Current projects and collaborations.

Current projects


Apollo is a browser-based tool for visualization and editing of sequence annotations.


We are collaborating with the BIRN project at UCSD to develop tools that utilize ontologies to query across distributed relational databases of images at multiple scales used for the study of Neurological Disease.

Cell Ontology

The cell ontology (CL) represents cell types across a variety of taxa. CL is integrated with other OBO library ontologies such as GO and uberon.

Gene Ontology

The Gene Ontology (GO) project is a collaborative effort to address the need for consistent descriptions of gene products in different databases.


GMOD is the Generic Model Organism Database Toolkit, a collection of software tools for creating and managing genome-scale biological databases.


We are also working on the modENCODE project--the model organism Encyclopedia of DNA Elements.

OBO Foundry

The Open Biomedical Ontologies (OBO) Foundry is a collaborative experiment: to produce well-structured vocabularies for shared use across different biological and medical domains.


One natural outgrowth of the GO project was the necessity to move from annotating the function of individual gene products to annotating protein families.


The PATO project provides a means of describing and comparing phenotypes across a variety of species

Past projects