Published in Database (Oxford) on January 17, 2013
PubTator: a web-based text mining tool for assisting biocuration. Nucleic Acids Res (2013) 3.02
Biocuration workflows and text mining: overview of the BioCreative 2012 Workshop Track II. Database (Oxford) (2012) 2.00
Accelerating literature curation with text-mining tools: a case study of using PubTator to curate genes in PubMed abstracts. Database (Oxford) (2012) 1.89
Finding our way through phenotypes. PLoS Biol (2015) 1.53
Overview of the gene ontology task at BioCreative IV. Database (Oxford) (2014) 1.46
BioCreative-2012 virtual issue. Database (Oxford) (2012) 1.26
BioC interoperability track overview. Database (Oxford) (2014) 1.11
Managing the data deluge: data-driven GO category assignment improves while complexity of functional annotation increases. Database (Oxford) (2013) 1.06
GNormPlus: An Integrative Approach for Tagging Genes, Gene Families, and Protein Domains. Biomed Res Int (2015) 1.02
BC4GO: a full-text corpus for the BioCreative IV GO task. Database (Oxford) (2014) 1.01
Community challenges in biomedical text mining over 10 years: success, failure and the future. Brief Bioinform (2015) 1.00
Scaling drug indication curation through crowdsourcing. Database (Oxford) (2015) 0.97
Assisting manual literature curation for protein-protein interactions using BioQRator. Database (Oxford) (2014) 0.96
Big data in medicine is driving big changes. Yearb Med Inform (2014) 0.94
OntoGene web services for biomedical text mining. BMC Bioinformatics (2014) 0.92
Crowdsourcing in biomedicine: challenges and opportunities. Brief Bioinform (2015) 0.91
Toward Synthesizing Our Knowledge of Morphology: Using Ontologies and Machine Reasoning to Extract Presence/Absence Evolutionary Phenotypes across Studies. Syst Biol (2015) 0.89
Biomedical relation extraction: from binary to complex. Comput Math Methods Med (2014) 0.89
Overview of the interactive task in BioCreative V. Database (Oxford) (2016) 0.88
tmBioC: improving interoperability of text-mining tools with BioC. Database (Oxford) (2014) 0.87
Construction of phosphorylation interaction networks by text mining of full-length articles using the eFIP system. Database (Oxford) (2015) 0.86
EXTRACT: interactive extraction of environment metadata and term suggestion for metagenomic sample annotation. Database (Oxford) (2016) 0.85
Micropublications: a semantic model for claims, evidence, arguments and annotations in biomedical communications. J Biomed Semantics (2014) 0.84
tagtog: interactive and text-mining-assisted annotation of gene mentions in PLOS full-text articles. Database (Oxford) (2014) 0.83
T-HOD: a literature-based candidate gene database for hypertension, obesity and diabetes. Database (Oxford) (2013) 0.83
Manually curated database of rice proteins. Nucleic Acids Res (2013) 0.82
Moving the mountain: analysis of the effort required to transform comparative anatomy into computable anatomy. Database (Oxford) (2015) 0.82
BioCreative V BioC track overview: collaborative biocurator assistant task for BioGRID. Database (Oxford) (2016) 0.82
OntoMate: a text-mining tool aiding curation at the Rat Genome Database. Database (Oxford) (2015) 0.82
Cataloging the biomedical world of pain through semi-automated curation of molecular interactions. Database (Oxford) (2013) 0.80
Accessing biomedical literature in the current information landscape. Methods Mol Biol (2014) 0.79
Pressing needs of biomedical text mining in biocuration and beyond: opportunities and challenges. Database (Oxford) (2016) 0.75
Biocuration with insufficient resources and fixed timelines. Database (Oxford) (2015) 0.75
Overview of BioCreAtIvE: critical assessment of information extraction for biology. BMC Bioinformatics (2005) 14.50
An application of hierarchical kappa-type statistics in the assessment of majority agreement among multiple observers. Biometrics (1977) 9.41
Evaluation of text-mining systems for biology: overview of the Second BioCreative community challenge. Genome Biol (2008) 3.54
An Overview of BioCreative II.5. IEEE/ACM Trans Comput Biol Bioinform (2010) 3.01
Semi-automated curation of protein subcellular localization: a text mining-based approach to Gene Ontology (GO) Cellular Component curation. BMC Bioinformatics (2009) 2.74
Text mining for the biocuration workflow. Database (Oxford) (2012) 2.37
Overview of the BioCreative III Workshop. BMC Bioinformatics (2011) 2.31
GeneTUKit: a software for document-level gene normalization. Bioinformatics (2011) 2.28
Literature mining and database annotation of protein phosphorylation using a rule-based system. Bioinformatics (2005) 2.16
BioCreative III interactive task: an overview. BMC Bioinformatics (2011) 2.16
Phenex: ontological annotation of phenotypic diversity. PLoS One (2010) 2.13
Accelerating literature curation with text-mining tools: a case study of using PubTator to curate genes in PubMed abstracts. Database (Oxford) (2012) 1.89
NeXML: rich, extensible, and verifiable representation of comparative data and metadata. Syst Biol (2012) 1.86
SR4GN: a species recognition software tool for gene normalization. PLoS One (2012) 1.57
Biocurators and biocuration: surveying the 21st century challenges. Database (Oxford) (2012) 1.46
eGIFT: mining gene information from the literature. BMC Bioinformatics (2010) 1.32
Open semantic annotation of scientific publications using DOMEO. J Biomed Semantics (2012) 1.31
Using ODIN for a PharmGKB revalidation experiment. Database (Oxford) (2012) 1.29
Text mining in the biocuration workflow: applications for literature curation at WormBase, dictyBase and TAIR. Database (Oxford) (2012) 1.19
Integration of gene normalization stages and co-reference resolution using a Markov logic network. Bioinformatics (2011) 1.13
The eFIP system for text mining of protein interaction networks of phosphorylated proteins. Database (Oxford) (2012) 1.07
HypertenGene: extracting key hypertension genes from biomedical literature with position and automatically-generated template features. BMC Bioinformatics (2009) 1.05
PPInterFinder--a mining tool for extracting causal relations on human proteins from literature. Database (Oxford) (2013) 0.95
Reactome knowledgebase of human biological pathways and processes. Nucleic Acids Res (2008) 15.69
The Arabidopsis Information Resource (TAIR): gene structure and function annotation. Nucleic Acids Res (2007) 14.24
Reactome: a knowledge base of biologic pathways and processes. Genome Biol (2007) 13.36
Database resources of the National Center for Biotechnology Information. Nucleic Acids Res (2009) 12.51
Prepublication data sharing. Nature (2009) 12.24
Annotation of functional variation in personal genomes using RegulomeDB. Genome Res (2012) 11.47
Reactome: a database of reactions, pathways and biological processes. Nucleic Acids Res (2010) 11.23
OBO-Edit--an ontology editor for biologists. Bioinformatics (2007) 11.04
Database resources of the National Center for Biotechnology Information. Nucleic Acids Res (2010) 10.97
Big data: The future of biocuration. Nature (2008) 10.81
Tagging gene and protein names in biomedical text. Bioinformatics (2002) 10.03
The BioPAX community standard for pathway data sharing. Nat Biotechnol (2010) 9.19
A unified nomenclature for yeast autophagy-related genes. Dev Cell (2003) 9.18
Gene Ontology annotations at SGD: new data sources and annotation methods. Nucleic Acids Res (2007) 9.03
Database resources of the National Center for Biotechnology Information. Nucleic Acids Res (2011) 8.62
Saccharomyces Genome Database: the genomics resource of budding yeast. Nucleic Acids Res (2011) 8.57
The Reactome pathway knowledgebase. Nucleic Acids Res (2013) 8.56
The BioGRID Interaction Database: 2011 update. Nucleic Acids Res (2010) 8.46
Sentiment Analysis of Suicide Notes: A Shared Task. Biomed Inform Insights (2012) 8.27
The minimum information required for reporting a molecular interaction experiment (MIMIx). Nat Biotechnol (2007) 8.24
The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools. Nucleic Acids Res (2011) 8.18
The evolution of transcriptional regulation in eukaryotes. Mol Biol Evol (2003) 7.72
The Zebrafish Information Network: the zebrafish model organism database. Nucleic Acids Res (2006) 7.66
MINT, the molecular interaction database: 2009 update. Nucleic Acids Res (2009) 7.19
WormBase: better software, richer content. Nucleic Acids Res (2006) 6.78
GENETAG: a tagged corpus for gene/protein named entity recognition. BMC Bioinformatics (2005) 6.19
Evaluation of BioCreAtIvE assessment of task 2. BMC Bioinformatics (2005) 6.02
Overview of BioCreative II gene mention recognition. Genome Biol (2008) 5.67
The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data. Nucleic Acids Res (2013) 5.66
Dissecting virulence: systematic and functional analyses of a pathogenicity island. Proc Natl Acad Sci U S A (2004) 5.34
PubMed related articles: a probabilistic topic-based model for content similarity. BMC Bioinformatics (2007) 5.30
WormBase: a cross-species database for comparative genomics. Nucleic Acids Res (2003) 5.28
WormBase: a comprehensive resource for nematode research. Nucleic Acids Res (2009) 5.20
The UniProt-GO Annotation database in 2011. Nucleic Acids Res (2011) 5.19
Genome-wide association study identifies variants in the ABO locus associated with susceptibility to pancreatic cancer. Nat Genet (2009) 5.14
Overview of BioCreative II gene normalization. Genome Biol (2008) 5.05
A genome-wide association study identifies pancreatic cancer susceptibility loci on chromosomes 13q22.1, 1q32.1 and 5p15.33. Nat Genet (2010) 4.89
GeneWays: a system for extracting, analyzing, visualizing, and integrating molecular pathway data. J Biomed Inform (2004) 4.57
Habitat-Lite: a GSC case study based on free text terms for environmental metadata. OMICS (2008) 4.40
The MIntAct project--IntAct as a common curation platform for 11 molecular interaction databases. Nucleic Acids Res (2013) 4.39
The Zebrafish Information Network: the zebrafish model organism database provides expanded support for genotypes and phenotypes. Nucleic Acids Res (2007) 4.30
Biomedical language processing: what's beyond PubMed? Mol Cell (2006) 4.27
Manual curation is not sufficient for annotation of genomic databases. Bioinformatics (2007) 4.16
WormBase: a multi-species resource for nematode biology and genomics. Nucleic Acids Res (2004) 4.14
WormBase: new content and better access. Nucleic Acids Res (2006) 4.01
WormBase 2012: more genomes, more data, new website. Nucleic Acids Res (2011) 3.87
WormBase: a comprehensive data resource for Caenorhabditis biology and genomics. Nucleic Acids Res (2005) 3.82
WormBase 2007. Nucleic Acids Res (2007) 3.69
Detectable clonal mosaicism and its relationship to aging and cancer. Nat Genet (2012) 3.69
Phenotype ontologies: the bridge between genomics and evolution. Trends Ecol Evol (2007) 3.68
Antibiotic-induced perturbations of the intestinal microbiota alter host susceptibility to enteric infection. Infect Immun (2008) 3.68
Genome Snapshot: a new resource at the Saccharomyces Genome Database (SGD) presenting an overview of the Saccharomyces cerevisiae genome. Nucleic Acids Res (2006) 3.59
Risk factors for hepatocellular carcinoma: synergism of alcohol with viral hepatitis and diabetes mellitus. Hepatology (2002) 3.59
MicroRNAs in plasma of pancreatic ductal adenocarcinoma patients as novel blood-based biomarkers of disease. Cancer Prev Res (Phila) (2009) 3.55
BioThesaurus: a web-based thesaurus of protein and gene names. Bioinformatics (2005) 3.43
Saccharomyces Genome Database provides mutant phenotype data. Nucleic Acids Res (2009) 3.38
Linking entries in protein interaction database to structured text: the FEBS Letters experiment. FEBS Lett (2008) 3.35
Expanded protein information at SGD: new pages and proteome browser. Nucleic Acids Res (2006) 3.31
Understanding PubMed user search behavior through log analysis. Database (Oxford) (2009) 3.27
Protein interaction data curation: the International Molecular Exchange (IMEx) consortium. Nat Methods (2012) 3.17
The Protein-Protein Interaction tasks of BioCreative III: classification/ranking of articles and linking bio-ontology concepts to full text. BMC Bioinformatics (2011) 3.03
PubTator: a web-based text mining tool for assisting biocuration. Nucleic Acids Res (2013) 3.02
An Overview of BioCreative II.5. IEEE/ACM Trans Comput Biol Bioinform (2010) 3.01
The gene normalization task in BioCreative III. BMC Bioinformatics (2011) 2.89
DNorm: disease name normalization with pairwise learning to rank. Bioinformatics (2013) 2.83
OpenDMAP: an open source, ontology-driven concept analysis engine, with applications to capturing knowledge regarding protein transport, protein interactions and cell-type-specific gene expression. BMC Bioinformatics (2008) 2.81
Introducing meta-services for biomedical information extraction. Genome Biol (2008) 2.78
Recommending MeSH terms for annotating biomedical articles. J Am Med Inform Assoc (2011) 2.77
Plasma protein profiling for diagnosis of pancreatic cancer reveals the presence of host response proteins. Clin Cancer Res (2005) 2.76
Semi-automated curation of protein subcellular localization: a text mining-based approach to Gene Ontology (GO) Cellular Component curation. BMC Bioinformatics (2009) 2.74
PpAtg30 tags peroxisomes for turnover by selective autophagy. Dev Cell (2008) 2.73
Text mining and manual curation of chemical-gene-disease networks for the comparative toxicogenomics database (CTD). BMC Bioinformatics (2009) 2.72
BioC: a minimalist approach to interoperability for biomedical text processing. Database (Oxford) (2013) 2.69
Fusion of FIG to the receptor tyrosine kinase ROS in a glioblastoma with an interstitial del(6)(q21q21). Genes Chromosomes Cancer (2003) 2.67