I am a Senior Research Associate at the Center for Computational Biomedicine in the Harvard Medical School. My research revolves around knowledge representation and reasoning. I am especially interested in the application of ontologies to improve the discovery, integration and meta-analysis of heterogeneous, evolving biomedical datasets originating from multiple sources.
I worked at the Center for Biomedical Informatics Research, in the School of Medicine, where I was primarily involved in the Protégé project. I steered the research activities of the Protégé group, and I coordinated and led projects to build enterprise knowledge graphs with industrial collaborators. I organized and taught the Protégé Short Course on building, reasoning, and querying ontologies with Protégé and WebProtégé.
I worked in the Protégé and the Center for Expanded Data Annotation and Retrieval (CEDAR) projects, led by Mark Musen. I developed Protégé extensions that allow users to collaboratively build OWL ontologies using Protégé. These extensions are used in the development of the National Cancer Institute Thesaurus. I built tools for transforming data from spreadsheets and forms into ontology statements.
I worked on an N8 Consortium project to build an intelligent system for browsing and discovering scientific equipment. This project involved the development of an OWL ontology to describe scientific equipment available within institutions of the N8 Consortium, and a prototype Web application for faceted-browsing of equipment based on the ontology. This project was supervised by Robert Stevens.
I was a Teaching Assistant on the following courses:
In my thesis Impact Analysis in Description Logic Ontologies, I investigated methods to detect and present changes between description logic (DL) ontologies represented in OWL. I defined a new diff method that detects changes to asserted and inferred axioms, as well as changes to the meaning of terms. Then I investigated how axiom changes affect DL reasoner performance. I defined a new method to isolate small ontology subsets whose interaction with the remainder is highly performance-degrading—so called hot spots. I was supervised by Uli Sattler and Bijan Parsia.
I received a Kilburn scholarship. In my Masters dissertation, I investigated the feasibility of collaboratively developing OWL ontologies using semantic wikis. I evaluated semantic wikis equipped with reasoning and SPARQL querying capabilities. This project was supervised by Alan Rector and Robert Stevens.
Completed with 1st class Honours. I received an award for the Best Achievement in the Field of Computational Biology. My final year project was supervised by Frans Coenen.
I frequently review papers for multiple conferences and workshops:
I am a member of the editorial board for the Semantic Web Journal. I also review for the following journals:
Born and raised in a small town in the south coast of Portugal, I spent much of my free time sailing (competitively). These days I rather enjoy being underwater instead, and scuba diving has become my main hobby. I dived a bit all over the world: Red Sea, Great Barrier Reef, Caribbean Sea, cenotes in Mexico, Blue Hole in Belize,... More recently I have been learning to ski.