KEfED Database Construction

Here we describe the development of a database representation of KEfED data based on generating a linked set of context / value relations.

June 2016

  1. Dry Run II Papers from MITRE

July 2015

  1. Two-Hop Ras BioPax Model

May 2015


April 2015

  1. Open Access Pathway Logic Papers and Figures
  2. Extended Coprecipitation Frames v2

January 2015

  1. Coprecipitation Frames v2
  2. List of Experimental Motif Types + Definitions
  3. KEfED Database Construction

December 2014

  1. KEfED Modeling of Coprecipitation Ras Papers
  2. Initial Extraction Study of Results-Based Epistemics

October 2014

  1. Pathway Logic Experiment Types
  2. Building a Database of Observations from Result Text
  3. Deploying the BioScholar System
  4. Reading Against a Model of Experimental Evidence

August 2014

  1. Developing NL Annotations for KEfED Elements
  2. Epistemics and Fragments
  3. Generating the Big Mechanisms Evaluation Corpus
  4. A Generative Story for Scientific Text from Experimental Data


Curating models & data into the previous BioScholar system based on a simple JSON store is now outdated and should be updated into the current KEfED VPDMf model. The goal here is not to fully rely on the VPDMf architecture (which is a little cumbersome), but to implement the data simply as a relational database store with minimal overhead.

Backup of previous data:

Changes to the model

  1. Removed additional data constructs (such as StatisticalAssertion). If needed, we will add these back in. It is likely that we will develop these as data workflow elements that occur downstream of primary measurements.
  2. Altered the curation elements in vpdmf-bioscholar.xml