Published in Genome Biol on January 08, 2010
Disease Ontology: a backbone for disease semantic integration. Nucleic Acids Res (2011) 6.03
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
Cross-product extensions of the Gene Ontology. J Biomed Inform (2010) 4.00
PhenomeNET: a whole-phenome approach to disease gene discovery. Nucleic Acids Res (2011) 2.67
The Mammalian Phenotype Ontology as a unifying standard for experimental and high-throughput phenotyping data. Mamm Genome (2012) 2.43
Improved exome prioritization of disease genes through cross-species phenotype comparison. Genome Res (2013) 2.24
Phenex: ontological annotation of phenotypic diversity. PLoS One (2010) 2.13
The teleost anatomy ontology: anatomical representation for the genomics age. Syst Biol (2010) 2.07
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
The cognitive paradigm ontology: design and application. Neuroinformatics (2012) 1.89
NeXML: rich, extensible, and verifiable representation of comparative data and metadata. Syst Biol (2012) 1.86
Three ontologies to define phenotype measurement data. Front Genet (2012) 1.74
Ontologies as integrative tools for plant science. Am J Bot (2012) 1.71
Worm Phenotype Ontology: integrating phenotype data within and beyond the C. elegans community. BMC Bioinformatics (2011) 1.69
ZFIN, the Zebrafish Model Organism Database: increased support for mutants and transgenics. Nucleic Acids Res (2012) 1.69
Interoperability between phenotype and anatomy ontologies. Bioinformatics (2010) 1.58
Standardized description of scientific evidence using the Evidence Ontology (ECO). Database (Oxford) (2014) 1.57
Construction and accessibility of a cross-species phenotype ontology along with gene annotations for biomedical research. F1000Res (2013) 1.52
The Human Phenotype Ontology: Semantic Unification of Common and Rare Disease. Am J Hum Genet (2015) 1.52
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
ParameciumDB in 2011: new tools and new data for functional and comparative genomics of the model ciliate Paramecium tetraurelia. Nucleic Acids Res (2010) 1.44
MouseFinder: Candidate disease genes from mouse phenotype data. Hum Mutat (2012) 1.41
Phenotypic overlap in the contribution of individual genes to CNV pathogenicity revealed by cross-species computational analysis of single-gene mutations in humans, mice and zebrafish. Dis Model Mech (2012) 1.39
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
Phenotype ontologies for mouse and man: bridging the semantic gap. Dis Model Mech (2010) 1.28
A semantic model for species description applied to the ensign wasps (hymenoptera: evaniidae) of New Caledonia. Syst Biol (2013) 1.26
Interoperability between biomedical ontologies through relation expansion, upper-level ontologies and automatic reasoning. PLoS One (2011) 1.24
Improving ontologies by automatic reasoning and evaluation of logical definitions. BMC Bioinformatics (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
A unified anatomy ontology of the vertebrate skeletal system. PLoS One (2012) 1.22
A revision of Evaniscus (Hymenoptera, Evaniidae) using ontology-based semantic phenotype annotation. Zookeys (2012) 1.20
The ontology of craniofacial development and malformation for translational craniofacial research. Am J Med Genet C Semin Med Genet (2013) 1.19
Phenotype ontologies and cross-species analysis for translational research. PLoS Genet (2014) 1.19
Reasoning over taxonomic change: exploring alignments for the Perelleschus use case. PLoS One (2015) 1.17
FYPO: the fission yeast phenotype ontology. Bioinformatics (2013) 1.17
Integrating systems biology models and biomedical ontologies. BMC Syst Biol (2011) 1.16
Developing a kidney and urinary pathway knowledge base. J Biomed Semantics (2011) 1.13
Evaluation of research in biomedical ontologies. Brief Bioinform (2012) 1.12
Towards a bioinformatics of patterning: a computational approach to understanding regulative morphogenesis. Biol Open (2012) 1.12
Aber-OWL: a framework for ontology-based data access in biology. BMC Bioinformatics (2015) 1.08
The mouse pathology ontology, MPATH; structure and applications. J Biomed Semantics (2013) 1.05
A knowledge based approach to matching human neurodegenerative disease and animal models. Front Neuroinform (2013) 1.04
PHENOPSIS DB: an information system for Arabidopsis thaliana phenotypic data in an environmental context. BMC Plant Biol (2011) 1.03
Semantic integration of physiology phenotypes with an application to the Cellular Phenotype Ontology. Bioinformatics (2012) 1.03
Applying the functional abnormality ontology pattern to anatomical functions. J Biomed Semantics (2010) 1.02
Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial Ontology. J Biomed Semantics (2014) 1.01
EXACT2: the semantics of biomedical protocols. BMC Bioinformatics (2014) 0.99
The RIKEN integrated database of mammals. Nucleic Acids Res (2010) 0.99
Improving disease gene prioritization by comparing the semantic similarity of phenotypes in mice with those of human diseases. PLoS One (2012) 0.98
iBeetle-Base: a database for RNAi phenotypes in the red flour beetle Tribolium castaneum. Nucleic Acids Res (2014) 0.98
Manteia, a predictive data mining system for vertebrate genes and its applications to human genetic diseases. Nucleic Acids Res (2013) 0.97
Semantically enabling a genome-wide association study database. J Biomed Semantics (2012) 0.97
eNanoMapper: harnessing ontologies to enable data integration for nanomaterial risk assessment. J Biomed Semantics (2015) 0.97
The role of ontologies in biological and biomedical research: a functional perspective. Brief Bioinform (2015) 0.96
The influence of disease categories on gene candidate predictions from model organism phenotypes. J Biomed Semantics (2014) 0.94
The iBeetle large-scale RNAi screen reveals gene functions for insect development and physiology. Nat Commun (2015) 0.93
Mouse model phenotypes provide information about human drug targets. Bioinformatics (2013) 0.93
Cross-Ontology multi-level association rule mining in the Gene Ontology. PLoS One (2012) 0.92
Systematic analysis of experimental phenotype data reveals gene functions. PLoS One (2013) 0.92
The Software Ontology (SWO): a resource for reproducibility in biomedical data analysis, curation and digital preservation. J Biomed Semantics (2014) 0.91
A bioinformatics expert system linking functional data to anatomical outcomes in limb regeneration. Regeneration (Oxf) (2014) 0.90
An integrative, translational approach to understanding rare and orphan genetically based diseases. Interface Focus (2013) 0.90
Laboratory mouse models for the human genome-wide associations. PLoS One (2010) 0.90
Supporting the annotation of chronic obstructive pulmonary disease (COPD) phenotypes with text mining workflows. J Biomed Semantics (2015) 0.90
Toward Synthesizing Our Knowledge of Morphology: Using Ontologies and Machine Reasoning to Extract Presence/Absence Evolutionary Phenotypes across Studies. Syst Biol (2015) 0.89
Ontology-based cross-species integration and analysis of Saccharomyces cerevisiae phenotypes. J Biomed Semantics (2012) 0.88
Analysis of the human diseasome using phenotype similarity between common, genetic, and infectious diseases. Sci Rep (2015) 0.86
Querying phenotype-genotype relationships on patient datasets using semantic web technology: the example of Cerebrotendinous xanthomatosis. BMC Med Inform Decis Mak (2012) 0.86
Computational tools for comparative phenomics: the role and promise of ontologies. Mamm Genome (2012) 0.85
New approaches to the representation and analysis of phenotype knowledge in human diseases and their animal models. Brief Funct Genomics (2011) 0.85
A UML profile for the OBO relation ontology. BMC Genomics (2012) 0.85
Automatically transforming pre- to post-composed phenotypes: EQ-lising HPO and MP. J Biomed Semantics (2013) 0.84
Analyzing gene expression data in mice with the Neuro Behavior Ontology. Mamm Genome (2013) 0.84
Linking gene expression to phenotypes via pathway information. J Biomed Semantics (2015) 0.84
Decomposing phenotype descriptions for the human skeletal phenome. Biomed Inform Insights (2013) 0.84
Toward knowledge support for analysis and interpretation of complex traits. Genome Biol (2013) 0.84
H2DB: a heritability database across multiple species by annotating trait-associated genomic loci. Nucleic Acids Res (2012) 0.83
TrOn: an anatomical ontology for the beetle Tribolium castaneum. PLoS One (2013) 0.83
Moving the mountain: analysis of the effort required to transform comparative anatomy into computable anatomy. Database (Oxford) (2015) 0.82
Reporting phenotypes in mouse models when considering body size as a potential confounder. J Biomed Semantics (2016) 0.82
An ontology approach to comparative phenomics in plants. Plant Methods (2015) 0.82
Linking tissues to phenotypes using gene expression profiles. Database (Oxford) (2014) 0.82
Modeling biochemical pathways in the gene ontology. Database (Oxford) (2016) 0.81
Molecularly and clinically related drugs and diseases are enriched in phenotypically similar drug-disease pairs. Genome Med (2014) 0.81
Disease insights through cross-species phenotype comparisons. Mamm Genome (2015) 0.80
The cellular microscopy phenotype ontology. J Biomed Semantics (2016) 0.79
Trends in computational biology—2010. Nat Biotechnol (2011) 0.79
Modeling functional Magnetic Resonance Imaging (fMRI) experimental variables in the Ontology of Experimental Variables and Values (OoEVV). Neuroimage (2013) 0.79
Using ontologies to study cell transitions. J Biomed Semantics (2013) 0.79
An ontology for microbial phenotypes. BMC Microbiol (2014) 0.79
Annotation of phenotypic diversity: decoupling data curation and ontology curation using Phenex. J Biomed Semantics (2014) 0.79
PhenoMiner: from text to a database of phenotypes associated with OMIM diseases. Database (Oxford) (2015) 0.79
Capturing phenotypes for precision medicine. Cold Spring Harb Mol Case Stud (2015) 0.78
Phenoscape: Identifying Candidate Genes for Evolutionary Phenotypes. Mol Biol Evol (2015) 0.78
Computable visually observed phenotype ontological framework for plants. BMC Bioinformatics (2011) 0.78
RARGE II: an integrated phenotype database of Arabidopsis mutant traits using a controlled vocabulary. Plant Cell Physiol (2013) 0.78
Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet (2000) 336.52
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
A reference ontology for biomedical informatics: the Foundational Model of Anatomy. J Biomed Inform (2003) 21.77
ChEBI: a database and ontology for chemical entities of biological interest. Nucleic Acids Res (2007) 13.08
An ontology for cell types. Genome Biol (2005) 11.71
The Mammalian Phenotype Ontology as a tool for annotating, analyzing and comparing phenotypic information. Genome Biol (2004) 11.18
OBO-Edit--an ontology editor for biologists. Bioinformatics (2007) 11.04
The Human Phenotype Ontology: a tool for annotating and analyzing human hereditary disease. Am J Hum Genet (2008) 8.78
Using ontologies to describe mouse phenotypes. Genome Biol (2004) 7.03
Genome assembly comparison identifies structural variants in the human genome. Nat Genet (2006) 6.93
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
Obol: integrating language and meaning in bio-ontologies. Comp Funct Genomics (2004) 5.53
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
Framework for a protein ontology. BMC Bioinformatics (2007) 5.24
Linking human diseases to animal models using ontology-based phenotype annotation. PLoS Biol (2009) 5.17
The Human Genome Project: lessons from large-scale biology. Science (2003) 4.69
The Zebrafish Information Network: the zebrafish model organism database provides expanded support for genotypes and phenotypes. Nucleic Acids Res (2007) 4.30
EMAP and EMAGE: a framework for understanding spatially organized data. Neuroinformatics (2003) 3.91
Phenotype ontologies: the bridge between genomics and evolution. Trends Ecol Evol (2007) 3.68
Biological ontologies in rice databases. An introduction to the activities in Gramene and Oryzabase. Plant Cell Physiol (2005) 2.06
Representing default knowledge in biomedical ontologies: application to the integration of anatomy and phenotype ontologies. BMC Bioinformatics (2007) 1.84
Practical application of ontologies to annotate and analyse large scale raw mouse phenotype data. BMC Bioinformatics (2009) 1.70
An anatomical ontology for amphibians. Pac Symp Biocomput (2007) 1.42
Genome-wide analysis of human disease alleles reveals that their locations are correlated in paralogous proteins. PLoS Comput Biol (2008) 1.20
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
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
An ontology for cell types. Genome Biol (2005) 11.71
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
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
The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data. Nucleic Acids Res (2013) 5.66
Uberon, an integrative multi-species anatomy ontology. Genome Biol (2012) 5.43
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
On the reproducibility of science: unique identification of research resources in the biomedical literature. PeerJ (2013) 5.11
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
Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Brief Bioinform (2011) 3.90
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 RNA Ontology Consortium: an open invitation to the RNA community. RNA (2006) 3.60
The DrosDel deletion collection: a Drosophila genomewide chromosomal deficiency resource. Genetics (2007) 3.08
Sequence ontology annotation guide. Comp Funct Genomics (2004) 2.77
PhenomeNET: a whole-phenome approach to disease gene discovery. Nucleic Acids Res (2011) 2.67
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
Improved exome prioritization of disease genes through cross-species phenotype comparison. Genome Res (2013) 2.24
Entity/quality-based logical definitions for the human skeletal phenome using PATO. Conf Proc IEEE Eng Med Biol Soc (2009) 2.20
modMine: flexible access to modENCODE data. Nucleic Acids Res (2011) 2.18
Relations of maternal socialization and toddlers' effortful control to children's adjustment and social competence. Dev Psychol (2007) 2.12
The teleost anatomy ontology: anatomical representation for the genomics age. Syst Biol (2010) 2.07
Towards BioDBcore: a community-defined information specification for biological databases. Nucleic Acids Res (2010) 1.97
Survey-based naming conventions for use in OBO Foundry ontology development. BMC Bioinformatics (2009) 1.90
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
The environment ontology: contextualising biological and biomedical entities. J Biomed Semantics (2013) 1.76
Mouse Phenotype Database Integration Consortium: integration [corrected] of mouse phenome data resources. Mamm Genome (2007) 1.75
Web Apollo: a web-based genomic annotation editing platform. Genome Biol (2013) 1.69
EMPReSS: European mouse phenotyping resource for standardized screens. Bioinformatics (2005) 1.69
On the Use of Gene Ontology Annotations to Assess Functional Similarity among Orthologs and Paralogs: A Short Report. PLoS Comput Biol (2012) 1.65
Exploring the elephant: histopathology in high-throughput phenotyping of mutant mice. Dis Model Mech (2011) 1.62
The relations of effortful control and ego control to children's resiliency and social functioning. Dev Psychol (2003) 1.54
MouseFinder: Candidate disease genes from mouse phenotype data. Hum Mutat (2012) 1.41
The modENCODE Data Coordination Center: lessons in harvesting comprehensive experimental details. Database (Oxford) (2011) 1.39
Phenotypic overlap in the contribution of individual genes to CNV pathogenicity revealed by cross-species computational analysis of single-gene mutations in humans, mice and zebrafish. Dis Model Mech (2012) 1.39
The relations of effortful control and reactive control to children's externalizing problems: a longitudinal assessment. J Pers (2003) 1.37
A common layer of interoperability for biomedical ontologies based on OWL EL. Bioinformatics (2011) 1.35
Mouse, man, and meaning: bridging the semantics of mouse phenotype and human disease. Mamm Genome (2009) 1.31
Phenotype ontologies for mouse and man: bridging the semantic gap. Dis Model Mech (2010) 1.28
Identifying aberrant pathways through integrated analysis of knowledge in pharmacogenomics. Bioinformatics (2012) 1.27
Towards BioDBcore: a community-defined information specification for biological databases. Database (Oxford) (2011) 1.24
Interoperability between biomedical ontologies through relation expansion, upper-level ontologies and automatic reasoning. PLoS One (2011) 1.24
Improving ontologies by automatic reasoning and evaluation of logical definitions. BMC Bioinformatics (2011) 1.24
A unified anatomy ontology of the vertebrate skeletal system. PLoS One (2012) 1.22
Mouse genetic and phenotypic resources for human genetics. Hum Mutat (2012) 1.18
Integrating systems biology models and biomedical ontologies. BMC Syst Biol (2011) 1.16
Interactions between serotonin transporter gene haplotypes and quality of mothers' parenting predict the development of children's noncompliance. Dev Psychol (2011) 1.12
Evaluation of research in biomedical ontologies. Brief Bioinform (2012) 1.12
Differential susceptibility and the early development of aggression: interactive effects of respiratory sinus arrhythmia and environmental quality. Dev Psychol (2011) 1.12
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
Deletions of chromosomal regulatory boundaries are associated with congenital disease. Genome Biol (2014) 1.07
The mouse pathology ontology, MPATH; structure and applications. J Biomed Semantics (2013) 1.05
A knowledge based approach to matching human neurodegenerative disease and animal models. Front Neuroinform (2013) 1.04
Semantic integration of physiology phenotypes with an application to the Cellular Phenotype Ontology. Bioinformatics (2012) 1.03
Disease model curation improvements at Mouse Genome Informatics. Database (Oxford) (2012) 1.02
The zebrafish anatomy and stage ontologies: representing the anatomy and development of Danio rerio. J Biomed Semantics (2014) 1.01
The Vertebrate Trait Ontology: a controlled vocabulary for the annotation of trait data across species. J Biomed Semantics (2013) 1.01
Leukaemia inhibitory factor (LIF) is functionally linked to axotrophin and both LIF and axotrophin are linked to regulatory immune tolerance. FEBS Lett (2005) 1.00
Improving disease gene prioritization by comparing the semantic similarity of phenotypes in mice with those of human diseases. PLoS One (2012) 0.98
The Drosophila phenotype ontology. J Biomed Semantics (2013) 0.96
The role of ontologies in biological and biomedical research: a functional perspective. Brief Bioinform (2015) 0.96
Physiological Regulation and Fearfulness as Predictors of Young Children's Empathy-related Reactions. Soc Dev (2010) 0.95
Linking PharmGKB to phenotype studies and animal models of disease for drug repurposing. Pac Symp Biocomput (2012) 0.93
Mouse model phenotypes provide information about human drug targets. Bioinformatics (2013) 0.93
Relations among maternal socialization, effortful control, and maladjustment in early childhood. Dev Psychopathol (2010) 0.92
Systematic analysis of experimental phenotype data reveals gene functions. PLoS One (2013) 0.92