The role of ontologies in biological and biomedical research: a functional perspective

AISO: Annotation of Image Segments with Ontologies

(2015) Nikhil Lingutla et al.   Journal of Biomedical Semantics

Large-scale biomedical concept recognition: an evaluation of current automatic annotators and their parameters

(2014) Christopher Funk et al.   BMC BIOINFORMATICS

OMIT: Dynamic, Semi-Automated Ontology Development for the microRNA Domain

(2014) Jingshan Huang et al.   PLoS One

Effective diagnosis of genetic disease by computational phenotype analysis of the disease-associated genome

(2014) T. Zemojtel et al.   Science Translational Medicine

Overview of the gene ontology task at BioCreative IV

(2014) Y. Mao et al.   Database-The Journal of Biological Databases and Curation

Annotation of phenotypic diversity: decoupling data curation and ontology curation using Phenex

(2014) James P Balhoff et al.   Journal of Biomedical Semantics

Evolving BioAssay Ontology (BAO): modularization, integration and applications

(2014) Saminda Abeyruwan et al.   Journal of Biomedical Semantics

The semantic measures library and toolkit: fast computation of semantic similarity and relatedness using biomedical ontologies

(2013) S. Harispe et al.   BIOINFORMATICS

Brain: biomedical knowledge manipulation

(2013) Samuel Croset et al.   BIOINFORMATICS

XperimentR: painless annotation of a biological experiment for the laboratory scientist

(2013) Chris D Tomlinson et al.   BMC BIOINFORMATICS

Mojo Hand, a TALEN design tool for genome editing applications

(2013) Kevin L Neff et al.   BMC BIOINFORMATICS

PhenoTips: Patient Phenotyping Software for Clinical and Research Use

(2013) Marta Girdea et al.   HUMAN MUTATION

The Incredible ELK

(2013) Yevgeny Kazakov et al.   JOURNAL OF AUTOMATED REASONING

Semantator: Semantic annotator for converting biomedical text to linked data

(2013) Cui Tao et al.   JOURNAL OF BIOMEDICAL INFORMATICS

Analyzing gene expression data in mice with the Neuro Behavior Ontology

(2013) Robert Hoehndorf et al.   MAMMALIAN GENOME

A large-scale evaluation of computational protein function prediction

(2013) Predrag Radivojac et al.   NATURE METHODS

The International Mouse Phenotyping Consortium Web Portal, a unified point of access for knockout mice and related phenotyping data

(2013) Gautier Koscielny et al.   NUCLEIC ACIDS RESEARCH

Evaluation and Cross-Comparison of Lexical Entities of Biological Interest (LexEBI)

(2013) Dietrich Rebholz-Schuhmann et al.   PLoS One

An integrative, translational approach to understanding rare and orphan genetically based diseases

(2013) R. Hoehndorf et al.   Interface Focus

NCBO Technology: Powering semantically aware applications

(2013) Patricia L Whetzel et al.   Journal of Biomedical Semantics

Evaluation of research in biomedical ontologies

(2012) R. Hoehndorf et al.   BRIEFINGS IN BIOINFORMATICS

Towards an encyclopaedia of mammalian gene function: the International Mouse Phenotyping Consortium

(2012) S. D. M. Brown et al.   Disease Models & Mechanisms

500,000 fish phenotypes: The new informatics landscape for evolutionary and developmental biology of the vertebrate skeleton

(2012) P. Mabee et al.   JOURNAL OF APPLIED ICHTHYOLOGY

A gene ontology inferred from molecular networks

(2012) Janusz Dutkowski et al.   NATURE BIOTECHNOLOGY

Text-mining solutions for biomedical research: enabling integrative biology

(2012) Dietrich Rebholz-Schuhmann et al.   NATURE REVIEWS GENETICS

Gene Ontology Annotations and Resources

(2012)   NUCLEIC ACIDS RESEARCH

Chapter 13: Mining Electronic Health Records in the Genomics Era

(2012) Joshua C. Denny   PLoS Computational Biology

Uberon, an integrative multi-species anatomy ontology

(2012) Christopher J Mungall et al.   GENOME BIOLOGY

Applying semantic web technologies for phenome-wide scan using an electronic health record linked Biobank

(2012) Jyotishman Pathak et al.   Journal of Biomedical Semantics

A common layer of interoperability for biomedical ontologies based on OWL EL

(2011) R. Hoehndorf et al.   BIOINFORMATICS

IntelliGO: a new vector-based semantic similarity measure including annotation origin

(2011) Sidahmed Benabderrahmane et al.   BMC BIOINFORMATICS

Integrating systems biology models and biomedical ontologies

(2011) Robert Hoehndorf et al.   BMC Systems Biology

Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium

(2011) P. Gaudet et al.   BRIEFINGS IN BIOINFORMATICS

The National Center for Biomedical Ontology

(2011) Mark A Musen et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

PhenomeNET: a whole-phenome approach to disease gene discovery

(2011) R. Hoehndorf et al.   NUCLEIC ACIDS RESEARCH

Interoperability between Biomedical Ontologies through Relation Expansion, Upper-Level Ontologies and Automatic Reasoning

(2011) Robert Hoehndorf et al.   PLoS One

Interoperability between phenotype and anatomy ontologies

(2010) R. Hoehndorf et al.   BIOINFORMATICS

Cytoscape 2.8: new features for data integration and network visualization

(2010) M. E. Smoot et al.   BIOINFORMATICS

Relations as patterns: bridging the gap between OBO and OWL

(2010) Robert Hoehndorf et al.   BMC BIOINFORMATICS

The BioPAX community standard for pathway data sharing

(2010) Emek Demir et al.   NATURE BIOTECHNOLOGY

Evolutionary Characters, Phenotypes and Ontologies: Curating Data from the Systematic Biology Literature

(2010) Wasila M. Dahdul et al.   PLoS One

Semantic Similarity for Automatic Classification of Chemical Compounds

(2010) João D. Ferreira et al.   PLoS Computational Biology

Integrating phenotype ontologies across multiple species

(2010) Christopher J Mungall et al.   GENOME BIOLOGY

HIERARCHICAL CLASSIFICATION OF GENE ONTOLOGY TERMS USING THE GOstruct METHOD

(2010) ARTEM SOKOLOV et al.   Journal of Bioinformatics and Computational Biology

Clinical Diagnostics in Human Genetics with Semantic Similarity Searches in Ontologies

(2009) Sebastian Köhler et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Ontology quality assurance through analysis of term transformations

(2009) K. Verspoor et al.   BIOINFORMATICS

The ontology of biological sequences

(2009) Robert Hoehndorf et al.   BMC BIOINFORMATICS

FunSimMat update: new features for exploring functional similarity

(2009) Andreas Schlicker et al.   NUCLEIC ACIDS RESEARCH

BioPortal: ontologies and integrated data resources at the click of a mouse

(2009) N. F. Noy et al.   NUCLEIC ACIDS RESEARCH

Linking Human Diseases to Animal Models Using Ontology-Based Phenotype Annotation

(2009) Nicole L. Washington et al.   PLOS BIOLOGY

Semantic Similarity in Biomedical Ontologies

(2009) Catia Pesquita et al.   PLoS Computational Biology

AmiGO: online access to ontology and annotation data

(2008) Seth Carbon et al.   BIOINFORMATICS

OpenDMAP: An open source, ontology-driven concept analysis engine, with applications to capturing knowledge regarding protein transport, protein interactions and cell-type-specific gene expression

(2008) Lawrence Hunter et al.   BMC BIOINFORMATICS

Forty years of SNOMED: a literature review

(2008) Ronald Cornet et al.   BMC Medical Informatics and Decision Making

Drug Target Identification Using Side-Effect Similarity

(2008) M. Campillos et al.   SCIENCE