Published in Nat Biotechnol on November 01, 2007
The NHGRI GWAS Catalog, a curated resource of SNP-trait associations. Nucleic Acids Res (2013) 14.23
Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project. Nat Biotechnol (2008) 12.96
BioPortal: ontologies and integrated data resources at the click of a mouse. Nucleic Acids Res (2009) 10.58
A gross anatomy ontology for hymenoptera. PLoS One (2010) 9.11
The Human Phenotype Ontology: a tool for annotating and analyzing human hereditary disease. Am J Hum Genet (2008) 8.78
WikiPathways: pathway editing for the people. PLoS Biol (2008) 8.13
A standard variation file format for human genome sequences. Genome Biol (2010) 7.83
The comprehensive antibiotic resistance database. Antimicrob Agents Chemother (2013) 6.41
Modeling sample variables with an Experimental Factor Ontology. Bioinformatics (2010) 6.27
Gene Ontology annotations and resources. Nucleic Acids Res (2012) 6.13
The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data. Nucleic Acids Res (2013) 5.66
ISA software suite: supporting standards-compliant experimental annotation and enabling curation at the community level. Bioinformatics (2010) 5.60
Integrating phenotype ontologies across multiple species. Genome Biol (2010) 5.46
Uberon, an integrative multi-species anatomy ontology. Genome Biol (2012) 5.43
The NIFSTD and BIRNLex vocabularies: building comprehensive ontologies for neuroscience. Neuroinformatics (2008) 5.38
Modeling biomedical experimental processes with OBI. J Biomed Semantics (2010) 5.36
Linking human diseases to animal models using ontology-based phenotype annotation. PLoS Biol (2009) 5.17
BioLit: integrating biological literature with databases. Nucleic Acids Res (2008) 4.85
The Ontology Lookup Service: more data and better tools for controlled vocabulary queries. Nucleic Acids Res (2008) 4.73
Toward interoperable bioscience data. Nat Genet (2012) 4.72
InnateDB: facilitating systems-level analyses of the mammalian innate immune response. Mol Syst Biol (2008) 4.61
Megascience. 'Omics data sharing. Science (2009) 4.36
Cross-product extensions of the Gene Ontology. J Biomed Inform (2010) 4.00
Biomedical ontologies in action: role in knowledge management, data integration and decision support. Yearb Med Inform (2008) 3.96
The Protein Ontology: a structured representation of protein forms and complexes. Nucleic Acids Res (2010) 3.74
OMERO: flexible, model-driven data management for experimental biology. Nat Methods (2012) 3.72
Logical development of the cell ontology. BMC Bioinformatics (2011) 3.68
Saccharomyces Genome Database provides mutant phenotype data. Nucleic Acids Res (2009) 3.38
Toward an ontological treatment of disease and diagnosis. Summit on Translat Bioinforma (2009) 3.24
Clinical diagnostics in human genetics with semantic similarity searches in ontologies. Am J Hum Genet (2009) 3.01
The mammalian phenotype ontology: enabling robust annotation and comparative analysis. Wiley Interdiscip Rev Syst Biol Med (2010) 3.00
A gene ontology inferred from molecular networks. Nat Biotechnol (2013) 2.95
Gene Ontology annotations: what they mean and where they come from. BMC Bioinformatics (2008) 2.84
PomBase: a comprehensive online resource for fission yeast. Nucleic Acids Res (2011) 2.84
Controlled vocabularies and semantics in systems biology. Mol Syst Biol (2011) 2.79
Next-generation phenotyping: requirements and strategies for enhancing our understanding of genotype-phenotype relationships and its relevance to crop improvement. Theor Appl Genet (2013) 2.75
PhenomeNET: a whole-phenome approach to disease gene discovery. Nucleic Acids Res (2011) 2.67
Evolution of the Sequence Ontology terms and relationships. J Biomed Inform (2010) 2.60
The National Center for Biomedical Ontology. J Am Med Inform Assoc (2011) 2.55
Identifiers.org and MIRIAM Registry: community resources to provide persistent identification. Nucleic Acids Res (2011) 2.48
VectorBase: improvements to a bioinformatics resource for invertebrate vector genomics. Nucleic Acids Res (2011) 2.45
OntoFox: web-based support for ontology reuse. BMC Res Notes (2010) 2.39
The Protein Feature Ontology: a tool for the unification of protein feature annotations. Bioinformatics (2008) 2.33
The EMBRACE web service collection. Nucleic Acids Res (2010) 2.26
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A review of auditing methods applied to the content of controlled biomedical terminologies. J Biomed Inform (2009) 2.18
BioAssay Ontology (BAO): a semantic description of bioassays and high-throughput screening results. BMC Bioinformatics (2011) 2.13
The teleost anatomy ontology: anatomical representation for the genomics age. Syst Biol (2010) 2.07
Invertebrate neurophylogeny: suggested terms and definitions for a neuroanatomical glossary. Front Zool (2010) 2.04
MAGETabulator, a suite of tools to support the microarray data format MAGE-TAB. Bioinformatics (2008) 2.03
EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats. Bioinformatics (2013) 2.02
Accessing and integrating data and knowledge for biomedical research. Yearb Med Inform (2008) 1.98
From Peer-Reviewed to Peer-Reproduced in Scholarly Publishing: The Complementary Roles of Data Models and Workflows in Bioinformatics. PLoS One (2015) 1.95
Natural Language Processing methods and systems for biomedical ontology learning. J Biomed Inform (2010) 1.95
Concept annotation in the CRAFT corpus. BMC Bioinformatics (2012) 1.94
Evolutionary characters, phenotypes and ontologies: curating data from the systematic biology literature. PLoS One (2010) 1.93
PhenoDigm: analyzing curated annotations to associate animal models with human diseases. Database (Oxford) (2013) 1.92
Phevor combines multiple biomedical ontologies for accurate identification of disease-causing alleles in single individuals and small nuclear families. Am J Hum Genet (2014) 1.92
Threats to validity in the design and conduct of preclinical efficacy studies: a systematic review of guidelines for in vivo animal experiments. PLoS Med (2013) 1.92
An open annotation ontology for science on web 3.0. J Biomed Semantics (2011) 1.91
Survey-based naming conventions for use in OBO Foundry ontology development. BMC Bioinformatics (2009) 1.90
The cognitive paradigm ontology: design and application. Neuroinformatics (2012) 1.89
Recent progress in automatically extracting information from the pharmacogenomic literature. Pharmacogenomics (2010) 1.88
On experiences of i2b2 (Informatics for integrating biology and the bedside) database with Japanese clinical patients' data. Bioinformation (2011) 1.82
The environment ontology: contextualising biological and biomedical entities. J Biomed Semantics (2013) 1.76
Three ontologies to define phenotype measurement data. Front Genet (2012) 1.74
Calling International Rescue: knowledge lost in literature and data landslide! Biochem J (2009) 1.71
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
Worm Phenotype Ontology: integrating phenotype data within and beyond the C. elegans community. BMC Bioinformatics (2011) 1.69
VectorBase: an updated bioinformatics resource for invertebrate vectors and other organisms related with human diseases. Nucleic Acids Res (2014) 1.68
Text-mining solutions for biomedical research: enabling integrative biology. Nat Rev Genet (2012) 1.68
Cognitive neuroscience 2.0: building a cumulative science of human brain function. Trends Cogn Sci (2010) 1.67
The plant ontology as a tool for comparative plant anatomy and genomic analyses. Plant Cell Physiol (2012) 1.65
An ontology for Xenopus anatomy and development. BMC Dev Biol (2008) 1.64
Pathbase and the MPATH ontology. Community resources for mouse histopathology. Vet Pathol (2010) 1.64
The what, where, how and why of gene ontology--a primer for bioinformaticians. Brief Bioinform (2011) 1.61
The RICORDO approach to semantic interoperability for biomedical data and models: strategy, standards and solutions. BMC Res Notes (2011) 1.59
Gateways to the FANTOM5 promoter level mammalian expression atlas. Genome Biol (2015) 1.58
Standardized description of scientific evidence using the Evidence Ontology (ECO). Database (Oxford) (2014) 1.57
The SWAN biomedical discourse ontology. J Biomed Inform (2008) 1.57
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
Construction of an annotated corpus to support biomedical information extraction. BMC Bioinformatics (2009) 1.55
OntoCAT--simple ontology search and integration in Java, R and REST/JavaScript. BMC Bioinformatics (2011) 1.54
The Pathogen-Host Interactions database (PHI-base): additions and future developments. Nucleic Acids Res (2014) 1.53
Building a biomedical ontology recommender web service. J Biomed Semantics (2010) 1.53
Ethical and practical issues associated with aggregating databases. PLoS Med (2008) 1.53
Finding our way through phenotypes. PLoS Biol (2015) 1.53
The chemical information ontology: provenance and disambiguation for chemical data on the biological semantic web. PLoS One (2011) 1.52
Construction and accessibility of a cross-species phenotype ontology along with gene annotations for biomedical research. F1000Res (2013) 1.52
Genotype-phenotype databases: challenges and solutions for the post-genomic era. Nat Rev Genet (2009) 1.52
Relations as patterns: bridging the gap between OBO and OWL. BMC Bioinformatics (2010) 1.50
Variable locus length in the human genome leads to ascertainment bias in functional inference for non-coding elements. Bioinformatics (2009) 1.49
Hematopoietic cell types: prototype for a revised cell ontology. J Biomed Inform (2010) 1.48
DcGO: database of domain-centric ontologies on functions, phenotypes, diseases and more. Nucleic Acids Res (2012) 1.47
Meeting Report: BioSharing at ISMB 2010. Stand Genomic Sci (2010) 1.47
Early immunologic correlates of HIV protection can be identified from computational analysis of complex multivariate T-cell flow cytometry assays. Bioinformatics (2012) 1.46
Utopia documents: linking scholarly literature with research data. Bioinformatics (2010) 1.43
Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat Genet (2001) 63.36
The consensus coding sequences of human breast and colorectal cancers. Science (2006) 60.02
The Unified Medical Language System (UMLS): integrating biomedical terminology. Nucleic Acids Res (2004) 25.99
Relations in biomedical ontologies. Genome Biol (2005) 22.07
The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene Ontology. Nucleic Acids Res (2004) 18.75
The Gene Ontology (GO) project in 2006. Nucleic Acids Res (2006) 13.79
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The Gene Ontology Annotation (GOA) project: implementation of GO in SWISS-PROT, TrEMBL, and InterPro. Genome Res (2003) 12.81
An ontology for cell types. Genome Biol (2005) 11.71
Biodynamic ontology: applying BFO in the biomedical domain. Stud Health Technol Inform (2004) 7.92
The MGED Ontology: a resource for semantics-based description of microarray experiments. Bioinformatics (2006) 7.37
Extension and integration of the gene ontology (GO): combining GO vocabularies with external vocabularies. Genome Res (2002) 5.67
Obol: integrating language and meaning in bio-ontologies. Comp Funct Genomics (2004) 5.53
Building national electronic medical record systems via the World Wide Web. J Am Med Inform Assoc (1996) 5.45
Cyberinfrastructure: empowering a "third way" in biomedical research. Science (2005) 5.43
eVOC: a controlled vocabulary for unifying gene expression data. Genome Res (2003) 5.41
Framework for a protein ontology. BMC Bioinformatics (2007) 5.24
A terminological and ontological analysis of the NCI Thesaurus. Methods Inf Med (2005) 5.11
A framework for using reference ontologies as a foundation for the semantic web. AMIA Annu Symp Proc (2006) 4.21
E-neuroscience: challenges and triumphs in integrating distributed data from molecules to brains. Nat Neurosci (2004) 4.13
The Unified Medical Language System: toward a collaborative approach for solving terminologic problems. J Am Med Inform Assoc (1998) 4.03
National Center for Biomedical Ontology: advancing biomedicine through structured organization of scientific knowledge. OMICS (2006) 3.96
Phenotype ontologies: the bridge between genomics and evolution. Trends Ecol Evol (2007) 3.68
The RNA Ontology Consortium: an open invitation to the RNA community. RNA (2006) 3.60
Development of FuGO: an ontology for functional genomics investigations. OMICS (2006) 3.59
A strategy capitalizing on synergies: the Reporting Structure for Biological Investigation (RSBI) working group. OMICS (2006) 3.51
Mistakes in medical ontologies: where do they come from and how can they be detected? Stud Health Technol Inform (2004) 3.19
Modular organization of protein interaction networks. Bioinformatics (2006) 2.68
Facts from text--is text mining ready to deliver? PLoS Biol (2005) 2.66
Linking of digital images to phylogenetic data matrices using a morphological ontology. Syst Biol (2007) 2.42
Ontologies for biologists: a community model for the annotation of genomic data. Cold Spring Harb Symp Quant Biol (2003) 2.42
Components of the antigen processing and presentation pathway revealed by gene expression microarray analysis following B cell antigen receptor (BCR) stimulation. BMC Bioinformatics (2006) 2.09
Enrichment of OBO ontologies. J Biomed Inform (2006) 1.95
Spatial location and its relevance for terminological inferences in bio-ontologies. BMC Bioinformatics (2007) 1.93
HL7 RIM: an incoherent standard. Stud Health Technol Inform (2006) 1.92
Pathway and ontology analysis: emerging approaches connecting transcriptome data and clinical endpoints. Curr Mol Med (2005) 1.70
The generic genome browser: a building block for a model organism system database. Genome Res (2002) 42.64
The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol (2008) 31.04
Relations in biomedical ontologies. Genome Biol (2005) 22.07
The Sequence Ontology: a tool for the unification of genome annotations. Genome Biol (2005) 18.20
EnsMart: a generic system for fast and flexible access to biological data. Genome Res (2004) 17.64
Reactome knowledgebase of human biological pathways and processes. Nucleic Acids Res (2008) 15.69
ArrayExpress--a public repository for microarray gene expression data at the EBI. Nucleic Acids Res (2003) 15.48
Reactome: a knowledge base of biologic pathways and processes. Genome Biol (2007) 13.36
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
ArrayExpress update--from an archive of functional genomics experiments to the atlas of gene expression. Nucleic Acids Res (2008) 12.45
Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science (2010) 12.39
FlyBase: enhancing Drosophila Gene Ontology annotations. Nucleic Acids Res (2008) 12.15
An ontology for cell types. Genome Biol (2005) 11.71
OBO-Edit--an ontology editor for biologists. Bioinformatics (2007) 11.04
AmiGO: online access to ontology and annotation data. Bioinformatics (2008) 10.77
BioPortal: ontologies and integrated data resources at the click of a mouse. Nucleic Acids Res (2009) 10.58
Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science (2010) 9.78
Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster. Science (2002) 9.43
The BioPAX community standard for pathway data sharing. Nat Biotechnol (2010) 9.19
PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium. Nucleic Acids Res (2009) 9.14
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
A standard variation file format for human genome sequences. Genome Biol (2010) 7.83
Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications. Nat Biotechnol (2011) 7.53
A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB. BMC Bioinformatics (2006) 7.53
The MGED Ontology: a resource for semantics-based description of microarray experiments. Bioinformatics (2006) 7.37
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
JBrowse: a next-generation genome browser. Genome Res (2009) 6.77
A promoter-level mammalian expression atlas. Nature (2014) 6.25
The transposable elements of the Drosophila melanogaster euchromatin: a genomics perspective. Genome Biol (2002) 5.80
The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data. Nucleic Acids Res (2013) 5.66
ISA software suite: supporting standards-compliant experimental annotation and enabling curation at the community level. Bioinformatics (2010) 5.60
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
Modeling biomedical experimental processes with OBI. J Biomed Semantics (2010) 5.36
RNAML: a standard syntax for exchanging RNA information. RNA (2002) 5.34
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
Toward interoperable bioscience data. Nat Genet (2012) 4.72
The neuroscience information framework: a data and knowledge environment for neuroscience. Neuroinformatics (2008) 4.60
Drosophila crinkled, mutations of which disrupt morphogenesis and cause lethality, encodes fly myosin VIIA. Genetics (2004) 4.51
Pre-existing immunity against swine-origin H1N1 influenza viruses in the general human population. Proc Natl Acad Sci U S A (2009) 4.47
Advancing translational research with the Semantic Web. BMC Bioinformatics (2007) 4.38
Megascience. 'Omics data sharing. Science (2009) 4.36
Diagnostic Criteria for Temporomandibular Disorders (DC/TMD) for Clinical and Research Applications: recommendations of the International RDC/TMD Consortium Network* and Orofacial Pain Special Interest Group†. J Oral Facial Pain Headache (2014) 4.25
A framework for using reference ontologies as a foundation for the semantic web. AMIA Annu Symp Proc (2006) 4.21
The first RSBI (ISA-TAB) workshop: "can a simple format work for complex studies?". OMICS (2008) 4.15
Tools for the automatic identification and classification of RNA base pairs. Nucleic Acids Res (2003) 4.12
Cross-product extensions of the Gene Ontology. J Biomed Inform (2010) 4.00
The Genomic Standards Consortium. PLoS Biol (2011) 3.99
National Center for Biomedical Ontology: advancing biomedicine through structured organization of scientific knowledge. OMICS (2006) 3.96
Federated access to heterogeneous information resources in the Neuroscience Information Framework (NIF). Neuroinformatics (2008) 3.94
Submission of microarray data to public repositories. PLoS Biol (2004) 3.83
Evaluation of fluorescence-based thermal shift assays for hit identification in drug discovery. Anal Biochem (2004) 3.73
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
Logical development of the cell ontology. BMC Bioinformatics (2011) 3.68
Development of FuGO: an ontology for functional genomics investigations. OMICS (2006) 3.59
The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics. Nat Biotechnol (2007) 3.55
A strategy capitalizing on synergies: the Reporting Structure for Biological Investigation (RSBI) working group. OMICS (2006) 3.51
The role of foundational relations in the alignment of biomedical ontologies. Stud Health Technol Inform (2004) 3.44
Minimum information specification for in situ hybridization and immunohistochemistry experiments (MISFISHIE). Nat Biotechnol (2008) 3.43
MIFlowCyt: the minimum information about a Flow Cytometry Experiment. Cytometry A (2008) 3.33
MetaboLights--an open-access general-purpose repository for metabolomics studies and associated meta-data. Nucleic Acids Res (2012) 3.32
Critical assessment of automated flow cytometry data analysis techniques. Nat Methods (2013) 3.30
BioHealthBase: informatics support in the elucidation of influenza virus host pathogen interactions and virulence. Nucleic Acids Res (2007) 3.28
Toward an ontological treatment of disease and diagnosis. Summit on Translat Bioinforma (2009) 3.24
Standards for microarray data: an open letter. Environ Health Perspect (2004) 3.15
Formalization of taxon-based constraints to detect inconsistencies in annotation and ontology development. BMC Bioinformatics (2010) 3.10
The DrosDel deletion collection: a Drosophila genomewide chromosomal deficiency resource. Genetics (2007) 3.08
Influenza research database: an integrated bioinformatics resource for influenza research and surveillance. Influenza Other Respir Viruses (2012) 3.04
National Institute of Allergy and Infectious Diseases bioinformatics resource centers: new assets for pathogen informatics. Infect Immun (2007) 3.02
On ontologies for biologists: the Gene Ontology--untangling the web. Novartis Found Symp (2002) 2.94
Summary recommendations for standardization and reporting of metabolic analyses. Nat Biotechnol (2005) 2.90