Event-based text mining for biology and functional genomics

A method for integrating and ranking the evidence for biochemical pathways by mining reactions from text

(2013) Makoto Miwa et al.   BIOINFORMATICS

Wide coverage biomedical event extraction using multiple partially overlapping corpora

(2013) Makoto Miwa et al.   BMC BIOINFORMATICS

Finding novel pharmaceuticals in the systems biology era using multiple effective drug targets, phenotypic screening and knowledge of transporters: where drug discovery went wrong and how to fix it

(2013) Douglas B. Kell   FEBS Journal

The DDI corpus: An annotated corpus with pharmacological substances and drug–drug interactions

(2013) María Herrero-Zazo et al.   JOURNAL OF BIOMEDICAL INFORMATICS

An analysis of a ‘community-driven’ reconstruction of the human metabolic network

(2013) Neil Swainston et al.   Metabolomics

Network link prediction by global silencing of indirect correlations

(2013) Baruch Barzel et al.   NATURE BIOTECHNOLOGY

A community-driven global reconstruction of human metabolism

(2013) Ines Thiele et al.   NATURE BIOTECHNOLOGY

Large-Scale Event Extraction from Literature with Multi-Level Gene Normalization

(2013) Sofie Van Landeghem et al.   PLoS One

Boosting automatic event extraction from the literature using domain adaptation and coreference resolution

(2012) M. Miwa et al.   BIOINFORMATICS

Event extraction across multiple levels of biological organization

(2012) Sampo Pyysalo et al.   BIOINFORMATICS

Extracting semantically enriched events from biomedical literature

(2012) Makoto Miwa et al.   BMC BIOINFORMATICS

The promiscuous binding of pharmaceutical drugs and their transporter-mediated uptake into cells: what we (need to) know and how we can do so

(2012) Douglas B. Kell et al.   DRUG DISCOVERY TODAY

GeneView: a comprehensive semantic search engine for PubMed

(2012) P. Thomas et al.   NUCLEIC ACIDS RESEARCH

Discovering and visualizing indirect associations between biomedical concepts

(2011) Y. Tsuruoka et al.   BIOINFORMATICS

The BioLexicon: a large-scale terminological resource for biomedical text mining

(2011) Paul Thompson et al.   BMC BIOINFORMATICS

Enriching a biomedical event corpus with meta-knowledge annotation

(2011) Paul Thompson et al.   BMC BIOINFORMATICS

Mining the Gene Wiki for functional genomic knowledge

(2011) Benjamin M Good et al.   BMC GENOMICS

EXTRACTING BIO-MOLECULAR EVENTS FROM LITERATURE-THE BIONLP’09 SHARED TASK

(2011) Jin-Dong Kim et al.   COMPUTATIONAL INTELLIGENCE

Using a shallow linguistic kernel for drug–drug interaction extraction

(2011) Isabel Segura-Bedmar et al.   JOURNAL OF BIOMEDICAL INFORMATICS

2010 i2b2/VA challenge on concepts, assertions, and relations in clinical text

(2011) Özlem Uzuner et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

Disease Ontology: a backbone for disease semantic integration

(2011) L. M. Schriml et al.   NUCLEIC ACIDS RESEARCH

PathText: a text mining integrator for biological pathway visualizations

(2010) B. Kemper et al.   BIOINFORMATICS

Complex event extraction at PubMed scale

(2010) J. Bjorne et al.   BIOINFORMATICS

An Overview of BioCreative II.5

(2010) F Leitner et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Reconstruction annotation jamborees: a community approach to systems biology

(2010) Ines Thiele et al.   Molecular Systems Biology

The FEBS Letters/BioCreative II.5 experiment: making biological information accessible

(2010) Florian Leitner et al.   NATURE BIOTECHNOLOGY

Event extraction for systems biology by text mining the literature

(2010) Sophia Ananiadou et al.   TRENDS IN BIOTECHNOLOGY

EVENT EXTRACTION WITH COMPLEX EVENT CLASSIFICATION USING RICH FEATURES

(2010) MAKOTO MIWA et al.   Journal of Bioinformatics and Computational Biology

KiPar, a tool for systematic information retrieval regarding parameters for kinetic modelling of yeast metabolic pathways

(2009) Irena Spasić et al.   BIOINFORMATICS

Construction of an annotated corpus to support biomedical information extraction

(2009) Paul Thompson et al.   BMC BIOINFORMATICS

FactBank: a corpus annotated with event factuality

(2009) Roser Saurí et al.   Language Resources and Evaluation

MedlineRanker: flexible ranking of biomedical literature

(2009) Jean-Fred Fontaine et al.   NUCLEIC ACIDS RESEARCH

The Universal Protein Resource (UniProt) in 2010

(2009)   NUCLEIC ACIDS RESEARCH

A Parsimony Approach to Biological Pathway Reconstruction/Inference for Genomes and Metagenomes

(2009) Yuzhen Ye et al.   PLoS Computational Biology

Multi-dimensional classification of biomedical text: Toward automated, practical provision of high-utility text to diverse users

(2008) H. Shatkay et al.   BIOINFORMATICS

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

(2008) A. Ozgur et al.   BIOINFORMATICS

Corpus annotation for mining biomedical events from literature

(2008) Jin-Dong Kim et al.   BMC BIOINFORMATICS

Feature Forest Models for Probabilistic HPSG Parsing

(2008) Yusuke Miyao et al.   COMPUTATIONAL LINGUISTICS

A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology

(2008) Markus J Herrgård et al.   NATURE BIOTECHNOLOGY

Defrosting the Digital Library: Bibliographic Tools for the Next Generation Web

(2008) Duncan Hull et al.   PLoS Computational Biology