Published in Nucleic Acids Res on November 17, 2009
UniProt Knowledgebase: a hub of integrated protein data. Database (Oxford) (2011) 11.43
Reactome: a database of reactions, pathways and biological processes. Nucleic Acids Res (2010) 11.23
PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium. Nucleic Acids Res (2009) 9.14
Entrez Gene: gene-centered information at NCBI. Nucleic Acids Res (2010) 9.09
The Reactome pathway knowledgebase. Nucleic Acids Res (2013) 8.56
The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools. Nucleic Acids Res (2011) 8.18
Disease Ontology: a backbone for disease semantic integration. Nucleic Acids Res (2011) 6.03
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
The UniProt-GO Annotation database in 2011. Nucleic Acids Res (2011) 5.19
EcoCyc: a comprehensive database of Escherichia coli biology. Nucleic Acids Res (2010) 4.68
The Mouse Genome Database (MGD): premier model organism resource for mammalian genomics and genetics. Nucleic Acids Res (2010) 4.58
Community cyberinfrastructure for Advanced Microbial Ecology Research and Analysis: the CAMERA resource. Nucleic Acids Res (2010) 4.39
Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Brief Bioinform (2011) 3.90
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
ZFIN: enhancements and updates to the Zebrafish Model Organism Database. Nucleic Acids Res (2010) 3.02
PomBase: a comprehensive online resource for fission yeast. Nucleic Acids Res (2011) 2.84
ConsensusPathDB: toward a more complete picture of cell biology. Nucleic Acids Res (2010) 2.79
UniPathway: a resource for the exploration and annotation of metabolic pathways. Nucleic Acids Res (2011) 2.45
The 2010 Nucleic Acids Research Database Issue and online Database Collection: a community of data resources. Nucleic Acids Res (2009) 2.42
Diverse roles and interactions of the SWI/SNF chromatin remodeling complex revealed using global approaches. PLoS Genet (2011) 2.38
Annotating cancer variants and anti-cancer therapeutics in reactome. Cancers (Basel) (2012) 2.35
The mouse Gene Expression Database (GXD): 2011 update. Nucleic Acids Res (2010) 2.07
CATH: comprehensive structural and functional annotations for genome sequences. Nucleic Acids Res (2014) 2.03
OrthoDB: the hierarchical catalog of eukaryotic orthologs in 2011. Nucleic Acids Res (2010) 2.02
DroID 2011: a comprehensive, integrated resource for protein, transcription factor, RNA and gene interactions for Drosophila. Nucleic Acids Res (2010) 1.86
MatrixDB, the extracellular matrix interaction database. Nucleic Acids Res (2010) 1.79
The mouse Gene Expression Database (GXD): 2014 update. Nucleic Acids Res (2013) 1.78
neXtProt: a knowledge platform for human proteins. Nucleic Acids Res (2011) 1.77
The representation of heart development in the gene ontology. Dev Biol (2011) 1.77
Ontologies as integrative tools for plant science. Am J Bot (2012) 1.71
The BRENDA Tissue Ontology (BTO): the first all-integrating ontology of all organisms for enzyme sources. Nucleic Acids Res (2010) 1.71
ViralZone: a knowledge resource to understand virus diversity. Nucleic Acids Res (2010) 1.66
The Reactome BioMart. Database (Oxford) (2011) 1.66
On the Use of Gene Ontology Annotations to Assess Functional Similarity among Orthologs and Paralogs: A Short Report. PLoS Comput Biol (2012) 1.65
Ontologies in quantitative biology: a basis for comparison, integration, and discovery. PLoS Biol (2010) 1.62
The what, where, how and why of gene ontology--a primer for bioinformaticians. Brief Bioinform (2011) 1.61
Quality of computationally inferred gene ontology annotations. PLoS Comput Biol (2012) 1.57
A MOD(ern) perspective on literature curation. Mol Genet Genomics (2010) 1.56
Solving the Problem: Genome Annotation Standards before the Data Deluge. Stand Genomic Sci (2011) 1.54
Ontology searching and browsing at the Rat Genome Database. Database (Oxford) (2012) 1.51
A guide to best practices for Gene Ontology (GO) manual annotation. Database (Oxford) (2013) 1.49
AgBase: supporting functional modeling in agricultural organisms. Nucleic Acids Res (2010) 1.48
Chapter 5: Network biology approach to complex diseases. PLoS Comput Biol (2012) 1.45
Minimum information about a bioactive entity (MIABE). Nat Rev Drug Discov (2011) 1.44
The Mouse Tumor Biology Database (MTB): a central electronic resource for locating and integrating mouse tumor pathology data. Vet Pathol (2011) 1.44
Execution of the meiotic noncoding RNA expression program and the onset of gametogenesis in yeast require the conserved exosome subunit Rrp6. Proc Natl Acad Sci U S A (2010) 1.39
GeneWeaver: a web-based system for integrative functional genomics. Nucleic Acids Res (2011) 1.39
FungiDB: an integrated functional genomics database for fungi. Nucleic Acids Res (2011) 1.37
ExoCarta: A Web-Based Compendium of Exosomal Cargo. J Mol Biol (2015) 1.37
ScerTF: a comprehensive database of benchmarked position weight matrices for Saccharomyces species. Nucleic Acids Res (2011) 1.37
EMAP/EMAPA ontology of mouse developmental anatomy: 2013 update. J Biomed Semantics (2013) 1.35
Host genetic variation impacts microbiome composition across human body sites. Genome Biol (2015) 1.32
Expression2Kinases: mRNA profiling linked to multiple upstream regulatory layers. Bioinformatics (2011) 1.31
Insights into the maize pan-genome and pan-transcriptome. Plant Cell (2014) 1.30
CharProtDB: a database of experimentally characterized protein annotations. Nucleic Acids Res (2011) 1.29
BioCreative-2012 virtual issue. Database (Oxford) (2012) 1.26
Information content-based gene ontology semantic similarity approaches: toward a unified framework theory. Biomed Res Int (2013) 1.26
Multiple apical plasma membrane constituents are associated with susceptibility to meconium ileus in individuals with cystic fibrosis. Nat Genet (2012) 1.26
Functional analysis beyond enrichment: non-redundant reciprocal linkage of genes and biological terms. PLoS One (2011) 1.25
IDOMAL: an ontology for malaria. Malar J (2010) 1.23
The Gene Ontology (GO) Cellular Component Ontology: integration with SAO (Subcellular Anatomy Ontology) and other recent developments. J Biomed Semantics (2013) 1.22
Phenotype ontologies and cross-species analysis for translational research. PLoS Genet (2014) 1.19
Pathway and network analysis of cancer genomes. Nat Methods (2015) 1.17
Using computational predictions to improve literature-based Gene Ontology annotations: a feasibility study. Database (Oxford) (2011) 1.17
DFLAT: functional annotation for human development. BMC Bioinformatics (2014) 1.17
IntelliGO: a new vector-based semantic similarity measure including annotation origin. BMC Bioinformatics (2010) 1.16
Integrating systems biology models and biomedical ontologies. BMC Syst Biol (2011) 1.16
The impact of focused Gene Ontology curation of specific mammalian systems. PLoS One (2011) 1.11
Genome-scale phylogenetic function annotation of large and diverse protein families. Genome Res (2011) 1.10
The systematic annotation of the three main GPCR families in Reactome. Database (Oxford) (2010) 1.09
vHOG, a multispecies vertebrate ontology of homologous organs groups. Bioinformatics (2012) 1.07
Nematode.net update 2011: addition of data sets and tools featuring next-generation sequencing data. Nucleic Acids Res (2011) 1.07
Correlating traits of gene retention, sequence divergence, duplicability and essentiality in vertebrates, arthropods, and fungi. Genome Biol Evol (2010) 1.07
Oxidative injury is a common consequence of BMPR2 mutations. Pulm Circ (2011) 1.06
Using the gene ontology to scan multilevel gene sets for associations in genome wide association studies. Genet Epidemiol (2011) 1.06
An integrated ontology resource to explore and study host-virus relationships. PLoS One (2014) 1.06
Minimotif Miner 3.0: database expansion and significantly improved reduction of false-positive predictions from consensus sequences. Nucleic Acids Res (2011) 1.06
Building an efficient curation workflow for the Arabidopsis literature corpus. Database (Oxford) (2012) 1.05
TcoF-DB: dragon database for human transcription co-factors and transcription factor interacting proteins. Nucleic Acids Res (2010) 1.05
The mouse pathology ontology, MPATH; structure and applications. J Biomed Semantics (2013) 1.05
A topology-based metric for measuring term similarity in the gene ontology. Adv Bioinformatics (2012) 1.04
How the gene ontology evolves. BMC Bioinformatics (2011) 1.04
Detecting local ligand-binding site similarity in nonhomologous proteins by surface patch comparison. Proteins (2012) 1.03
Logical Gene Ontology Annotations (GOAL): exploring gene ontology annotations with OWL. J Biomed Semantics (2012) 1.03
Semantic integration of physiology phenotypes with an application to the Cellular Phenotype Ontology. Bioinformatics (2012) 1.03
The DNA methylome and transcriptome of different brain regions in schizophrenia and bipolar disorder. PLoS One (2014) 1.01
Using nanoinformatics methods for automatically identifying relevant nanotoxicology entities from the literature. Biomed Res Int (2012) 1.01
Transcriptomic events involved in melon mature-fruit abscission comprise the sequential induction of cell-wall degrading genes coupled to a stimulation of endo and exocytosis. PLoS One (2013) 1.01
Systematic approaches towards the development of host-directed antiviral therapeutics. Int J Mol Sci (2011) 1.01
COLOMBOS: access port for cross-platform bacterial expression compendia. PLoS One (2011) 1.00
Idiopathic and heritable PAH perturb common molecular pathways, correlated with increased MSX1 expression. Pulm Circ (2011) 1.00
New mode of energy metabolism in the seventh order of methanogens as revealed by comparative genome analysis of “Candidatus methanoplasma termitum”. Appl Environ Microbiol (2015) 1.00
Generation and analysis of a mouse intestinal metatranscriptome through Illumina based RNA-sequencing. PLoS One (2012) 0.99
The gene expression database for mouse development (GXD): putting developmental expression information at your fingertips. Dev Dyn (2014) 0.99
Preliminary evaluation of the CellFinder literature curation pipeline for gene expression in kidney cells and anatomical parts. Database (Oxford) (2013) 0.99
Bio-crude transcriptomics: gene discovery and metabolic network reconstruction for the biosynthesis of the terpenome of the hydrocarbon oil-producing green alga, Botryococcus braunii race B (Showa). BMC Genomics (2012) 0.99
MetaBase--the wiki-database of biological databases. Nucleic Acids Res (2011) 0.98
Assessment of community-submitted ontology annotations from a novel database-journal partnership. Database (Oxford) (2012) 0.98
OBO-Edit--an ontology editor for biologists. Bioinformatics (2007) 11.04
AmiGO: online access to ontology and annotation data. Bioinformatics (2008) 10.77
PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium. Nucleic Acids Res (2009) 9.14
The Gene Ontology's Reference Genome Project: a unified framework for functional annotation across species. PLoS Comput Biol (2009) 7.95
The Plant-Associated Microbe Gene Ontology (PAMGO) Consortium: community development of new Gene Ontology terms describing biological processes involved in microbe-host interactions. BMC Microbiol (2009) 3.14
Creating the gene ontology resource: design and implementation. Genome Res (2001) 55.73
The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res (2004) 54.37
The Gene Ontology (GO) project in 2006. Nucleic Acids Res (2006) 13.79
The Gene Ontology project in 2008. Nucleic Acids Res (2007) 11.71
Gene Ontology Consortium: going forward. Nucleic Acids Res (2014) 7.76
Gene Ontology annotations and resources. Nucleic Acids Res (2012) 6.13
The Gene Ontology: enhancements for 2011. Nucleic Acids Res (2011) 5.82
On the Use of Gene Ontology Annotations to Assess Functional Similarity among Orthologs and Paralogs: A Short Report. PLoS Comput Biol (2012) 1.65