Published in BMC Bioinformatics on February 05, 2009
BioPortal: ontologies and integrated data resources at the click of a mouse. Nucleic Acids Res (2009) 10.58
BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications. Nucleic Acids Res (2011) 6.59
The open biomedical annotator. Summit on Translat Bioinforma (2009) 4.19
Creating mappings for ontologies in biomedicine: simple methods work. AMIA Annu Symp Proc (2009) 2.93
Comparison of concept recognizers for building the Open Biomedical Annotator. BMC Bioinformatics (2009) 2.83
The National Center for Biomedical Ontology. J Am Med Inform Assoc (2011) 2.55
Annotation and query of tissue microarray data using the NCI Thesaurus. BMC Bioinformatics (2007) 2.03
Bayesian approach to transforming public gene expression repositories into disease diagnosis databases. Proc Natl Acad Sci U S A (2010) 1.84
Annotation Analysis for Testing Drug Safety Signals using Unstructured Clinical Notes. J Biomed Semantics (2012) 1.83
Comparison of ontology-based semantic-similarity measures. AMIA Annu Symp Proc (2008) 1.69
Building a biomedical ontology recommender web service. J Biomed Semantics (2010) 1.53
curatedOvarianData: clinically annotated data for the ovarian cancer transcriptome. Database (Oxford) (2013) 1.40
The Translational Medicine Ontology and Knowledge Base: driving personalized medicine by bridging the gap between bench and bedside. J Biomed Semantics (2011) 1.37
NCBO Technology: Powering semantically aware applications. J Biomed Semantics (2013) 1.31
NCBO Resource Index: Ontology-Based Search and Mining of Biomedical Resources. Web Semant (2011) 1.27
Programming cells: towards an automated 'Genetic Compiler'. Curr Opin Biotechnol (2010) 1.20
Informatics and standards for nanomedicine technology. Wiley Interdiscip Rev Nanomed Nanobiotechnol (2011) 1.19
An ontology-neutral framework for enrichment analysis. AMIA Annu Symp Proc (2010) 1.15
The Lexicon Builder Web service: Building Custom Lexicons from two hundred Biomedical Ontologies. AMIA Annu Symp Proc (2010) 1.10
Analyzing patterns of drug use in clinical notes for patient safety. AMIA Jt Summits Transl Sci Proc (2012) 1.10
UMLS-Query: a perl module for querying the UMLS. AMIA Annu Symp Proc (2008) 1.10
Content-based microarray search using differential expression profiles. BMC Bioinformatics (2010) 1.07
Translational bioinformatics: linking the molecular world to the clinical world. Clin Pharmacol Ther (2012) 1.05
Leveraging biomedical ontologies and annotation services to organize microbiome data from Mammalian hosts. AMIA Annu Symp Proc (2010) 1.01
Comparison of automated and human assignment of MeSH terms on publicly-available molecular datasets. J Biomed Inform (2011) 0.99
Chapter 9: Analyses using disease ontologies. PLoS Comput Biol (2012) 0.98
Markov Chain Ontology Analysis (MCOA). BMC Bioinformatics (2012) 0.97
Getting started in text mining: part two. PLoS Comput Biol (2009) 0.97
Using ontology-based annotation to profile disease research. J Am Med Inform Assoc (2012) 0.94
Vitamin D and the RNA transcriptome: more than mRNA regulation. Front Physiol (2014) 0.88
Facilitating transparency in spinal cord injury studies using data standards and ontologies. Neural Regen Res (2014) 0.86
Improving gene expression similarity measurement using pathway-based analytic dimension. BMC Genomics (2009) 0.82
Using ontology databases for scalable query answering, inconsistency detection, and data integration. J Intell Inf Syst (2011) 0.78
Statistical algorithms for ontology-based annotation of scientific literature. J Biomed Semantics (2014) 0.78
Vitamin D receptor and RXR in the post-genomic era. J Cell Physiol (2015) 0.76
Selected proceedings of the First Summit on Translational Bioinformatics 2008. BMC Bioinformatics (2009) 0.75
Assessing Metadata Quality of a Federally Sponsored Health Data Repository. AMIA Annu Symp Proc (2017) 0.75
Surveillance for the prevention of chronic diseases through information association. BMC Med Genomics (2014) 0.75
Using LASSO Regression to Predict Rheumatoid Arthritis Treatment Efficacy. AMIA Jt Summits Transl Sci Proc (2016) 0.75
Effective mapping of biomedical text to the UMLS Metathesaurus: the MetaMap program. Proc AMIA Symp (2001) 40.22
The Unified Medical Language System (UMLS): integrating biomedical terminology. Nucleic Acids Res (2004) 25.99
Creation and implications of a phenome-genome network. Nat Biotechnol (2006) 5.79
Text mining and ontologies in biomedicine: making sense of raw text. Brief Bioinform (2005) 3.36
Tissue microarray: a new technology for amplification of tissue resources. Cancer J (2001) 3.19
Software tools for high-throughput analysis and archiving of immunohistochemistry staining data obtained with tissue microarrays. Am J Pathol (2002) 3.11
Finding disease-related genomic experiments within an international repository: first steps in translational bioinformatics. AMIA Annu Symp Proc (2006) 2.88
The SAPHIRE server: a new algorithm and implementation. Proc Annu Symp Comput Appl Med Care (1995) 2.48
Ontology-based annotation and query of tissue microarray data. AMIA Annu Symp Proc (2006) 2.05
Annotation and query of tissue microarray data using the NCI Thesaurus. BMC Bioinformatics (2007) 2.03
The Stanford Tissue Microarray Database. Nucleic Acids Res (2007) 1.96
A comparative evaluation of full-text, concept-based, and context-sensitive search. J Am Med Inform Assoc (2007) 1.92
Knowledge-based methods to help clinicians find answers in MEDLINE. J Am Med Inform Assoc (2007) 1.78
Tissue microarrays for predictive molecular pathology. J Clin Pathol (2002) 1.65
Integration of genomic technologies for accelerated cancer drug development. Biotechniques (2003) 1.36
Coordinated reduction of genes of oxidative metabolism in humans with insulin resistance and diabetes: Potential role of PGC1 and NRF1. Proc Natl Acad Sci U S A (2003) 17.10
Personal omics profiling reveals dynamic molecular and medical phenotypes. Cell (2012) 12.32
BioPortal: ontologies and integrated data resources at the click of a mouse. Nucleic Acids Res (2009) 10.58
Clinical assessment incorporating a personal genome. Lancet (2010) 10.18
Performance comparison of exome DNA sequencing technologies. Nat Biotechnol (2011) 7.11
The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models. Nat Biotechnol (2010) 7.08
Analysis of matched mRNA measurements from two different microarray technologies. Bioinformatics (2002) 7.07
BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications. Nucleic Acids Res (2011) 6.59
Ten years of pathway analysis: current approaches and outstanding challenges. PLoS Comput Biol (2012) 6.38
Performance comparison of whole-genome sequencing platforms. Nat Biotechnol (2011) 5.79
Discovery and preclinical validation of drug indications using compendia of public gene expression data. Sci Transl Med (2011) 5.77
Computational repositioning of the anticonvulsant topiramate for inflammatory bowel disease. Sci Transl Med (2011) 5.30
Cell type-specific gene expression differences in complex tissues. Nat Methods (2010) 4.75
An Environment-Wide Association Study (EWAS) on type 2 diabetes mellitus. PLoS One (2010) 4.42
The open biomedical annotator. Summit on Translat Bioinforma (2009) 4.19
National Center for Biomedical Ontology: advancing biomedicine through structured organization of scientific knowledge. OMICS (2006) 3.96
FoxO3 regulates neural stem cell homeostasis. Cell Stem Cell (2009) 3.54
Expression-based genome-wide association study links the receptor CD44 in adipose tissue with type 2 diabetes. Proc Natl Acad Sci U S A (2012) 3.27
Network-based elucidation of human disease similarities reveals common functional modules enriched for pluripotent drug targets. PLoS Comput Biol (2010) 3.23
The SAGE Guideline Model: achievements and overview. J Am Med Inform Assoc (2007) 3.22
Phased whole-genome genetic risk in a family quartet using a major allele reference sequence. PLoS Genet (2011) 3.20
Protein-Protein Docking Benchmark 2.0: an update. Proteins (2005) 3.13
Bardet-Biedl syndrome type 4 (BBS4)-null mice implicate Bbs4 in flagella formation but not global cilia assembly. Proc Natl Acad Sci U S A (2004) 3.01
Creating mappings for ontologies in biomedicine: simple methods work. AMIA Annu Symp Proc (2009) 2.93
Challenges in the clinical application of whole-genome sequencing. Lancet (2010) 2.92
Finding disease-related genomic experiments within an international repository: first steps in translational bioinformatics. AMIA Annu Symp Proc (2006) 2.88
Comparison of concept recognizers for building the Open Biomedical Annotator. BMC Bioinformatics (2009) 2.83
Systematic survey reveals general applicability of "guilt-by-association" within gene coexpression networks. BMC Bioinformatics (2005) 2.83
Protégé-2000: an open-source ontology-development and knowledge-acquisition environment. AMIA Annu Symp Proc (2003) 2.73
Prediction of preadipocyte differentiation by gene expression reveals role of insulin receptor substrates and necdin. Nat Cell Biol (2005) 2.68
Hematopoietic stem cell quiescence is maintained by compound contributions of the retinoblastoma gene family. Cell Stem Cell (2008) 2.67
Computerized recruiting for clinical trials in real time. Ann Emerg Med (2003) 2.59
Breast cancer on the world wide web: cross sectional survey of quality of information and popularity of websites. BMJ (2002) 2.53
Integrating statistical pair potentials into protein complex prediction. Proteins (2007) 2.53
Exploiting drug-disease relationships for computational drug repositioning. Brief Bioinform (2011) 2.52
Quantifying the relationship between co-expression, co-regulation and gene function. BMC Bioinformatics (2004) 2.51
Silver nanoparticles: partial oxidation and antibacterial activities. J Biol Inorg Chem (2007) 2.50
Progressive histological damage in renal allografts is associated with expression of innate and adaptive immunity genes. Kidney Int (2011) 2.50
AILUN: reannotating gene expression data automatically. Nat Methods (2007) 2.47
A drug repositioning approach identifies tricyclic antidepressants as inhibitors of small cell lung cancer and other neuroendocrine tumors. Cancer Discov (2013) 2.46
MicroRNA profiling of human-induced pluripotent stem cells. Stem Cells Dev (2009) 2.44
Proteomic analysis of the mode of antibacterial action of silver nanoparticles. J Proteome Res (2006) 2.43
Systematic evaluation of environmental factors: persistent pollutants and nutrients correlated with serum lipid levels. Int J Epidemiol (2012) 2.42
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
Structural requirements for the assembly of Norwalk virus-like particles. J Virol (2002) 2.38
Translational bioinformatics: linking knowledge across biological and clinical realms. J Am Med Inform Assoc (2011) 2.36
Multifunctional Alloys Obtained via a Dislocation-Free Plastic Deformation Mechanism. Science (2003) 2.33
Dynamic microRNA expression programs during cardiac differentiation of human embryonic stem cells: role for miR-499. Circ Cardiovasc Genet (2010) 2.24
RDOCK: refinement of rigid-body protein docking predictions. Proteins (2003) 2.24
Reproducibility of gene expression across generations of Affymetrix microarrays. BMC Bioinformatics (2003) 2.20
A nutrient-wide association study on blood pressure. Circulation (2012) 2.19
WebProtégé: A Collaborative Ontology Editor and Knowledge Acquisition Tool for the Web. Semant Web (2013) 2.17
Conserved mechanisms across development and tumorigenesis revealed by a mouse development perspective of human cancers. Genes Dev (2004) 2.16
Challenges in converting frame-based ontology into OWL: the Foundational Model of Anatomy case-study. AMIA Annu Symp Proc (2005) 2.10
Non-synonymous and synonymous coding SNPs show similar likelihood and effect size of human disease association. PLoS One (2010) 2.10
The Biomedical Resource Ontology (BRO) to enable resource discovery in clinical and translational research. J Biomed Inform (2010) 2.10
Ontology-based annotation and query of tissue microarray data. AMIA Annu Symp Proc (2006) 2.05
Supporting the Collaborative Authoring of ICD-11 with WebProtégé. AMIA Annu Symp Proc (2010) 2.05
Annotation and query of tissue microarray data using the NCI Thesaurus. BMC Bioinformatics (2007) 2.03
Leveraging models of cell regulation and GWAS data in integrative network-based association studies. Nat Genet (2012) 2.02
Autoimmune disease classification by inverse association with SNP alleles. PLoS Genet (2009) 1.96
Protégé: a tool for managing and using terminology in radiology applications. J Digit Imaging (2007) 1.95
Disease signatures are robust across tissues and experiments. Mol Syst Biol (2009) 1.93
Genome-scale expression profiling of Hutchinson-Gilford progeria syndrome reveals widespread transcriptional misregulation leading to mesodermal/mesenchymal defects and accelerated atherosclerosis. Aging Cell (2004) 1.87
In silico research in the era of cloud computing. Nat Biotechnol (2010) 1.81
Population genetic inference from personal genome data: impact of ancestry and admixture on human genomic variation. Am J Hum Genet (2012) 1.75
Translating research into practice: organizational issues in implementing automated decision support for hypertension in three medical centers. J Am Med Inform Assoc (2004) 1.75
Knowledge-based bioterrorism surveillance. Proc AMIA Symp (2002) 1.74
Unified Medical Language System term occurrences in clinical notes: a large-scale corpus analysis. J Am Med Inform Assoc (2012) 1.73
Use of description logic classification to reason about consequences of penetrating injuries. AMIA Annu Symp Proc (2005) 1.72
Arabidopsis ASA1 is important for jasmonate-mediated regulation of auxin biosynthesis and transport during lateral root formation. Plant Cell (2009) 1.71
Ethnic differences in the relationship between insulin sensitivity and insulin response: a systematic review and meta-analysis. Diabetes Care (2013) 1.70
Protein microarrays identify antibodies to protein kinase Czeta that are associated with a greater risk of allograft loss in pediatric renal transplant recipients. Kidney Int (2009) 1.68
A Comprehensive Analysis of Five Million UMLS Metathesaurus Terms Using Eighteen Million MEDLINE Citations. AMIA Annu Symp Proc (2010) 1.68
Contextualizing heterogeneous data for integration and inference. AMIA Annu Symp Proc (2003) 1.67
OBO to OWL: a protege OWL tab to read/save OBO ontologies. Bioinformatics (2007) 1.67
The basic helix-loop-helix transcription factor MYC2 directly represses PLETHORA expression during jasmonate-mediated modulation of the root stem cell niche in Arabidopsis. Plant Cell (2011) 1.65
Translational bioinformatics in the cloud: an affordable alternative. Genome Med (2010) 1.61
ZDOCK and RDOCK performance in CAPRI rounds 3, 4, and 5. Proteins (2005) 1.61
Enabling integrative genomic analysis of high-impact human diseases through text mining. Pac Symp Biocomput (2008) 1.61
FitSNPs: highly differentially expressed genes are more likely to have variants associated with disease. Genome Biol (2008) 1.58