Coprecipitation Frames v2

Here we describe the annotation process + annotations for IE extraction frames based on co-precipitation experiments.

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

Coprecipitation experiments and model fragments.

Simple mapping between coprecipitation studies and BioPax pathway models (for a Tfx_IP_IB motif). The right hand side shows the typical interpretation of data as a controlled binding event

Experimental and Interpretive Frames

Based on separating interpretive and observational frames for knowledge derived from a given experimental type, we present (A) an IE frame for data expressed in the paper as experimental knowledge (which might refer to the major parts of the experimental procedure, the context for measurements or measurements themselves) and (B) an IE frame for data expressed as an interpretation (or implication).

In this case, data is expressed as experimental data from coprecipitation experiments (i.e., experiments in which a coprecipitation step gave rise to measurements of the concentration of complexes)

Coprecipitation experiment frame

At this stage, we use a flat annotation structure where multiple slots can be populated from a single sentence, in order to attempt to construct three things from the text (A) features that permit us to classify the experiment according to it’s type and subtype (i.e., a coprecipitation experiment specialization), (B) contextual values of independent variables that anchor a given measurement and (C) the measurement value itself.


Binding interpretation frame

We found a great many more annotations of this type because the focus of these relatively simple experiments in the narrative of a given paper is whether two (or more) molecules bind together to form a complex.

	binds-strength # how strong is the binding between the constituents
	binds-catalysis # how does the catalysis work (inhibits, activates, etc.)
	binds-constituent1 # molecules binding together
	binds-controller # molecule acting as a catalyst
	binds-complex # molecule formed as a complex
	binds-site # site on constituent molecule's DNA where an event happens. This may or may not be binding related. 

Annotated Data

This data comprises brat files from 18 articles, containing information from 103 experimental passages / figure descriptions. We also include brat configuration files (annotation.conf, kb_shortcuts.conf and visual.conf) that determine and assist how these annotations are used within the brat annotation tool.