My research interests lie in the application of Semantic Web technologies to improve the knowledge management in life sciences.
I am or have been involved in the following developments:
- OPPL Galaxy: this tool can be used to execute OPPL scripts as part of Galaxy. It can be found in Ontology Manipulation in the Galaxy Toolshed. [http://toolshed.g2.bx.psu.edu/]
- Bioinformatics Knowledge Blog: This is a compilation of peer reviewed tutorials. [http://bioinformatics.knowledgeblog.org]
- Ontogenesis Knowledge Blog: This was an experiment on publishing papers about ontologies (Including peer review) using blogs, as part of the Ontogenesis network. [http://ontogenesis.knowledgeblog.org/]
- OGO: OGO integrates orthology information with diseases from OMIM, exploiting OWL, SPARQL and OBO ontologies. [http://miuras.inf.um.es:9080/OGO-1.0/]
- OGOLOD is a Linked Data version of OGO. [http://miuras.inf.um.es/~ogo/ogolod.html]
- ODPs catalogue: A repository of ontology engineering best practices, focused on biological knowledge. [http://odps.sf.net]
- BioGateway: An RDF store holding information integrated from different bioinformatics resources, like the OBO ontologies, GOA files and SwissProt. [http://www.semantic-systems-biology.org/biogateway]
- CCO: The Cell Cycle Ontology is an application ontology that describes different aspects of the cell cycle, integrating information from UniProt, IntAct, GOA, NCBI taxonomy and GO. [http://cellcycleontology.org]
- OPPL: The Ontology Pre-Processor Language is a scripting language for defining and performing axiomatic changes in OWL ontologies, thus offering an abstraction of the OWL API that works directly with axioms instead of programmatic procedures. [http://oppl.sourceforge.net/]
- ONTO-PERL: An API for manipulating OBO ontologies, written in Perl. [http://search.cpan.org/~easr/]
- GONG: Gene Ontology Next Generation is a methodology for enriching OBO ontologies by adding OWL axioms based on dissecting the structure of the term names with regular expressions. [http://www.gong.manchester.ac.uk]
