.pharmgkb.org/ https://string-db.org/ https://commons.wikimedia.org/wiki/File:Mad_scientist_transparent_background.svg
- 4. PubRunner Keeping text mining up-to-date PubMed Abstracts PubRunner Text mining tool Public FTP or Zenodo Private Server Download XML files Upload results Run tool Get results www.pubrunner.org website Update status of tool and location of latest results http://www.pubrunner.org https://github.com/NCBI-Hackathons/PubRunner
- 5. NutriChem “There is rising evidence of an inverse association between chronic diseases and diets characterized by rich fruit and vegetable consumption.” http://sbb.hku.hk/services/NutriChem-2.0 Jensen, Kasper, Gianni Panagiotou, and Irene Kouskoumvekaki. "NutriChem: a systems chemical biology resource to explore the medicinal value of plant-based foods." Nucleic acids research 43.D1 (2014): D940-D945. Disclaimer: We are not involved in the development of this tool
- 6. What we’d like to do Show the power of text mining on PubAg PubMed PubAg PubRunner NutriChem jake.lever@nih.gov ben.busby@nih.gov What we need: Access to all PubAg abstracts, preferably through FTP