PhenomicDB: a new cross-species genotype/phenotype resource

Abstract

Phenotypes are an important subject of biomedical research for which many repositories have already been created. Most of these databases are either dedicated to a single species or to a single disease of interest. With the advent of technologies to generate phenotypes in a high-throughput manner, not only is the volume of phenotype data growing fast but also the need to organize these data in more useful ways. We have created PhenomicDB (freely available at ), a multi-species genotype/phenotype database, which shows phenotypes associated with their corresponding genes and grouped by gene orthologies across a variety of species. We have enhanced PhenomicDB recently by additionally incorporating quantitative and descriptive RNA interference (RNAi) screening data, by enabling the usage of phenotype ontology terms and by providing information on assays and cell lines. We envision that integration of classical phenotypes with high-throughput data will bring new momentum and insights to our understanding. Modern analysis tools under development may help exploiting this wealth of information to transform it into knowledge and, eventually, into novel therapeutic approaches.

Uniform standards for genome databases in forest and fruit trees

“…NCBI has launched dbGaP (Zhang et al 2008), a public database to archive genotype and clinical phenotype data from human studies. The Complex Trait Consortium has launched GeneNetwork (Wu (Groth et al 2007). None of the existing tools currently handle plant data or geographic information which is vital for the increasing number of landscape genomics studies.…”

Phenotype ontologies for mouse and man: bridging the semantic gap

“…A good example is PhenomicDB (Groth et al, 2007), which contains one of the most wide-ranging cross-species datasets on gene/phenotype associations. This database combines data from OMIM, the Mouse Genome Database (MGD), WormBase, FlyBase, the Comprehensive Yeast Genome Database (CYGD), the Zebrafish Information Network (ZFIN), and the MIPS Arabidopsis thaliana database (MAtDB).…”

“…It is also crucial if human phenotypes are to be compared with those from model organisms. The deficiency in cross-species interoperability of phenotype description formalisms is well demonstrated by the analysis of cross-species phenoclustering that was carried out using PhenomicDB by Groth et al (Groth et al, 2007), discussed above. More than 90% of the clusters they generated contained genes from a single species and there was a tendency for genes to fall into species-specific clusters.…”

Array comparative genomic hybridization and computational genome annotation in constitutional cytogenetics: suggesting candidate genes for novel submicroscopic chromosomal imbalance syndromes

“…Other noteworthy resources include PhenomicDB 31 and PhenoGO. 32 PhenomicDB's value lies in how it integrates phenotype information from multiple species-oriented databases into one repository.…”