Published in BMC Bioinformatics on July 09, 2012
The CHEMDNER corpus of chemicals and drugs and its annotation principles. J Cheminform (2015) 1.96
BioLemmatizer: a lemmatization tool for morphological processing of biomedical text. J Biomed Semantics (2012) 1.90
NCBI disease corpus: a resource for disease name recognition and concept normalization. J Biomed Inform (2014) 1.83
Large-scale biomedical concept recognition: an evaluation of current automatic annotators and their parameters. BMC Bioinformatics (2014) 1.52
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
Protein Ontology: a controlled structured network of protein entities. Nucleic Acids Res (2013) 1.33
Large-scale event extraction from literature with multi-level gene normalization. PLoS One (2013) 1.30
A modular framework for biomedical concept recognition. BMC Bioinformatics (2013) 1.14
Anatomical entity mention recognition at literature scale. Bioinformatics (2013) 1.07
BC4GO: a full-text corpus for the BioCreative IV GO task. Database (Oxford) (2014) 1.01
Evaluating a variety of text-mined features for automatic protein function prediction with GOstruct. J Biomed Semantics (2015) 1.00
Collective instance-level gene normalization on the IGN corpus. PLoS One (2013) 1.00
Processing biological literature with customizable Web services supporting interoperable formats. Database (Oxford) (2014) 0.99
Egas: a collaborative and interactive document curation platform. Database (Oxford) (2014) 0.90
Automated annotation of functional imaging experiments via multi-label classification. Front Neurosci (2013) 0.90
Representing annotation compositionality and provenance for the Semantic Web. J Biomed Semantics (2013) 0.88
Generation of silver standard concept annotations from biomedical texts with special relevance to phenotypes. PLoS One (2015) 0.85
Evaluating gold standard corpora against gene/protein tagging solutions and lexical resources. J Biomed Semantics (2013) 0.85
A document processing pipeline for annotating chemical entities in scientific documents. J Cheminform (2015) 0.82
NOBLE - Flexible concept recognition for large-scale biomedical natural language processing. BMC Bioinformatics (2016) 0.81
Finding pathway-modulating genes from a novel Ontology Fingerprint-derived gene network. Nucleic Acids Res (2014) 0.80
An analysis on the entity annotations in biological corpora. F1000Res (2014) 0.80
Evaluation and cross-comparison of lexical entities of biological interest (LexEBI). PLoS One (2013) 0.79
Assessing the impact of case sensitivity and term information gain on biomedical concept recognition. PLoS One (2015) 0.78
Gene Ontology synonym generation rules lead to increased performance in biomedical concept recognition. J Biomed Semantics (2016) 0.77
DeTEXT: A Database for Evaluating Text Extraction from Biomedical Literature Figures. PLoS One (2015) 0.75
Text mining resources for the life sciences. Database (Oxford) (2016) 0.75
A Framework for Collaborative Curation of Neuroscientific Literature. Front Neuroinform (2017) 0.75
A multilingual gold-standard corpus for biomedical concept recognition: the Mantra GSC. J Am Med Inform Assoc (2015) 0.75
Annotating patient clinical records with syntactic chunks and named entities: the Harvey Corpus. Lang Resour Eval (2016) 0.75
Recognizing chemicals in patents: a comparative analysis. J Cheminform (2016) 0.75
Tutorial on Protein Ontology Resources. Methods Mol Biol (2017) 0.75
Automatically Detecting Acute Myocardial Infarction Events from EHR Text: A Preliminary Study. AMIA Annu Symp Proc (2014) 0.75
Coreference annotation and resolution in the Colorado Richly Annotated Full Text (CRAFT) corpus of biomedical journal articles. BMC Bioinformatics (2017) 0.75
Semantic annotation in biomedicine: the current landscape. J Biomed Semantics (2017) 0.75
A neural network multi-task learning approach to biomedical named entity recognition. BMC Bioinformatics (2017) 0.75
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Database resources of the National Center for Biotechnology Information. Nucleic Acids Res (2008) 21.36
The Sequence Ontology: a tool for the unification of genome annotations. Genome Biol (2005) 18.20
ChEBI: a database and ontology for chemical entities of biological interest. Nucleic Acids Res (2007) 13.08
An ontology for cell types. Genome Biol (2005) 11.71
Investigating semantic similarity measures across the Gene Ontology: the relationship between sequence and annotation. Bioinformatics (2003) 9.47
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GENIA corpus--semantically annotated corpus for bio-textmining. Bioinformatics (2003) 8.89
Literature mining for the biologist: from information retrieval to biological discovery. Nat Rev Genet (2006) 8.23
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MedPost: a part-of-speech tagger for bioMedical text. Bioinformatics (2004) 6.53
GENETAG: a tagged corpus for gene/protein named entity recognition. BMC Bioinformatics (2005) 6.19
Corpus annotation for mining biomedical events from literature. BMC Bioinformatics (2008) 5.84
The Gene Ontology: enhancements for 2011. Nucleic Acids Res (2011) 5.82
The Mouse Genome Database (MGD): comprehensive resource for genetics and genomics of the laboratory mouse. Nucleic Acids Res (2011) 5.60
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Biomedical ontologies in action: role in knowledge management, data integration and decision support. Yearb Med Inform (2008) 3.96
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Information extraction from full text scientific articles: where are the keywords? BMC Bioinformatics (2003) 2.64
BioRAT: extracting biological information from full-length papers. Bioinformatics (2004) 2.63
Evolution of the Sequence Ontology terms and relationships. J Biomed Inform (2010) 2.60
Can bibliographic pointers for known biological data be found automatically? Protein interactions as a case study. Comp Funct Genomics (2001) 2.21
Building a semantically annotated corpus of clinical texts. J Biomed Inform (2009) 2.03
GO PaD: the Gene Ontology Partition Database. Nucleic Acids Res (2006) 1.98
CALBC silver standard corpus. J Bioinform Comput Biol (2010) 1.74
Domain-specific language models and lexicons for tagging. J Biomed Inform (2005) 1.72
Construction of an annotated corpus to support biomedical information extraction. BMC Bioinformatics (2009) 1.55
Biomedical discovery acceleration, with applications to craniofacial development. PLoS Comput Biol (2009) 1.49
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
Alzforum and SWAN: the present and future of scientific web communities. Brief Bioinform (2007) 1.42
The ontology of biological taxa. Bioinformatics (2008) 1.17
A reappraisal of sentence and token splitting for life sciences documents. Stud Health Technol Inform (2007) 1.04
The Cell Line Ontology and its use in tagging cell line names in biomedical text. AMIA Annu Symp Proc (2007) 1.00
Parenthetically speaking: classifying the contents of parentheses for text mining. AMIA Annu Symp Proc (2011) 0.96
Desiderata for ontologies to be used in semantic annotation of biomedical documents. J Biomed Inform (2010) 0.91
Protein name tagging guidelines: lessons learned. Comp Funct Genomics (2005) 0.91
In the pursuit of a semantic similarity metric based on UMLS annotations for articles in PubMed Central Open Access. J Biomed Inform (2015) 0.82
The Mouse Genome Database (MGD): mouse biology and model systems. Nucleic Acids Res (2007) 9.75
The Mouse Genome Database (MGD): integrating biology with the genome. Nucleic Acids Res (2004) 8.91
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The Mouse Genome Database (MGD): from genes to mice--a community resource for mouse biology. Nucleic Acids Res (2005) 8.19
The mouse Gene Expression Database (GXD): updates and enhancements. Nucleic Acids Res (2004) 7.26
A promoter-level mammalian expression atlas. Nature (2014) 6.25
Overview of BioCreative II gene mention recognition. Genome Biol (2008) 5.67
Extension and integration of the gene ontology (GO): combining GO vocabularies with external vocabularies. Genome Res (2002) 5.67
The Mouse Genome Database (MGD): comprehensive resource for genetics and genomics of the laboratory mouse. Nucleic Acids Res (2011) 5.60
A global analysis of Caenorhabditis elegans operons. Nature (2002) 5.29
Overview of BioCreative II gene normalization. Genome Biol (2008) 5.05
A critical assessment of Mus musculus gene function prediction using integrated genomic evidence. Genome Biol (2008) 4.78
A large-scale evaluation of computational protein function prediction. Nat Methods (2013) 4.61
The mouse genome database (MGD): new features facilitating a model system. Nucleic Acids Res (2006) 4.52
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
Manual curation is not sufficient for annotation of genomic databases. Bioinformatics (2007) 4.16
The Protein Ontology: a structured representation of protein forms and complexes. Nucleic Acids Res (2010) 3.74
Logical development of the cell ontology. BMC Bioinformatics (2011) 3.68
Mesenchymal stem cell implantation in a swine myocardial infarct model: engraftment and functional effects. Ann Thorac Surg (2002) 3.62
Stroke and encephalopathy after cardiac surgery: an update. Stroke (2005) 2.91
The gene normalization task in BioCreative III. BMC Bioinformatics (2011) 2.89
The structural and content aspects of abstracts versus bodies of full text journal articles are different. BMC Bioinformatics (2010) 2.88
Gene Ontology annotations: what they mean and where they come from. BMC Bioinformatics (2008) 2.84
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
Text mining and manual curation of chemical-gene-disease networks for the comparative toxicogenomics database (CTD). BMC Bioinformatics (2009) 2.72
Rules and guidelines for mouse gene, allele, and mutation nomenclature: a condensed version. Genomics (2002) 2.72
BioC: a minimalist approach to interoperability for biomedical text processing. Database (Oxford) (2013) 2.69
Connecting sequence and biology in the laboratory mouse. Genome Res (2003) 2.69
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 Mouse Genome Database: enhancements and updates. Nucleic Acids Res (2009) 2.44
AMIA Board white paper: definition of biomedical informatics and specification of core competencies for graduate education in the discipline. J Am Med Inform Assoc (2012) 2.40
Text mining for the biocuration workflow. Database (Oxford) (2012) 2.37
U-Compare: share and compare text mining tools with UIMA. Bioinformatics (2009) 2.28
Clinical outcomes of noninfectious sternal dehiscence after median sternotomy. Ann Thorac Surg (2006) 2.25
Ontology engineering. Nat Biotechnol (2010) 2.24
A procedure for assessing GO annotation consistency. Bioinformatics (2005) 2.11
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
Ontology development for biological systems: immunology. Bioinformatics (2007) 2.03
Watershed strokes after cardiac surgery: diagnosis, etiology, and outcome. Stroke (2006) 1.98
The mouse genome database: genotypes, phenotypes, and models of human disease. Nucleic Acids Res (2012) 1.98
Towards BioDBcore: a community-defined information specification for biological databases. Nucleic Acids Res (2010) 1.97
Concept recognition for extracting protein interaction relations from biomedical text. Genome Biol (2008) 1.93
Coronary artery bypass grafting with or without surgical ventricular restoration: a comparison. Ann Thorac Surg (2008) 1.92
Evaluation of lexical methods for detecting relationships between concepts from multiple ontologies. Pac Symp Biocomput (2006) 1.90
BioLemmatizer: a lemmatization tool for morphological processing of biomedical text. J Biomed Semantics (2012) 1.90
An overview of the BioCreative 2012 Workshop Track III: interactive text mining task. Database (Oxford) (2013) 1.82
Finding GeneRIFs via gene ontology annotations. Pac Symp Biocomput (2006) 1.77
Increased mortality at low-volume orthotopic heart transplantation centers: should current standards change? Ann Thorac Surg (2008) 1.68
A 32-year experience with surgical repair of sinus of valsalva aneurysms. J Card Surg (2005) 1.68
Impact of the lung allocation score on resource utilization after lung transplantation in the United States. J Heart Lung Transplant (2010) 1.67
On the Use of Gene Ontology Annotations to Assess Functional Similarity among Orthologs and Paralogs: A Short Report. PLoS Comput Biol (2012) 1.65
Valproic acid prevents brain injury in a canine model of hypothermic circulatory arrest: a promising new approach to neuroprotection during cardiac surgery. Ann Thorac Surg (2006) 1.64
Delirium after coronary artery bypass graft surgery and late mortality. Ann Neurol (2010) 1.63
Application of haptic feedback to robotic surgery. J Laparoendosc Adv Surg Tech A (2004) 1.62
GeneRIF quality assurance as summary revision. Pac Symp Biocomput (2007) 1.60
Cognitive and neurologic outcomes after coronary-artery bypass surgery. N Engl J Med (2012) 1.58
Simple score to assess the risk of rejection after orthotopic heart transplantation. Circulation (2012) 1.57
Do management strategies for coronary artery disease influence 6-year cognitive outcomes? Ann Thorac Surg (2009) 1.56
Ontological visualization of protein-protein interactions. BMC Bioinformatics (2005) 1.56
Large-scale biomedical concept recognition: an evaluation of current automatic annotators and their parameters. BMC Bioinformatics (2014) 1.52
Biomedical discovery acceleration, with applications to craniofacial development. PLoS Comput Biol (2009) 1.49
Hematopoietic cell types: prototype for a revised cell ontology. J Biomed Inform (2010) 1.48
A method for increasing expressivity of Gene Ontology annotations using a compositional approach. BMC Bioinformatics (2014) 1.48
Ontology quality assurance through analysis of term transformations. Bioinformatics (2009) 1.47
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
Aortic valve replacement and concomitant coronary artery bypass: assessing the impact of multiple grafts. Ann Thorac Surg (2007) 1.46
Pilot implementation of a perioperative protocol to guide operating room-to-intensive care unit patient handoffs. J Cardiothorac Vasc Anesth (2011) 1.45
Intraoperative hemoglobin levels and transfusion independently predict stroke after cardiac operations. Ann Thorac Surg (2011) 1.45
Subjective memory symptoms in surgical and nonsurgical coronary artery patients: 6-year follow-up. Ann Thorac Surg (2009) 1.43
Covert video surveillance -- a response to Professor Southall and Dr. Samuels. J Med Ethics (1996) 1.42
Cognition 6 years after surgical or medical therapy for coronary artery disease. Ann Neurol (2008) 1.41
Pharmacological preconditioning ameliorates neurological injury in a model of spinal cord ischemia. Ann Thorac Surg (2002) 1.41
Intrinsic evaluation of text mining tools may not predict performance on realistic tasks. Pac Symp Biocomput (2008) 1.40
Influence of pretransplant panel-reactive antibody on outcomes in 8,160 heart transplant recipients in recent era. Ann Thorac Surg (2007) 1.39
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
Protein Ontology: a controlled structured network of protein entities. Nucleic Acids Res (2013) 1.33
Corpus refactoring: a feasibility study. J Biomed Discov Collab (2007) 1.29
Cognitive changes with coronary artery disease: a prospective study of coronary artery bypass graft patients and nonsurgical controls. Ann Thorac Surg (2003) 1.29
Literature mining of protein-residue associations with graph rules learned through distant supervision. J Biomed Semantics (2012) 1.25
The PhenoGen informatics website: tools for analyses of complex traits. BMC Genet (2007) 1.25
Towards BioDBcore: a community-defined information specification for biological databases. Database (Oxford) (2011) 1.24
Gene Ontology annotation of sequence-specific DNA binding transcription factors: setting the stage for a large-scale curation effort. Database (Oxford) (2013) 1.24
EuroSCORE predicts short- and mid-term mortality in combined aortic valve replacement and coronary artery bypass patients. J Card Surg (2010) 1.22
Molecular subtypes of osteosarcoma identified by reducing tumor heterogeneity through an interspecies comparative approach. Bone (2011) 1.21