Published in Genome Biol on September 01, 2008
Overview of the protein-protein interaction annotation extraction task of BioCreative II. Genome Biol (2008) 6.38
Linking genes to literature: text mining, information extraction, and retrieval applications for biology. Genome Biol (2008) 4.36
The structural and content aspects of abstracts versus bodies of full text journal articles are different. BMC Bioinformatics (2010) 2.88
Introducing meta-services for biomedical information extraction. Genome Biol (2008) 2.78
SR4GN: a species recognition software tool for gene normalization. PLoS One (2012) 1.57
Biomedical discovery acceleration, with applications to craniofacial development. PLoS Comput Biol (2009) 1.49
A realistic assessment of methods for extracting gene/protein interactions from free text. BMC Bioinformatics (2009) 1.46
Improving accuracy for identifying related PubMed queries by an integrated approach. J Biomed Inform (2008) 1.30
Using rule-based natural language processing to improve disease normalization in biomedical text. J Am Med Inform Assoc (2012) 1.27
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
Exploring species-based strategies for gene normalization. IEEE/ACM Trans Comput Biol Bioinform (2010) 0.97
Parenthetically speaking: classifying the contents of parentheses for text mining. AMIA Annu Symp Proc (2011) 0.96
Chapter 16: text mining for translational bioinformatics. PLoS Comput Biol (2013) 0.94
Automatically Detecting Failures in Natural Language Processing Tools for Online Community Text. J Med Internet Res (2015) 0.88
SimConcept: A Hybrid Approach for Simplifying Composite Named Entities in Biomedicine. ACM BCB (2015) 0.81
Methodological Issues in Predicting Pediatric Epilepsy Surgery Candidates Through Natural Language Processing and Machine Learning. Biomed Inform Insights (2016) 0.78
Dynamic programming re-ranking for PPI interactor and pair extraction in full-text articles. BMC Bioinformatics (2011) 0.77
Mapping Phenotypic Information in Heterogeneous Textual Sources to a Domain-Specific Terminological Resource. PLoS One (2016) 0.75
Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet (2000) 336.52
Entrez Gene: gene-centered information at NCBI. Nucleic Acids Res (2006) 20.92
Tagging gene and protein names in biomedical text. Bioinformatics (2002) 10.03
A simple algorithm for identifying abbreviation definitions in biomedical text. Pac Symp Biocomput (2003) 9.78
Toward information extraction: identifying protein names from biological papers. Pac Symp Biocomput (1998) 8.17
BioCreAtIvE task 1A: gene mention finding evaluation. BMC Bioinformatics (2005) 8.09
ABNER: an open source tool for automatically tagging genes, proteins and other entity names in text. Bioinformatics (2005) 6.92
Overview of BioCreAtIvE task 1B: normalized gene lists. BMC Bioinformatics (2005) 6.85
Overview of the protein-protein interaction annotation extraction task of BioCreative II. Genome Biol (2008) 6.38
Evaluation of BioCreAtIvE assessment of task 2. BMC Bioinformatics (2005) 6.02
Overview of BioCreative II gene mention recognition. Genome Biol (2008) 5.67
Overview of BioCreative II gene normalization. Genome Biol (2008) 5.05
Automatic extraction of biological information from scientific text: protein-protein interactions. Proc Int Conf Intell Syst Mol Biol (1999) 4.55
Disambiguating proteins, genes, and RNA in text: a machine learning approach. Bioinformatics (2001) 3.66
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
Gene name ambiguity of eukaryotic nomenclatures. Bioinformatics (2004) 2.72
BioCreAtIvE task1A: entity identification with a stochastic tagger. BMC Bioinformatics (2005) 2.05
Enhancing access to the Bibliome: the TREC 2004 Genomics Track. J Biomed Discov Collab (2006) 1.91
Finding GeneRIFs via gene ontology annotations. Pac Symp Biocomput (2006) 1.77
MINT and IntAct contribute to the Second BioCreative challenge: serving the text-mining community with high quality molecular interaction data. Genome Biol (2008) 1.76
Biological nomenclatures: a source of lexical knowledge and ambiguity. Pac Symp Biocomput (2004) 1.52
Corpus refactoring: a feasibility study. J Biomed Discov Collab (2007) 1.29
QIIME allows analysis of high-throughput community sequencing data. Nat Methods (2010) 85.34
PyCogent: a toolkit for making sense from sequence. Genome Biol (2007) 20.64
Human gut microbiome viewed across age and geography. Nature (2012) 19.31
Database resources of the National Center for Biotechnology Information. Nucleic Acids Res (2009) 12.51
Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat Biotechnol (2013) 11.05
Database resources of the National Center for Biotechnology Information. Nucleic Acids Res (2010) 10.97
Database resources of the National Center for Biotechnology Information. Nucleic Acids Res (2011) 8.62
Sentiment Analysis of Suicide Notes: A Shared Task. Biomed Inform Insights (2012) 8.27
Overview of BioCreative II gene mention recognition. Genome Biol (2008) 5.67
Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing. Nat Methods (2012) 5.41
Soil bacterial and fungal communities across a pH gradient in an arable soil. ISME J (2010) 5.37
Overview of BioCreative II gene normalization. Genome Biol (2008) 5.05
Defining seasonal marine microbial community dynamics. ISME J (2011) 4.61
Habitat-Lite: a GSC case study based on free text terms for environmental metadata. OMICS (2008) 4.40
Biomedical language processing: what's beyond PubMed? Mol Cell (2006) 4.27
Examining the global distribution of dominant archaeal populations in soil. ISME J (2010) 4.24
Manual curation is not sufficient for annotation of genomic databases. Bioinformatics (2007) 4.16
Cross-biome metagenomic analyses of soil microbial communities and their functional attributes. Proc Natl Acad Sci U S A (2012) 3.71
Understanding PubMed user search behavior through log analysis. Database (Oxford) (2009) 3.27
Impact of training sets on classification of high-throughput bacterial 16s rRNA gene surveys. ISME J (2011) 3.24
The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome. Gigascience (2012) 3.24
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
Cohabiting family members share microbiota with one another and with their dogs. Elife (2013) 2.92
The structural and content aspects of abstracts versus bodies of full text journal articles are different. BMC Bioinformatics (2010) 2.88
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
Text mining and manual curation of chemical-gene-disease networks for the comparative toxicogenomics database (CTD). BMC Bioinformatics (2009) 2.72
Sequencing our way towards understanding global eukaryotic biodiversity. Trends Ecol Evol (2012) 2.70
BioC: a minimalist approach to interoperability for biomedical text processing. Database (Oxford) (2013) 2.69
PrimerProspector: de novo design and taxonomic analysis of barcoded polymerase chain reaction primers. Bioinformatics (2011) 2.62
Implications of compositionality in the gene ontology for its curation and usage. Pac Symp Biocomput (2005) 2.54
MutationFinder: a high-performance system for extracting point mutation mentions from text. Bioinformatics (2007) 2.53
The under-recognized dominance of Verrucomicrobia in soil bacterial communities. Soil Biol Biochem (2011) 2.42
Text mining for the biocuration workflow. Database (Oxford) (2012) 2.37
Overview of the BioCreative III Workshop. BMC Bioinformatics (2011) 2.31
U-Compare: share and compare text mining tools with UIMA. Bioinformatics (2009) 2.28
BioCreative III interactive task: an overview. BMC Bioinformatics (2011) 2.16
Using QIIME to analyze 16S rRNA gene sequences from microbial communities. Curr Protoc Bioinformatics (2011) 2.15
An open-source framework for large-scale, flexible evaluation of biomedical text mining systems. J Biomed Discov Collab (2008) 2.07
BioCreAtIvE task1A: entity identification with a stochastic tagger. BMC Bioinformatics (2005) 2.05
Advancing our understanding of the human microbiome using QIIME. Methods Enzymol (2013) 2.04
Enrichment of OBO ontologies. J Biomed Inform (2006) 1.95
Concept annotation in the CRAFT corpus. BMC Bioinformatics (2012) 1.94
Semi-automatic semantic annotation of PubMed queries: a study on quality, efficiency, satisfaction. J Biomed Inform (2010) 1.91
Evaluation of lexical methods for detecting relationships between concepts from multiple ontologies. Pac Symp Biocomput (2006) 1.90
Accelerating literature curation with text-mining tools: a case study of using PubTator to curate genes in PubMed abstracts. Database (Oxford) (2012) 1.89
tmVar: a text mining approach for extracting sequence variants in biomedical literature. Bioinformatics (2013) 1.87
Using QIIME to analyze 16S rRNA gene sequences from microbial communities. Curr Protoc Microbiol (2012) 1.87
Bacterial communities associated with the lichen symbiosis. Appl Environ Microbiol (2010) 1.85
An overview of the BioCreative 2012 Workshop Track III: interactive text mining task. Database (Oxford) (2013) 1.82
A meta-analysis of changes in bacterial and archaeal communities with time. ISME J (2013) 1.80
Getting started in text mining. PLoS Comput Biol (2008) 1.79
A general architecture for intelligent tutoring of diagnostic classification problem solving. AMIA Annu Symp Proc (2003) 1.79
Evidence for a persistent microbial seed bank throughout the global ocean. Proc Natl Acad Sci U S A (2013) 1.78
Finding GeneRIFs via gene ontology annotations. Pac Symp Biocomput (2006) 1.77
Evaluation of an intelligent tutoring system in pathology: effects of external representation on performance gains, metacognition, and acceptance. J Am Med Inform Assoc (2007) 1.61
GeneRIF quality assurance as summary revision. Pac Symp Biocomput (2007) 1.60
SR4GN: a species recognition software tool for gene normalization. PLoS One (2012) 1.57
Large-scale biomedical concept recognition: an evaluation of current automatic annotators and their parameters. BMC Bioinformatics (2014) 1.52
Nominalization and alternations in biomedical language. PLoS One (2008) 1.52
Comparison of Illumina paired-end and single-direction sequencing for microbial 16S rRNA gene amplicon surveys. ISME J (2011) 1.52
Phylogenetic stratigraphy in the Guerrero Negro hypersaline microbial mat. ISME J (2012) 1.51
Identification of OBO nonalignments and its implications for OBO enrichment. Bioinformatics (2008) 1.49
Biomedical discovery acceleration, with applications to craniofacial development. PLoS Comput Biol (2009) 1.49
Ontology quality assurance through analysis of term transformations. Bioinformatics (2009) 1.47
Diversity, distribution and sources of bacteria in residential kitchens. Environ Microbiol (2012) 1.46
A corpus of full-text journal articles is a robust evaluation tool for revealing differences in performance of biomedical natural language processing tools. BMC Bioinformatics (2012) 1.46
Automated detection of heuristics and biases among pathologists in a computer-based system. Adv Health Sci Educ Theory Pract (2012) 1.46
Proteome Analyst: custom predictions with explanations in a web-based tool for high-throughput proteome annotations. Nucleic Acids Res (2004) 1.46
Collaborative cloud-enabled tools allow rapid, reproducible biological insights. ISME J (2012) 1.43
Intrinsic evaluation of text mining tools may not predict performance on realistic tasks. Pac Symp Biocomput (2008) 1.40
Temporal variability is a personalized feature of the human microbiome. Genome Biol (2014) 1.39
Empirical data on corpus design and usage in biomedical natural language processing. AMIA Annu Symp Proc (2005) 1.37
Approximate subgraph matching-based literature mining for biomedical events and relations. PLoS One (2013) 1.37
The textual characteristics of traditional and Open Access scientific journals are similar. BMC Bioinformatics (2009) 1.37
The interpersonal and intrapersonal diversity of human-associated microbiota in key body sites. J Allergy Clin Immunol (2012) 1.35
Gene expression profile identifies tyrosine kinase c-Met as a targetable mediator of antiangiogenic therapy resistance. Clin Cancer Res (2013) 1.35
Microarray analysis verifies two distinct phenotypes of glioblastomas resistant to antiangiogenic therapy. Clin Cancer Res (2012) 1.35
Improving links between literature and biological data with text mining: a case study with GEO, PDB and MEDLINE. Database (Oxford) (2012) 1.32
Conditionally rare taxa disproportionately contribute to temporal changes in microbial diversity. MBio (2014) 1.32