Published in Genome Biol on January 14, 2005
The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat Biotechnol (2007) 35.41
Relations in biomedical ontologies. Genome Biol (2005) 22.07
ArrayExpress update--from an archive of functional genomics experiments to the atlas of gene expression. Nucleic Acids Res (2008) 12.45
Gene Ontology Consortium: going forward. Nucleic Acids Res (2014) 7.76
The Adult Mouse Anatomical Dictionary: a tool for annotating and integrating data. Genome Biol (2005) 6.44
FlyBase: anatomical data, images and queries. Nucleic Acids Res (2006) 6.01
Bio-ontologies: current trends and future directions. Brief Bioinform (2006) 5.96
Integrating phenotype ontologies across multiple species. Genome Biol (2010) 5.46
Uberon, an integrative multi-species anatomy ontology. Genome Biol (2012) 5.43
Linking human diseases to animal models using ontology-based phenotype annotation. PLoS Biol (2009) 5.17
PRIDE: new developments and new datasets. Nucleic Acids Res (2007) 4.42
Cross-product extensions of the Gene Ontology. J Biomed Inform (2010) 4.00
Logical development of the cell ontology. BMC Bioinformatics (2011) 3.68
Minimum information specification for in situ hybridization and immunohistochemistry experiments (MISFISHIE). Nat Biotechnol (2008) 3.43
Automated acquisition of disease drug knowledge from biomedical and clinical documents: an initial study. J Am Med Inform Assoc (2007) 3.09
ZFIN: enhancements and updates to the Zebrafish Model Organism Database. Nucleic Acids Res (2010) 3.02
The mammalian phenotype ontology: enabling robust annotation and comparative analysis. Wiley Interdiscip Rev Syst Biol Med (2010) 3.00
The cell centered database project: an update on building community resources for managing and sharing 3D imaging data. J Struct Biol (2007) 3.00
Gene Ontology annotations: what they mean and where they come from. BMC Bioinformatics (2008) 2.84
Protein family expansions and biological complexity. PLoS Comput Biol (2006) 2.69
PhenomeNET: a whole-phenome approach to disease gene discovery. Nucleic Acids Res (2011) 2.67
Elucidation of seventeen human peripheral blood B-cell subsets and quantification of the tetanus response using a density-based method for the automated identification of cell populations in multidimensional flow cytometry data. Cytometry B Clin Cytom (2010) 2.38
Celsius: a community resource for Affymetrix microarray data. Genome Biol (2007) 2.38
The Plant Ontology Database: a community resource for plant structure and developmental stages controlled vocabulary and annotations. Nucleic Acids Res (2008) 2.28
Entity/quality-based logical definitions for the human skeletal phenome using PATO. Conf Proc IEEE Eng Med Biol Soc (2009) 2.20
Developmental fate and cellular maturity encoded in human regulatory DNA landscapes. Cell (2013) 2.16
The plant structure ontology, a unified vocabulary of anatomy and morphology of a flowering plant. Plant Physiol (2006) 2.03
A flexible framework for deriving assertions from electronic medical records. J Am Med Inform Assoc (2011) 2.02
Enrichment of OBO ontologies. J Biomed Inform (2006) 1.95
Concept annotation in the CRAFT corpus. BMC Bioinformatics (2012) 1.94
Evaluation of lexical methods for detecting relationships between concepts from multiple ontologies. Pac Symp Biocomput (2006) 1.90
Representing default knowledge in biomedical ontologies: application to the integration of anatomy and phenotype ontologies. BMC Bioinformatics (2007) 1.84
NeuroMorpho.Org implementation of digital neuroscience: dense coverage and integration with the NIF. Neuroinformatics (2008) 1.82
MOPED: Model Organism Protein Expression Database. Nucleic Acids Res (2011) 1.79
PhenoGO: assigning phenotypic context to gene ontology annotations with natural language processing. Pac Symp Biocomput (2006) 1.76
Calling International Rescue: knowledge lost in literature and data landslide! Biochem J (2009) 1.71
The BRENDA Tissue Ontology (BTO): the first all-integrating ontology of all organisms for enzyme sources. Nucleic Acids Res (2010) 1.71
An ontology for Xenopus anatomy and development. BMC Dev Biol (2008) 1.64
The RICORDO approach to semantic interoperability for biomedical data and models: strategy, standards and solutions. BMC Res Notes (2011) 1.59
Computational approaches to phenotyping: high-throughput phenomics. Proc Am Thorac Soc (2007) 1.57
A MOD(ern) perspective on literature curation. Mol Genet Genomics (2010) 1.56
Development and use of Ontologies Inside the Neuroscience Information Framework: A Practical Approach. Front Genet (2012) 1.56
An improved ontological representation of dendritic cells as a paradigm for all cell types. BMC Bioinformatics (2009) 1.56
OntoCAT--simple ontology search and integration in Java, R and REST/JavaScript. BMC Bioinformatics (2011) 1.54
Construction and accessibility of a cross-species phenotype ontology along with gene annotations for biomedical research. F1000Res (2013) 1.52
Large-scale biomedical concept recognition: an evaluation of current automatic annotators and their parameters. BMC Bioinformatics (2014) 1.52
Relations as patterns: bridging the gap between OBO and OWL. BMC Bioinformatics (2010) 1.50
Identification of OBO nonalignments and its implications for OBO enrichment. Bioinformatics (2008) 1.49
A guide to best practices for Gene Ontology (GO) manual annotation. Database (Oxford) (2013) 1.49
Hematopoietic cell types: prototype for a revised cell ontology. J Biomed Inform (2010) 1.48
Use of Gene Ontology Annotation to understand the peroxisome proteome in humans. Database (Oxford) (2013) 1.48
Early immunologic correlates of HIV protection can be identified from computational analysis of complex multivariate T-cell flow cytometry assays. Bioinformatics (2012) 1.46
A formal ontology of subcellular neuroanatomy. Front Neuroinform (2007) 1.44
MirZ: an integrated microRNA expression atlas and target prediction resource. Nucleic Acids Res (2009) 1.44
Mining of vaccine-associated IFN-γ gene interaction networks using the Vaccine Ontology. J Biomed Semantics (2011) 1.43
TermGenie - a web-application for pattern-based ontology class generation. J Biomed Semantics (2014) 1.37
A common layer of interoperability for biomedical ontologies based on OWL EL. Bioinformatics (2011) 1.35
The neuron classification problem. Brain Res Rev (2007) 1.34
A bioinformatics analysis of the cell line nomenclature. Bioinformatics (2008) 1.33
A multilevel data integration resource for breast cancer study. BMC Syst Biol (2010) 1.32
An anatomy ontology to represent biological knowledge in Dictyostelium discoideum. BMC Genomics (2008) 1.32
BAMS Neuroanatomical Ontology: Design and Implementation. Front Neuroinform (2008) 1.29
Identifying aberrant pathways through integrated analysis of knowledge in pharmacogenomics. Bioinformatics (2012) 1.27
BodyMap-Xs: anatomical breakdown of 17 million animal ESTs for cross-species comparison of gene expression. Nucleic Acids Res (2006) 1.25
Interoperability between biomedical ontologies through relation expansion, upper-level ontologies and automatic reasoning. PLoS One (2011) 1.24
The Gene Ontology (GO) Cellular Component Ontology: integration with SAO (Subcellular Anatomy Ontology) and other recent developments. J Biomed Semantics (2013) 1.22
An ontological approach to describing neurons and their relationships. Front Neuroinform (2012) 1.22
A unified anatomy ontology of the vertebrate skeletal system. PLoS One (2012) 1.22
Phenotype ontologies and cross-species analysis for translational research. PLoS Genet (2014) 1.19
The Stem Cell Discovery Engine: an integrated repository and analysis system for cancer stem cell comparisons. Nucleic Acids Res (2011) 1.18
Flow: Statistics, visualization and informatics for flow cytometry. Source Code Biol Med (2008) 1.17
Integrating systems biology models and biomedical ontologies. BMC Syst Biol (2011) 1.16
Combining rules and machine learning for extraction of temporal expressions and events from clinical narratives. J Am Med Inform Assoc (2013) 1.15
Developing a kidney and urinary pathway knowledge base. J Biomed Semantics (2011) 1.13
The BioLexicon: a large-scale terminological resource for biomedical text mining. BMC Bioinformatics (2011) 1.13
MIMAS: an innovative tool for network-based high density oligonucleotide microarray data management and annotation. BMC Bioinformatics (2006) 1.11
Populous: a tool for building OWL ontologies from templates. BMC Bioinformatics (2012) 1.10
Managing, analysing, and integrating big data in medical bioinformatics: open problems and future perspectives. Biomed Res Int (2014) 1.08
The Renal Gene Ontology Annotation Initiative. Organogenesis (2010) 1.06
Unsupervised biomedical named entity recognition: experiments with clinical and biological texts. J Biomed Inform (2013) 1.05
The mouse pathology ontology, MPATH; structure and applications. J Biomed Semantics (2013) 1.05
Requirements and ontology for a G protein-coupled receptor oligomerization knowledge base. BMC Bioinformatics (2007) 1.04
Manual Gene Ontology annotation workflow at the Mouse Genome Informatics Database. Database (Oxford) (2012) 1.03
Semantic integration of physiology phenotypes with an application to the Cellular Phenotype Ontology. Bioinformatics (2012) 1.03
A fault model for ontology mapping, alignment, and linking systems. Pac Symp Biocomput (2007) 1.03
Overview of the Cancer Genetics and Pathway Curation tasks of BioNLP Shared Task 2013. BMC Bioinformatics (2015) 1.03
Applying the functional abnormality ontology pattern to anatomical functions. J Biomed Semantics (2010) 1.02
PhenoGO: an integrated resource for the multiscale mining of clinical and biological data. BMC Bioinformatics (2009) 1.01
Muscle Research and Gene Ontology: New standards for improved data integration. BMC Med Genomics (2009) 1.01
The Vertebrate Trait Ontology: a controlled vocabulary for the annotation of trait data across species. J Biomed Semantics (2013) 1.01
Preliminary evaluation of the CellFinder literature curation pipeline for gene expression in kidney cells and anatomical parts. Database (Oxford) (2013) 0.99
Transcriptomine, a web resource for nuclear receptor signaling transcriptomes. Physiol Genomics (2012) 0.99
Composite annotations: requirements for mapping multiscale data and models to biomedical ontologies. Conf Proc IEEE Eng Med Biol Soc (2009) 0.98
The Porifera Ontology (PORO): enhancing sponge systematics with an anatomy ontology. J Biomed Semantics (2014) 0.98
The cell: an image library-CCDB: a curated repository of microscopy data. Nucleic Acids Res (2012) 0.97
MAO: a Multiple Alignment Ontology for nucleic acid and protein sequences. Nucleic Acids Res (2005) 0.97
Terminologies for text-mining; an experiment in the lipoprotein metabolism domain. BMC Bioinformatics (2008) 0.96
The Drosophila phenotype ontology. J Biomed Semantics (2013) 0.96
Cross-Ontology multi-level association rule mining in the Gene Ontology. PLoS One (2012) 0.92
Query enhancement through the practical application of ontology: the IEDB and OBI. J Biomed Semantics (2013) 0.91
Creating the gene ontology resource: design and implementation. Genome Res (2001) 55.73
Phenotypic data in FlyBase. Brief Bioinform (2001) 10.53
Drosophila crinkled, mutations of which disrupt morphogenesis and cause lethality, encodes fly myosin VIIA. Genetics (2004) 4.51
The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat Biotechnol (2007) 35.41
The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol (2008) 31.04
The Sequence Ontology: a tool for the unification of genome annotations. Genome Biol (2005) 18.20
MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes. Plant J (2004) 15.51
ChEBI: a database and ontology for chemical entities of biological interest. Nucleic Acids Res (2007) 13.08
Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project. Nat Biotechnol (2008) 12.96
FlyBase: enhancing Drosophila Gene Ontology annotations. Nucleic Acids Res (2008) 12.15
MetaCyc: a multiorganism database of metabolic pathways and enzymes. Nucleic Acids Res (2004) 10.71
The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases. Nucleic Acids Res (2007) 10.62
Systematic determination of patterns of gene expression during Drosophila embryogenesis. Genome Biol (2002) 8.89
Annotation of the Drosophila melanogaster euchromatic genome: a systematic review. Genome Biol (2002) 8.59
Assessment of genome-wide protein function classification for Drosophila melanogaster. Genome Res (2003) 8.39
AraCyc: a biochemical pathway database for Arabidopsis. Plant Physiol (2003) 7.59
Calling on a million minds for community annotation in WikiProteins. Genome Biol (2008) 7.11
EGASP: the human ENCODE Genome Annotation Assessment Project. Genome Biol (2006) 7.06
The transposable elements of the Drosophila melanogaster euchromatin: a genomics perspective. Genome Biol (2002) 5.80
MetaCyc: a multiorganism database of metabolic pathways and enzymes. Nucleic Acids Res (2006) 5.79
Integrating phenotype ontologies across multiple species. Genome Biol (2010) 5.46
The bacterial symbiont Wolbachia induces resistance to RNA viral infections in Drosophila melanogaster. PLoS Biol (2008) 5.42
FlyMine: an integrated database for Drosophila and Anopheles genomics. Genome Biol (2007) 5.23
Linking human diseases to animal models using ontology-based phenotype annotation. PLoS Biol (2009) 5.17
Functional annotation of the Arabidopsis genome using controlled vocabularies. Plant Physiol (2004) 5.17
Drosophila crinkled, mutations of which disrupt morphogenesis and cause lethality, encodes fly myosin VIIA. Genetics (2004) 4.51
National Center for Biomedical Ontology: advancing biomedicine through structured organization of scientific knowledge. OMICS (2006) 3.96
TAIR: a resource for integrated Arabidopsis data. Funct Integr Genomics (2002) 3.74
The DrosDel collection: a set of P-element insertions for generating custom chromosomal aberrations in Drosophila melanogaster. Genetics (2004) 3.71
Phenotype ontologies: the bridge between genomics and evolution. Trends Ecol Evol (2007) 3.68
The DrosDel deletion collection: a Drosophila genomewide chromosomal deficiency resource. Genetics (2007) 3.08
Ontologies in biology: design, applications and future challenges. Nat Rev Genet (2004) 3.02
MetaCyc and AraCyc. Metabolic pathway databases for plant research. Plant Physiol (2005) 3.00
Integration of brassinosteroid signal transduction with the transcription network for plant growth regulation in Arabidopsis. Dev Cell (2010) 2.96
Rational association of genes with traits using a genome-scale gene network for Arabidopsis thaliana. Nat Biotechnol (2010) 2.90
Taking the first steps towards a standard for reporting on phylogenies: Minimum Information About a Phylogenetic Analysis (MIAPA). OMICS (2006) 2.57
Plant Ontology (PO): a Controlled Vocabulary of Plant Structures and Growth Stages. Comp Funct Genomics (2005) 2.48
High-throughput fluorescent tagging of full-length Arabidopsis gene products in planta. Plant Physiol (2004) 2.48
Combined evidence annotation of transposable elements in genome sequences. PLoS Comput Biol (2005) 2.47
The ribosomal protein genes and Minute loci of Drosophila melanogaster. Genome Biol (2007) 2.40
The Plant Ontology Database: a community resource for plant structure and developmental stages controlled vocabulary and annotations. Nucleic Acids Res (2008) 2.28
Entity/quality-based logical definitions for the human skeletal phenome using PATO. Conf Proc IEEE Eng Med Biol Soc (2009) 2.20
The plant structure ontology, a unified vocabulary of anatomy and morphology of a flowering plant. Plant Physiol (2006) 2.03
Principles of genome evolution in the Drosophila melanogaster species group. PLoS Biol (2007) 1.89
Mapping and identification of essential gene functions on the X chromosome of Drosophila. EMBO Rep (2001) 1.83
Recurrent insertion and duplication generate networks of transposable element sequences in the Drosophila melanogaster genome. Genome Biol (2006) 1.81
Strategies for avoiding reinventing the precollege education and outreach wheel. Genetics (2004) 1.81
PatMatch: a program for finding patterns in peptide and nucleotide sequences. Nucleic Acids Res (2005) 1.67
Molecular and cellular approaches for the detection of protein-protein interactions: latest techniques and current limitations. Plant J (2008) 1.62
Community-based gene structure annotation. Trends Plant Sci (2005) 1.47
Freezing-sensitive tomato has a functional CBF cold response pathway, but a CBF regulon that differs from that of freezing-tolerant Arabidopsis. Plant J (2004) 1.42
Whole-plant growth stage ontology for angiosperms and its application in plant biology. Plant Physiol (2006) 1.31
A membrane protein/signaling protein interaction network for Arabidopsis version AMPv2. Front Physiol (2010) 1.30
Systems analysis of plant functional, transcriptional, physical interaction, and metabolic networks. Plant Cell (2012) 1.27
The rules of gene expression in plants: organ identity and gene body methylation are key factors for regulation of gene expression in Arabidopsis thaliana. BMC Genomics (2008) 1.22
Genomic signatures of specialized metabolism in plants. Science (2014) 1.19
Metabolomics as a Hypothesis-Generating Functional Genomics Tool for the Annotation of Arabidopsis thaliana Genes of "Unknown Function". Front Plant Sci (2012) 1.17
PlantMetabolomics.org: a web portal for plant metabolomics experiments. Plant Physiol (2010) 1.15
Systematic prediction of gene function in Arabidopsis thaliana using a probabilistic functional gene network. Nat Protoc (2011) 1.14
A novel system of fertility rescue in Drosophila hybrids reveals a link between hybrid lethality and female sterility. Genetics (2003) 1.11
Fragile regions and not functional constraints predominate in shaping gene organization in the genus Drosophila. Genome Res (2010) 1.08
Systematic analysis of Arabidopsis organelles and a protein localization database for facilitating fluorescent tagging of full-length Arabidopsis proteins. Plant Physiol (2006) 1.04
The low temperature-responsive, Solanum CBF1 genes maintain high identity in their upstream regions in a genomic environment undergoing gene duplications, deletions, and rearrangements. Plant Mol Biol (2008) 0.94
Taking stock of our models: the function and future of stock centres. Nat Rev Genet (2002) 0.92
Design, implementation and maintenance of a model organism database for Arabidopsis thaliana. Comp Funct Genomics (2004) 0.88
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Uncovering Arabidopsis membrane protein interactome enriched in transporters using mating-based split ubiquitin assays and classification models. Front Plant Sci (2012) 0.83
Molecular characterization of the singed wings locus of Drosophila melanogaster. BMC Genet (2004) 0.78
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Arabidopsis genomic information for interpreting wheat EST sequences. Funct Integr Genomics (2002) 0.78
A new hybrid rescue allele in Drosophila melanogaster. Genetica (2004) 0.76
Bioinformatics tools for the identification of gene clusters that biosynthesize specialized metabolites. Brief Bioinform (2017) 0.76
A quizzical view pays clear dividends. Nature (2002) 0.75
An open letter to the Health and Safety Executive. Nature (1976) 0.75