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PubMed-Scale Event Extraction for Post-Translational Modifications, Epigenetics and Protein Structural Relations

Jari Björne, Sofie van Landeghem, Sampo Pyysalo, Tomoko Ohta, Filip Ginter, Yves van de Peer, Sophia Ananiadou, Tapio Salakoski, PubMed-Scale Event Extraction for Post-Translational Modifications, Epigenetics and Protein Structural Relations. In: Kevin Bretonnel Cohen, Dina Demner-Fushman, Sophia Ananiadou, John Pestian (Eds.), Proceedings of the 2012 Workshop on Biomedical Natural Language Processing (BioNLP 2012), 82–90, Association for Computational Linguistics, 2012.

Abstract:

Recent efforts in biomolecular event extrac-
tion have mainly focused on core event types
involving genes and proteins, such as gene
expression, protein-protein interactions, and
protein catabolism. The BioNLP’11 Shared
Task extended the event extraction approach
to sub-protein events and relations in the Epi-
genetics and Post-translational Modifications
(EPI) and Protein Relations (REL) tasks. In
this study, we apply the Turku Event Ex-
traction System, the best-performing system
for these tasks, to all PubMed abstracts and
all available PMC full-text articles, extract-
ing 1.4M EPI events and 2.2M REL relations
from 21M abstracts and 372K articles. We
introduce several entity normalization algo-
rithms for genes, proteins, protein complexes
and protein components, aiming to uniquely
identify these biological entities. This nor-
malization effort allows direct mapping of
the extracted events and relations with post-
translational modifications from UniProt, epi-
genetics from PubMeth, functional domains
from InterPro and macromolecular structures
from PDB. The extraction of such detailed
protein information provides a unique text
mining dataset, offering the opportunity to fur-
ther deepen the information provided by ex-
isting PubMed-scale event extraction efforts.
The methods and data introduced in this study
are freely available from bionlp.utu.fi.

BibTeX entry:

@INPROCEEDINGS{inpBjVaPyOhGiVaAnSa12a,
  title = {PubMed-Scale Event Extraction for Post-Translational Modifications, Epigenetics and Protein Structural Relations},
  booktitle = {Proceedings of the 2012 Workshop on Biomedical Natural Language Processing (BioNLP 2012)},
  author = {Björne, Jari and Landeghem, Sofie van and Pyysalo, Sampo and Ohta, Tomoko and Ginter, Filip and Peer, Yves van de and Ananiadou, Sophia and Salakoski, Tapio},
  editor = {Cohen, Kevin Bretonnel and Demner-Fushman, Dina and Ananiadou, Sophia and Pestian, John},
  publisher = {Association for Computational Linguistics},
  pages = {82–90},
  year = {2012},
}

Belongs to TUCS Research Unit(s): Turku BioNLP Group

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