Sunday, August 25, 2013

The SciKnowMine Project: Bridging BioNLP and Biocuration

Biological Natural Language Processing ('BioNLP') holds great promise to support and accelerate biocuration (organizing published biomedical knowledge into online resources such as databases) but has not yet generated viable open technology for use within the community. This is an area of active research and is the subject of shared evaluations such as 'BioCreative 4'. As the closing meeting of an NSF-funded infrastructure project (called 'SciKnowMine', #0849977), we held a workshop to (A) present an implementation of a system for document triage that we are currently deploying to the Mouse Genome Informatics (MGI) system, (B) present and develop a strategic plan for open-source community-driven tools that bridge between curators committed to improving the quality of their informatics resources and computer science specialists developing novel NLP technology. The meeting was well-attended by many experts from both communities and in-keeping with the vision of this blog of examining the issues inherent in developing scientific breakthroughs by explicitly describing the paradigms that different disciplines inhabit, the workshop was fully designed around the theme of finding connecting points between these two inter-dependent paradigms.

The workshop page is here: 

And my introduction and talk (which goes into some detail about the way we use paradigms) is here:

and here: