Published in BMC Bioinformatics on January 31, 2008
All-paths graph kernel for protein-protein interaction extraction with evaluation of cross-corpus learning. BMC Bioinformatics (2008) 3.27
Using text to build semantic networks for pharmacogenomics. J Biomed Inform (2010) 2.19
A comprehensive benchmark of kernel methods to extract protein-protein interactions from literature. PLoS Comput Biol (2010) 2.03
Concept recognition for extracting protein interaction relations from biomedical text. Genome Biol (2008) 1.93
Recent progress in automatically extracting information from the pharmacogenomic literature. Pharmacogenomics (2010) 1.88
Text-mining solutions for biomedical research: enabling integrative biology. Nat Rev Genet (2012) 1.68
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
A realistic assessment of methods for extracting gene/protein interactions from free text. BMC Bioinformatics (2009) 1.46
Integration and publication of heterogeneous text-mined relationships on the Semantic Web. J Biomed Semantics (2011) 1.29
Challenges for automatically extracting molecular interactions from full-text articles. BMC Bioinformatics (2009) 1.11
Semantic role labeling for protein transport predicates. BMC Bioinformatics (2008) 1.10
Improving the extraction of complex regulatory events from scientific text by using ontology-based inference. J Biomed Semantics (2011) 1.04
Preliminary evaluation of the CellFinder literature curation pipeline for gene expression in kidney cells and anatomical parts. Database (Oxford) (2013) 0.99
U-Compare bio-event meta-service: compatible BioNLP event extraction services. BMC Bioinformatics (2011) 0.99
Detection of interaction articles and experimental methods in biomedical literature. BMC Bioinformatics (2011) 0.98
Exploring species-based strategies for gene normalization. IEEE/ACM Trans Comput Biol Bioinform (2010) 0.97
The role of ontologies in biological and biomedical research: a functional perspective. Brief Bioinform (2015) 0.96
Looking at cerebellar malformations through text-mined interactomes of mice and humans. PLoS Comput Biol (2009) 0.95
Chapter 16: text mining for translational bioinformatics. PLoS Comput Biol (2013) 0.94
A generalizable NLP framework for fast development of pattern-based biomedical relation extraction systems. BMC Bioinformatics (2014) 0.94
A UIMA wrapper for the NCBO annotator. Bioinformatics (2010) 0.93
Representing annotation compositionality and provenance for the Semantic Web. J Biomed Semantics (2013) 0.88
HIGH-PRECISION BIOLOGICAL EVENT EXTRACTION: EFFECTS OF SYSTEM AND OF DATA. Comput Intell (2011) 0.88
Simple tricks for improving pattern-based information extraction from the biomedical literature. J Biomed Semantics (2010) 0.88
Automatic extraction of nanoparticle properties using natural language processing: NanoSifter an application to acquire PAMAM dendrimer properties. PLoS One (2014) 0.87
RLIMS-P 2.0: A Generalizable Rule-Based Information Extraction System for Literature Mining of Protein Phosphorylation Information. IEEE/ACM Trans Comput Biol Bioinform (2015) 0.87
Ranking gene-drug relationships in biomedical literature using Latent Dirichlet Allocation. Pac Symp Biocomput (2012) 0.86
Construction of phosphorylation interaction networks by text mining of full-length articles using the eFIP system. Database (Oxford) (2015) 0.86
SimConcept: a hybrid approach for simplifying composite named entities in biomedical text. IEEE J Biomed Health Inform (2015) 0.84
KnowLife: a versatile approach for constructing a large knowledge graph for biomedical sciences. BMC Bioinformatics (2015) 0.83
Context-specific protein network miner--an online system for exploring context-specific protein interaction networks from the literature. PLoS One (2012) 0.83
A mutation-centric approach to identifying pharmacogenomic relations in text. J Biomed Inform (2012) 0.83
What the papers say: text mining for genomics and systems biology. Hum Genomics (2010) 0.82
Teaching computers to read the pharmacogenomics literature ... so you don't have to. Pharmacogenomics (2010) 0.82
SimConcept: A Hybrid Approach for Simplifying Composite Named Entities in Biomedicine. ACM BCB (2015) 0.81
Graph theory enables drug repurposing--how a mathematical model can drive the discovery of hidden mechanisms of action. PLoS One (2014) 0.80
Extraction of genotype-phenotype-drug relationships from text: from entity recognition to bioinformatics application. Pac Symp Biocomput (2010) 0.79
PIMiner: a web tool for extraction of protein interactions from biomedical literature. Int J Data Min Bioinform (2013) 0.77
Is the crowd better as an assistant or a replacement in ontology engineering? An exploration through the lens of the Gene Ontology. J Biomed Inform (2016) 0.75
AtPID: a genome-scale resource for genotype-phenotype associations in Arabidopsis. Nucleic Acids Res (2016) 0.75
Knowledge Author: facilitating user-driven, domain content development to support clinical information extraction. J Biomed Semantics (2016) 0.75
BioEve Search: A Novel Framework to Facilitate Interactive Literature Search. Adv Bioinformatics (2012) 0.75
Differential gene expression in disease: a comparison between high-throughput studies and the literature. BMC Med Genomics (2017) 0.75
Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet (2000) 336.52
Effective mapping of biomedical text to the UMLS Metathesaurus: the MetaMap program. Proc AMIA Symp (2001) 40.22
IntAct: an open source molecular interaction database. Nucleic Acids Res (2004) 15.02
The interaction of domain knowledge and linguistic structure in natural language processing: interpreting hypernymic propositions in biomedical text. J Biomed Inform (2003) 8.00
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
A gene network for navigating the literature. Nat Genet (2004) 6.43
Comparative experiments on learning information extractors for proteins and their interactions. Artif Intell Med (2005) 5.44
Overview of BioCreative II gene normalization. Genome Biol (2008) 5.05
Content-rich biological network constructed by mining PubMed abstracts. BMC Bioinformatics (2004) 4.97
GeneWays: a system for extracting, analyzing, visualizing, and integrating molecular pathway data. J Biomed Inform (2004) 4.57
Automatic extraction of biological information from scientific text: protein-protein interactions. Proc Int Conf Intell Syst Mol Biol (1999) 4.55
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
Extraction of regulatory gene/protein networks from Medline. Bioinformatics (2005) 3.43
Constructing biological knowledge bases by extracting information from text sources. Proc Int Conf Intell Syst Mol Biol (1999) 3.33
Extraction of protein interaction information from unstructured text using a context-free grammar. Bioinformatics (2003) 3.11
Extracting semantic predications from Medline citations for pharmacogenomics. Pac Symp Biocomput (2007) 3.04
Automated extraction of mutation data from the literature: application of MuteXt to G protein-coupled receptors and nuclear hormone receptors. Bioinformatics (2004) 3.03
Mining MEDLINE: abstracts, sentences, or phrases? Pac Symp Biocomput (2002) 2.82
Protégé-2000: an open-source ontology-development and knowledge-acquisition environment. AMIA Annu Symp Proc (2003) 2.73
Facts from text--is text mining ready to deliver? PLoS Biol (2005) 2.66
BioRAT: extracting biological information from full-length papers. Bioinformatics (2004) 2.63
PASBio: predicate-argument structures for event extraction in molecular biology. BMC Bioinformatics (2004) 2.41
Semantic relations asserting the etiology of genetic diseases. AMIA Annu Symp Proc (2003) 2.32
Can bibliographic pointers for known biological data be found automatically? Protein interactions as a case study. Comp Funct Genomics (2001) 2.21
Literature mining and database annotation of protein phosphorylation using a rule-based system. Bioinformatics (2005) 2.16
Event extraction from biomedical papers using a full parser. Pac Symp Biocomput (2001) 2.08
Mining functional information associated with expression arrays. Funct Integr Genomics (2001) 1.81
Extraction of transcript diversity from scientific literature. PLoS Comput Biol (2005) 1.64
Automatic extraction of gene/protein biological functions from biomedical text. Bioinformatics (2004) 1.59
Argument-predicate distance as a filter for enhancing precision in extracting predications on the genetic etiology of disease. BMC Bioinformatics (2006) 1.55
Bidirectional incremental parsing for automatic pathway identification with combinatory categorial grammar. Pac Symp Biocomput (2001) 1.54
A shallow parser based on closed-class words to capture relations in biomedical text. J Biomed Inform (2003) 1.53
An environment for relation mining over richly annotated corpora: the case of GENIA. BMC Bioinformatics (2006) 1.45
Beyond the clause: extraction of phosphorylation information from medline abstracts. Bioinformatics (2005) 1.42
Protein structures and information extraction from biological texts: the PASTA system. Bioinformatics (2003) 1.36
A critical review of PASBio's argument structures for biomedical verbs. BMC Bioinformatics (2006) 1.29
Improving protein function prediction methods with integrated literature data. BMC Bioinformatics (2008) 1.02
Assessing and combining reliability of protein interaction sources. Pac Symp Biocomput (2007) 0.88
Mayo clinical Text Analysis and Knowledge Extraction System (cTAKES): architecture, component evaluation and applications. J Am Med Inform Assoc (2010) 13.18
Database resources of the National Center for Biotechnology Information. Nucleic Acids Res (2009) 12.51
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
Overview of BioCreative II gene normalization. Genome Biol (2008) 5.05
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
Mayo clinic NLP system for patient smoking status identification. J Am Med Inform Assoc (2007) 3.92
Mesenchymal stem cell implantation in a swine myocardial infarct model: engraftment and functional effects. Ann Thorac Surg (2002) 3.62
Understanding PubMed user search behavior through log analysis. Database (Oxford) (2009) 3.27
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
Stroke and encephalopathy after cardiac surgery: an update. Stroke (2005) 2.91
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
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
BioC: a minimalist approach to interoperability for biomedical text processing. Database (Oxford) (2013) 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
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
Clinical outcomes of noninfectious sternal dehiscence after median sternotomy. Ann Thorac Surg (2006) 2.25
BioCreative III interactive task: an overview. BMC Bioinformatics (2011) 2.16
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
Watershed strokes after cardiac surgery: diagnosis, etiology, and outcome. Stroke (2006) 1.98
Concept annotation in the CRAFT corpus. BMC Bioinformatics (2012) 1.94
Word sense disambiguation across two domains: biomedical literature and clinical notes. J Biomed Inform (2008) 1.93
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
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
BioLemmatizer: a lemmatization tool for morphological processing of biomedical text. J Biomed Semantics (2012) 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
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
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
SR4GN: a species recognition software tool for gene normalization. PLoS One (2012) 1.57
Do management strategies for coronary artery disease influence 6-year cognitive outcomes? Ann Thorac Surg (2009) 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
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
Proteome Analyst: custom predictions with explanations in a web-based tool for high-throughput proteome annotations. Nucleic Acids Res (2004) 1.46
Intraoperative hemoglobin levels and transfusion independently predict stroke after cardiac operations. Ann Thorac Surg (2011) 1.45
Pilot implementation of a perioperative protocol to guide operating room-to-intensive care unit patient handoffs. J Cardiothorac Vasc Anesth (2011) 1.45
Subjective memory symptoms in surgical and nonsurgical coronary artery patients: 6-year follow-up. Ann Thorac Surg (2009) 1.43
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
The textual characteristics of traditional and Open Access scientific journals are similar. BMC Bioinformatics (2009) 1.37
Improving links between literature and biological data with text mining: a case study with GEO, PDB and MEDLINE. Database (Oxford) (2012) 1.32
Large-scale event extraction from literature with multi-level gene normalization. PLoS One (2013) 1.30
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
Extraction of data deposition statements from the literature: a method for automatically tracking research results. Bioinformatics (2011) 1.27
BioCreative-2012 virtual issue. Database (Oxford) (2012) 1.26
EuroSCORE predicts short- and mid-term mortality in combined aortic valve replacement and coronary artery bypass patients. J Card Surg (2010) 1.22
Encephalopathy and stroke after coronary artery bypass grafting: incidence, consequences, and prediction. Arch Neurol (2002) 1.20
The impact of center volume on survival in lung transplantation: an analysis of more than 10,000 cases. Ann Thorac Surg (2009) 1.20
A survey of current trends in computational drug repositioning. Brief Bioinform (2015) 1.18
Neurocognitive outcomes 3 years after coronary artery bypass graft surgery: a controlled study. Ann Thorac Surg (2007) 1.18
Association of operative time of day with outcomes after thoracic organ transplant. JAMA (2011) 1.16
Determining the utility of temporary pacing wires after coronary artery bypass surgery. Ann Thorac Surg (2005) 1.15
Inspiring medical students to pursue surgical careers: outcomes from our cardiothoracic surgery research program. Ann Thorac Surg (2009) 1.14
Extracting Rx information from clinical narrative. J Am Med Inform Assoc (2010) 1.14
Mutations in POFUT1, encoding protein O-fucosyltransferase 1, cause generalized Dowling-Degos disease. Am J Hum Genet (2013) 1.13
BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains. J Biomed Semantics (2014) 1.12
A context-blocks model for identifying clinical relationships in patient records. BMC Bioinformatics (2011) 1.10
Semantic role labeling for protein transport predicates. BMC Bioinformatics (2008) 1.10
Current issues in biomedical text mining and natural language processing. J Biomed Inform (2009) 1.09