Extracting Biological Pathway Models From NLP Event Representations

This paper describes an an open-source software system for the automatic conversion of NLP event representations to system biology structured data interchange formats such as SBML and BioPAX. It is part of a larger effort to make results of the NLP community available for system biology pathway modelers.

[1]  Burkhard Rost,et al.  tagtog: interactive and text-mining-assisted annotation of gene mentions in PLOS full-text articles , 2014, Database J. Biol. Databases Curation.

[2]  Michael Hucka,et al.  The Systems Biology Markup Language (SBML) Level 2 Version 2 , 2007 .

[3]  Hugh D. Spence,et al.  Minimum information requested in the annotation of biochemical models (MIRIAM) , 2005, Nature Biotechnology.

[4]  Zhiyong Lu,et al.  PubTator: a web-based text mining tool for assisting biocuration , 2013, Nucleic Acids Res..

[5]  Gary D. Bader,et al.  Using Biological Pathway Data with Paxtools , 2013, PLoS Comput. Biol..

[6]  N. Kikuchi,et al.  CellDesigner 3.5: A Versatile Modeling Tool for Biochemical Networks , 2008, Proceedings of the IEEE.

[7]  Falk Schreiber,et al.  VANTED: A system for advanced data analysis and visualization in the context of biological networks , 2006, BMC Bioinformatics.

[8]  Sarala M. Wimalaratne,et al.  The Systems Biology Graphical Notation , 2009, Nature Biotechnology.

[9]  Jari Björne,et al.  UTurku: Drug Named Entity Recognition and Drug-Drug Interaction Extraction Using SVM Classification and Domain Knowledge , 2013, *SEMEVAL.

[10]  Sampo Pyysalo,et al.  Overview of the Pathway Curation (PC) task of BioNLP Shared Task 2013 , 2013, BioNLP@ACL.

[11]  Sampo Pyysalo,et al.  A method for integrating and ranking the evidence for biochemical pathways by mining reactions from text , 2013, Bioinform..

[12]  Junichi Tsujii,et al.  Event extraction for systems biology by text mining the literature. , 2010, Trends in biotechnology.

[13]  Tapio Salakoski,et al.  EVEX: A PubMed-Scale Resource for Homology-Based Generalization of Text Mining Predictions , 2011, BioNLP@ACL.

[14]  Sampo Pyysalo,et al.  From Pathways to Biomolecular Events: Opportunities and Challenges , 2011, BioNLP@ACL.

[15]  Sampo Pyysalo,et al.  Overview of BioNLP Shared Task 2013 , 2013, BioNLP@ACL.

[16]  Rainer Breitling,et al.  What is Systems Biology? , 2010, Front. Physiology.

[17]  Kei-Hoi Cheung,et al.  The BioPAX community standard for pathway data sharing (Nature Biotechnology (2010) 28, (935-942)) , 2012 .

[18]  Kei-Hoi Cheung,et al.  BioPAX – A community standard for pathway data sharing , 2010, Nature Biotechnology.

[19]  Hiroaki Kitano,et al.  The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models , 2003, Bioinform..

[20]  Zhiyong Lu,et al.  Community challenges in biomedical text mining over 10 years: success, failure and the future , 2016, Briefings Bioinform..