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An integrated text mining framework for metabolic interaction network reconstruction

Autor

Bairong Shen

Wanwipa Vongsangnak

veröffentlicht in: PeerJ

Erscheinungsdatum: 2016-03-21

Hauptthema: Text Mining

Zitiert Artikel 30

Datum

Titel

Autor

2013-04-17

Large-scale event extraction from literature with multi-level gene normalization

Yves Van de Peer, Tapio Salakoski, Filip Ginter, Sofie Van Landeghem, Jari Björne, Sampo Pyysalo, Sophia Ananiadou, Chih-Hsuan Wei, Zhiyong Lu
2013-04-18

Preliminary evaluation of the CellFinder literature curation pipeline for gene expression in kidney cells and anatomical parts

Ulf Leser, Andreas Kurtz, Stefanie Seltmann, Mariana Neves, Fritz Lekschas, Harald Stachelscheid, Nancy Mah, Alexander Damaschun
2013-04-29

Genome-scale reconstruction and in silico analysis of Aspergillus terreus metabolism
2012-11-07

A survey of computational methods for protein complex prediction from protein interaction networks
2012-11-09

EcoCyc: fusing model organism databases with systems biology

Ian T. Paulsen, Peter D. Karp, Martin Peralta-Gil, Julio Collado-Vides, Alberto Santos-Zavaleta, Markus Krummenacker, César Bonavides-Martínez, Socorro Gama-Castro
2012-07-23

A text-mining system for extracting metabolic reactions from full-text articles

Irene Nobeli, Adrian M Smith, Adrian Shepherd
2012-06-26

Combining joint models for biomedical event extraction

Sebastian Riedel, Andrew McCallum, Christopher D. Manning
2012-06-17

BioContext: an integrated text mining system for large-scale extraction and contextualization of biomolecular events

Goran Nenadic, Casey M Bergman, Martin Gerner, Farzaneh Sarafraz
2012-06-04

Yeast 5 – an expanded reconstruction of the Saccharomyces cerevisiae metabolic network

Brandon Barker, Benjamin D Heavner, Kieran Smallbone, Pedro Pedrosa Mendes
2012

Text mining for the biocuration workflow

Lynette Hirschman, Martin Krallinger, Anália Lourenço, Alfonso Valencia, Andrew Chatr-Aryamontri, Cecilia Arighi, Eva Huala, Kevin Bretonnel Cohen, Cathy H. Wu, Thomas C. Wiegers, Gully A.P.C. Burns
2012-02-01

Using the reconstructed genome-scale human metabolic network to study physiology and pathology
2011

Integrated bio-entity network: a system for biological knowledge discovery
2011-10-11

A comprehensive genome-scale reconstruction of Escherichia coli metabolism--2011.

Joshua A. Lerman, Hojung Nam, Bernhard Palsson, Adam M. Feist, Jeffrey D Orth
2010-10-31

Mining metabolites: extracting the yeast metabolome from the literature

Pedro Pedrosa Mendes, Douglas Kell, Sophia Ananiadou, Jun'ichi Tsujii
2010-06-01

PathText: a text mining integrator for biological pathway visualizations

Yoshimasa Tsuruoka, Sophia Ananiadou, Jun'ichi Tsujii, Yukiko Matsuoka
2010-07-01

Extracting protein interactions from text with the unified AkaneRE event extraction system

Rune Sætre, Jun'ichi Tsujii
2009-10-08

PathBinder--text empirics and automatic extraction of biomolecular interactions
2009-07-28

A realistic assessment of methods for extracting gene/protein interactions from free text

Adrian Shepherd
2009-02

Reconstruction of biochemical networks in microorganisms
2009-08-07

Text mining biomedical literature for constructing gene regulatory networks.
2009-09-15

A genome-scale metabolic model of Arabidopsis and some of its properties

David Fell
2008-11-19

All-paths graph kernel for protein-protein interaction extraction with evaluation of cross-corpus learning

Jari Björne, Sampo Pyysalo, Filip Ginter, Tapio Salakoski, Tapio Pahikkala
2008-07-01

Identifying gene-disease associations using centrality on a literature mined gene-interaction network

Dragomir R. Radev, Arzucan Özgür
2008-03-25

Metabolic model integration of the bibliome, genome, metabolome and reactome of Aspergillus niger

Mikael Rørdam Andersen, Jens Nielsen
2008-01-01

BANNER: an executable survey of advances in biomedical named entity recognition
2007-08-07

Automatic reconstruction of a bacterial regulatory network using Natural Language Processing

Carlos Rodriguez-Penagos, Julio Collado-Vides
2007-07-01

Manual curation is not sufficient for annotation of genomic databases

Lawrence Hunter, George K Acquaah-Mensah, Kevin Bretonnel Cohen, William Baumgartner
2004-02-01

GeneWays: a system for extracting, analyzing, visualizing, and integrating molecular pathway data

Andrey Rzhetsky, Michael Krauthammer, W. John Wilbur, Carol Friedman
2000-01-01

Two applications of information extraction to biological science journal articles: enzyme interactions and protein structures

Robert Gaizauskas
1960-04

A Coefficient of Agreement for Nominal Scales

Artikel - wd:Q39460433

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