Ontology alignment, the task of identifying mappings between ontologies, is a key task for knowledge sharing between applications that use different ontologies. Manual alignment is time-consuming and difficult when dealing with large ontologies, which are common in biomedical domain, while automatic alignment shows low coverage. We present a tool with user-friendly GUI for semi-automatic ontology alignment, called NViz. It helps human experts focus on pairs of ontology clusters that are likely to have missing mappings. NViz utilizes a state of-the-art system of ontology alignment, called BOAT, and a hierarchical clustering method.

Watson W.K. Chua, Jung-jae Kim, Bui Duc Hieu

Bgee is a database to compare expression patterns between animals. We create homology relationships between anatomical ontologies, and store this information in a multi-species ontology. On the download page of Bgee, you will find the Homologous Organ Group ontology, the developmental Stages ontology, and the Homolonto software for ontology alignment.

Robinson-Rechavi lab

eTOX is a temporary consortium established in 2010 to share and use toxicology data. It is a pre-competitive collaboration which main goal is to create and distribute tools to predict drug side-effects based on pre-clinical experiments. Aims are a better in silico predictability of potential adverse events and a decrease of the use of animals in toxicological research. eTOX is funded by the Innovative Medicines Initiative (IMI).

Philippe MARC

Logic-based and Scalable Ontology Matching. LogMap is a highly scalable ontology matching system with `built-in' reasoning and diagnosis capabilities. Currently, LogMap is the only matching system that can sucessfully deal with semantically rich ontologies containing tens (and even hundreds) of thousands of classes. Furthermore, LogMap is able to produce a `clean' set of output mappings in many cases. Our experiments with the ontologies NCI, FMA and SNOMED CT confirm that our system can efficiently match even the largest existing bio-medical ontologies.

Ernesto Jimenez Ruiz and Bernardo Cuenca Grau

SemGen is a software tool for automating the modular composition and decomposition of biosimulation models. It uses BioPortal web services to provide model annotators access to reference ontology terms.

Maxwell Neal, Daniel Cook, John Gennari

Enabling navigation across a rich landscape of phenotypes, diseases, models, and genes for translational research.

Melissa Haendel, Chris Mungall, Maryann Martone, Harry Hochhesier, Damian Smedley, Peter Robinson

A web-based environment that discovers ontological structure from empirical data.

Elissa Chesler, Erich Baker, Michael Langston, Jeremy Jay