I'm the Associate Director of Knowledge Representation at the Center for Computational Biomedicine (CCB), Harvard Medical School.
My interests revolve around the theory and applications of knowledge representation and reasoning, natural language processing and semantic web techniques to facilitate the discovery, analysis and integration of heterogeneous, evolving datasets originating from multiple sources.
Before moving to Boston I was a Research Scientist at the Stanford Center for Biomedical Informatics Research, in the Protégé group.
I lead the Knowledge Representation group of the Center for Computational Biomedicine in its mission to develop ontology/knowledge graph-based solutions to facilitate search, annotation and reuse of scientific datasets both located on the Web and generated by research labs across the Harvard Medical School.
At the Stanford Center for Biomedical Informatics Research I was involved in the Protégé and CEDAR projects. I steered the research activities of the Protégé group, and coordinated and led projects to build enterprise knowledge graphs with industrial collaborators. I helped organizing and teaching 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. My role involved developing tools for building and populating ontologies from spreadsheet and form data, and Protégé extensions to enable collaboratively building ontologies using Protégé Desktop v5+. These extensions were designed and used for the development of the National Cancer Institute Thesaurus.
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 identify changes between (OWL) ontologies. I defined a diff method that detects changes to asserted and inferred axioms, and how those affect the meaning of terms. Then I investigated how axiom changes affect reasoning performance, and defined a new method to isolate small ontology subsets whose interaction with the remainder is highly performance-degrading—so called hot spots. My supervisors were Uli Sattler and Bijan Parsia.
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. My supervisors were Alan Rector and Robert Stevens.
Completed with 1st class Honors and an award for Best Achievement in the Field of Computational Biology. My final-year project involved web and database development, and 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 coastal town in southern Portugal, I spent much of my free time sailing and participating in competitions throughout the country. These days I enjoy being underwater instead, and scuba diving has become my main hobby. I'm a certified instructor and have dived a bit all over the world; in the Red Sea, Great Barrier Reef, Caribbean Sea, cenotes in Mexico, Blue Hole in Belize, etc. More recently I have been learning to ski.