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Extracting Evidence Fragments for Distant Supervision of Molecular Interactions

View ORCID ProfileGully A Burns, Pradeep Dasigi, View ORCID ProfileEduard H. Hovy
doi: https://doi.org/10.1101/192856
Gully A Burns
1USC Information Sciences Institute, Marina del Rey, CA 90292, USA
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  • For correspondence: burns@isi.edu
Pradeep Dasigi
2Language Technologies Institute – Carnegie Mellon University, Pittsburgh, PA 15213, USA ,
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  • For correspondence: pdasigi@cs.cmu.edu hovy@cs.cmu.edu
Eduard H. Hovy
2Language Technologies Institute – Carnegie Mellon University, Pittsburgh, PA 15213, USA ,
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  • ORCID record for Eduard H. Hovy
  • For correspondence: pdasigi@cs.cmu.edu hovy@cs.cmu.edu
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Abstract.

We describe a methodology for automatically extracting ‘evidence fragments’ from a set of biomedical experimental research articles. These fragments provide the primary description of evidence that is presented in the papers’ figures. They elucidate the goals, methods, results and interpretations of experiments that support the original scientific contributions the study being reported. Within this paper, we describe our methodology and showcase an example data set based on the European Bioinformatics Institute’s INTACT database (http://www.ebi.ac.uk/intact/). Using figure codes as anchors, we linked evidence fragments to INTACT data records as an example of distant supervision so that we could use INTACT’s preexisting, manually-curated structured interaction data to act as a gold standard for machine reading experiments. We report preliminary baseline event extraction measures from this collection based on a publicly available, machine reading system (REACH). We use semantic web standards for our data and provide open access to all source code.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted September 23, 2017.
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Extracting Evidence Fragments for Distant Supervision of Molecular Interactions
Gully A Burns, Pradeep Dasigi, Eduard H. Hovy
bioRxiv 192856; doi: https://doi.org/10.1101/192856
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Extracting Evidence Fragments for Distant Supervision of Molecular Interactions
Gully A Burns, Pradeep Dasigi, Eduard H. Hovy
bioRxiv 192856; doi: https://doi.org/10.1101/192856

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