Extended Coprecipitation Frames v2

Adding some data to the core annotated data for Binding / Coprecipitation.

June 2016

  1. Dry Run II Papers from MITRE

July 2015

  1. Two-Hop Ras BioPax Model

May 2015

  1. MINT + INTACT DATA

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

Extending the Molecular Interaction Corpus.

Here we extend the existing available annotated data with 14 extra files by broadening the search for papers involved in binding experiments beyond the set annotated within Pathway Logic.

All papers in expanded set

Annotated data

Here we present a larger set of papers marked up for coprecipitation experiments (this file includes the data presented previously).

Organization of the annotations (brat markup)

!Protocol
	process
	entity

!Coprecipitation-Context-Object
	cell-type
	transfection-molecule
	mutation-molecule
	incubation-reagent
	ip-molecule
	molecular-weight
	time-point
	assay-molecule
	immunodepletion
	mutation

!Coreference-Object
	coreference-target

!Measured-Object
	m-obj

!Binds-Objects
	binds-strength
	binds-catalysis
	binds-constituent1
	binds-constituent2
	binds-constituent3
	binds-controller
	binds-complex
	binds-site

!Measured-Value
	m-val
	m-comp
	
[attributes]

[relations]

<OVERLAP>	Arg1:<ENTITY>, Arg2:<ENTITY>, <OVL-TYPE>:<ANY>

[events]

How the reports for different frame elements distribute over the discourse types

Frame fact goal hypothesis implication method other-hypothesis other-implication other-result problem result Total
binds                     2499
binds-catalysis 1 8   9 11     9 6 49 93
binds-complex 3 13 3 19 28   1 10 1 41 119
binds-constituent1 8 70 12 92 180 2 2 82 29 320 797
binds-constituent2 7 64 8 90 172 5 2 75 26 300 749
binds-constituent3 1 9 1 10 12 1   9 3 18 64
binds-controller 1 16 2 31 41     14 3 86 194
binds-site   16 2 38 84 1 1 28   128 298
binds-strength 2 21 4 13 24     22 16 83 185
copi                     2817
assay-molecule   22   29 196     25 4 160 436
cell-type 2 26 1 23 130     31 14 91 318
coreference-target   14 1 30 55     18 1 68 187
entity   15   35 117   2 19   73 261
incubation-reagent   12   15 87     11 3 77 205
ip-molecule   21   37 181     26 3 158 426
m-comp       1 1         13 15
m-obj         1         2 3
m-val   10   13 30     9 2 87 151
molecular-weight       2 6         10 18
mutation     1   1           2
mutation-molecule         4           4
process   26   53 217     35   125 456
time-point   5     7     5 5 15 37
transfection-molecule   22   40 134   2 22 5 73 298
Grand Total 25 390 35 580 1719 9 10 450 121 1977 5316