Dry Run II Papers from MITRE

Dry Run Evaluation Papers from MITRE to identify level 1 statements

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
PMC1234335 16135815 n
PMC3178447 20179705 y
PMC3690480 23706742 y
PMC4345513 24602610 y
PMC534114 15550174 y
PMC4329006 25449683 y
PMC3595493 23392125 y
PMC4729484 26816343 y
PMC2841635 20333297 y
PMC4052680 24467442 y

Not all of these papers are available as *.nxml. All of them are available as PDF.

Running Preprocessing

Note that FRIES preprocessing does not seem to work currently. May need to update REACH.

Running SciDP on Soweto

The embeddings are here /usr1/shared/projects/bigmech/data/embeddings/pyysalo_et_al

Pradeep’s version of the code is here: /usr1/home/pdasigi/workspace/sciDP/

Importantly, this includes the model files: model_att=*, which we copy into a shared
version of sciDP here: /usr1/shared/projects/bigmech/tools/sciDP


python nn_passage_tagger.py /usr1/shared/projects/bigmech/data/embeddings/pyysalo_et_al/PubMed-and-PMC-w2
v.txt.gz --train_file /usr1/shared/projects/bigmech/data/discourse_tagging/train+test_data/passage_train.txt --use_attention


Setting up dependencies locally so that I can run sciDP:

Running the classifier:

   python nn_passage_tagger.py 
      --test_files /usr1/shared/projects/bigmech/corpora/2016-06-01-DryRun2MITRE/ --use_attention