The digital revolution in phenotyping

Linking gene expression to phenotypes via pathway information

(2015) Irene Papatheodorou et al.   Journal of Biomedical Semantics

Development and validation of a classification approach for extracting severity automatically from electronic health records

(2015) Mary Regina Boland et al.   Journal of Biomedical Semantics

Dose-Specific Adverse Drug Reaction Identification in Electronic Patient Records: Temporal Data Mining in an Inpatient Psychiatric Population

(2014) Robert Eriksson et al.   DRUG SAFETY

An overview of MetaMap: historical perspective and recent advances

(2014) Alan R Aronson et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

Disease Risk Factors Identified Through Shared Genetic Architecture and Electronic Medical Records

(2014) L. Li et al.   Science Translational Medicine

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

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

Human symptoms–disease network

(2014) XueZhong Zhou et al.   Nature Communications

Phenotype Ontologies and Cross-Species Analysis for Translational Research

(2014) Peter N. Robinson et al.   PLoS Genetics

Commentary on Shimoyama et al. (2012): three ontologies to define phenotype measurement data

(2014) John M. Hancock   Frontiers in Genetics

Mouse model phenotypes provide information about human drug targets

(2013) Robert Hoehndorf et al.   BIOINFORMATICS

Genome-wide Generation and Systematic Phenotyping of Knockout Mice Reveals New Roles for Many Genes

(2013) Jacqueline K. White et al.   CELL

Pharmacovigilance Using Clinical Notes

(2013) P LePendu et al.   CLINICAL PHARMACOLOGY & THERAPEUTICS

Ethnic Differences in the Relationship Between Insulin Sensitivity and Insulin Response: A systematic review and meta-analysis

(2013) K. Kodama et al.   DIABETES CARE

Improved exome prioritization of disease genes through cross-species phenotype comparison

(2013) P. N. Robinson et al.   GENOME RESEARCH

A genome- and phenome-wide association study to identify genetic variants influencing platelet count and volume and their pleiotropic effects

(2013) Khader Shameer et al.   HUMAN GENETICS

PhenoTips: Patient Phenotyping Software for Clinical and Research Use

(2013) Marta Girdea et al.   HUMAN MUTATION

Inferring characteristic phenotypes via class association rule mining in the bone dysplasia domain

(2013) Razan Paul et al.   JOURNAL OF BIOMEDICAL INFORMATICS

Systematic comparison of phenome-wide association study of electronic medical record data and genome-wide association study data

(2013) Joshua C Denny et al.   NATURE BIOTECHNOLOGY

The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data

(2013) Sebastian Köhler et al.   NUCLEIC ACIDS RESEARCH

The NHGRI GWAS Catalog, a curated resource of SNP-trait associations

(2013) Danielle Welter et al.   NUCLEIC ACIDS RESEARCH

Mining Skeletal Phenotype Descriptions from Scientific Literature

(2013) Tudor Groza et al.   PLoS One

Computational Phenotype Discovery Using Unsupervised Feature Learning over Noisy, Sparse, and Irregular Clinical Data

(2013) Thomas A. Lasko et al.   PLoS One

Learning to Recognize Phenotype Candidates in the Auto-Immune Literature Using SVM Re-Ranking

(2013) Nigel Collier et al.   PLoS One

PhenoDigm: analyzing curated annotations to associate animal models with human diseases

(2013) D. Smedley et al.   Database-The Journal of Biological Databases and Curation

Phenome-Wide Association Study (PheWAS) for Detection of Pleiotropy within the Population Architecture using Genomics and Epidemiology (PAGE) Network

(2013) Sarah A. Pendergrass et al.   PLoS Genetics

Toward knowledge support for analysis and interpretation of complex traits

(2013) Nigel Collier et al.   GENOME BIOLOGY

Personal Omics Profiling Reveals Dynamic Molecular and Medical Phenotypes

(2012) Rui Chen et al.   CELL

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

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

Representation of rare diseases in health information systems: The orphanet approach to serve a wide range of end users

(2012) Ana Rath et al.   HUMAN MUTATION

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

The Mammalian Phenotype Ontology as a unifying standard for experimental and high-throughput phenotyping data

(2012) Cynthia L. Smith et al.   MAMMALIAN GENOME

ZFIN, the Zebrafish Model Organism Database: increased support for mutants and transgenics

(2012) Douglas G. Howe et al.   NUCLEIC ACIDS RESEARCH

Decision Support Methods for Finding Phenotype — Disorder Associations in the Bone Dysplasia Domain

(2012) Razan Paul et al.   PLoS One

Argo: an integrative, interactive, text mining-based workbench supporting curation

(2012) R. Rak et al.   Database-The Journal of Biological Databases and Curation

Three Ontologies to Define Phenotype Measurement Data

(2012) Mary Shimoyama et al.   Frontiers in Genetics

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

(2011) Gary Schindelman et al.   BMC BIOINFORMATICS

A new face and new challenges for Online Mendelian Inheritance in Man (OMIM®)

(2011) Joanna Amberger et al.   HUMAN MUTATION

2010 i2b2/VA challenge on concepts, assertions, and relations in clinical text

(2011) Özlem Uzuner 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 phenotype and anatomy ontologies

(2010) R. Hoehndorf et al.   BIOINFORMATICS

PheWAS: demonstrating the feasibility of a phenome-wide scan to discover gene-disease associations

(2010) J. C. Denny et al.   BIOINFORMATICS

Mayo clinical Text Analysis and Knowledge Extraction System (cTAKES): architecture, component evaluation and applications

(2010) Guergana K Savova et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

A side effect resource to capture phenotypic effects of drugs

(2010) Michael Kuhn et al.   Molecular Systems Biology

The Mouse Genome Database (MGD): premier model organism resource for mammalian genomics and genetics

(2010) J. A. Blake et al.   NUCLEIC ACIDS RESEARCH

Finding and sharing: new approaches to registries of databases and services for the biomedical sciences

(2010) D. Smedley et al.   Database-The Journal of Biological Databases and Curation

Integrating phenotype ontologies across multiple species

(2010) Christopher J Mungall et al.   GENOME BIOLOGY

Clinical Diagnostics in Human Genetics with Semantic Similarity Searches in Ontologies

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

Practical application of ontologies to annotate and analyse large scale raw mouse phenotype data

(2009) Tim Beck et al.   BMC BIOINFORMATICS

Challenges in phenotype definition in the whole-genome era: multivariate models of memory and intelligence

(2009) F.W. Sabb et al.   NEUROSCIENCE

Potential etiologic and functional implications of genome-wide association loci for human diseases and traits

(2009) L. A. Hindorff et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

Mining phenotypes for gene function prediction

(2008) Philip Groth et al.   BMC BIOINFORMATICS

FlyBase: enhancing Drosophila Gene Ontology annotations

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