Evaluation of research in biomedical ontologies

Personal Omics Profiling Reveals Dynamic Molecular and Medical Phenotypes

(2012) Rui Chen et al.   CELL

Semantically enabling pharmacogenomic data for the realization of personalized medicine

(2012) Matthias Samwald et al.   PHARMACOGENOMICS

Data-Driven Prediction of Drug Effects and Interactions

(2012) N. P. Tatonetti et al.   Science Translational Medicine

Uberon, an integrative multi-species anatomy ontology

(2012) Christopher J Mungall et al.   GENOME BIOLOGY

Open biomedical pluralism: formalising knowledge about breast cancer phenotypes

(2012) Aleksandra Sojic et al.   Journal of Biomedical Semantics

Reasoning with bio-ontologies: using relational closure rules to enable practical querying

(2011) Ward Blondé et al.   BIOINFORMATICS

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

(2011) Sidahmed Benabderrahmane et al.   BMC BIOINFORMATICS

Worm Phenotype Ontology: Integrating phenotype data within and beyond the C. elegans community

(2011) Gary Schindelman et al.   BMC BIOINFORMATICS

Improving ontologies by automatic reasoning and evaluation of logical definitions

(2011) Sebastian Köhler et al.   BMC BIOINFORMATICS

Unintended consequences of existential quantifications in biomedical ontologies

(2011) Martin Boeker et al.   BMC BIOINFORMATICS

Integrating systems biology models and biomedical ontologies

(2011) Robert Hoehndorf et al.   BMC Systems Biology

The what, where, how and why of gene ontology--a primer for bioinformaticians

(2011) L. du Plessis et al.   BRIEFINGS IN BIOINFORMATICS

Literature mining, ontologies and information visualization for drug repurposing

(2011) C. Andronis et al.   BRIEFINGS IN BIOINFORMATICS

In silico repositioning of approved drugs for rare and neglected diseases

(2011) Sean Ekins et al.   DRUG DISCOVERY TODAY

Enabling enrichment analysis with the Human Disease Ontology

(2011) Paea LePendu et al.   JOURNAL OF BIOMEDICAL INFORMATICS

A conditional knockout resource for the genome-wide study of mouse gene function

(2011) William C. Skarnes et al.   NATURE

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

Creating a Buzz About Insect Genomes

(2011) G. E. Robinson et al.   SCIENCE

Benchmarking Ontologies: Bigger or Better?

(2011) Lixia Yao et al.   PLoS Computational Biology

Improving disease gene prioritization using the semantic similarity of Gene Ontology terms

(2010) Andreas Schlicker et al.   BIOINFORMATICS

Interoperability between phenotype and anatomy ontologies

(2010) R. Hoehndorf et al.   BIOINFORMATICS

Relations as patterns: bridging the gap between OBO and OWL

(2010) Robert Hoehndorf et al.   BMC BIOINFORMATICS

BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models

(2010) Chen Li et al.   BMC Systems Biology

Disambiguation in the biomedical domain: The role of ambiguity type

(2010) Mark Stevenson et al.   JOURNAL OF BIOMEDICAL INFORMATICS

Evolution of the Sequence Ontology terms and relationships

(2010) Christopher J. Mungall et al.   JOURNAL OF BIOMEDICAL INFORMATICS

Cross-product extensions of the Gene Ontology

(2010) Christopher J. Mungall et al.   JOURNAL OF BIOMEDICAL INFORMATICS

The BioPAX community standard for pathway data sharing

(2010) Emek Demir et al.   NATURE BIOTECHNOLOGY

Network medicine: a network-based approach to human disease

(2010) Albert-László Barabási et al.   NATURE REVIEWS GENETICS

ArrayExpress update--an archive of microarray and high-throughput sequencing-based functional genomics experiments

(2010) H. Parkinson et al.   NUCLEIC ACIDS RESEARCH

EcoCyc: a comprehensive database of Escherichia coli biology

(2010) I. M. Keseler et al.   NUCLEIC ACIDS RESEARCH

An Environment-Wide Association Study (EWAS) on Type 2 Diabetes Mellitus

(2010) Chirag J. Patel et al.   PLoS One

Integrating phenotype ontologies across multiple species

(2010) Christopher J Mungall et al.   GENOME BIOLOGY

Applying the functional abnormality ontology pattern to anatomical functions

(2010) Robert Hoehndorf et al.   Journal of Biomedical Semantics

Survey-based naming conventions for use in OBO Foundry ontology development

(2009) Daniel Schober et al.   BMC BIOINFORMATICS

The ontology of biological sequences

(2009) Robert Hoehndorf et al.   BMC BIOINFORMATICS

Genome 10K: A Proposal to Obtain Whole-Genome Sequence for 10 000 Vertebrate Species

(2009)   JOURNAL OF HEREDITY

Lessons from 60 years of pharmaceutical innovation

(2009) Bernard Munos   NATURE REVIEWS DRUG DISCOVERY

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

The ontology of biological taxa

(2008) S. Schulz et al.   BIOINFORMATICS

Evaluation of GO-based functional similarity measures using S. cerevisiae protein interaction and expression profile data

(2008) Tao Xu et al.   BMC BIOINFORMATICS

An ontology for Xenopus anatomy and development

(2008) Erik Segerdell et al.   BMC DEVELOPMENTAL BIOLOGY

Forty years of SNOMED: a literature review

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

Inter-Coder Agreement for Computational Linguistics

(2008) Ron Artstein et al.   COMPUTATIONAL LINGUISTICS

SNOMED reaching its adolescence: Ontologists’ and logicians’ health check

(2008) Stefan Schulz et al.   INTERNATIONAL JOURNAL OF MEDICAL INFORMATICS

State of the nation in data integration for bioinformatics

(2008) Carole Goble et al.   JOURNAL OF BIOMEDICAL INFORMATICS

OWL 2: The next step for OWL

(2008) Bernardo Cuenca Grau et al.   Journal of Web Semantics

FlyBase: enhancing Drosophila Gene Ontology annotations

(2008) S. Tweedie et al.   NUCLEIC ACIDS RESEARCH