I'm a Research Scientist at the Stanford Center for Biomedical Informatics Research, in the School of Medicine. I work in the Protégé project as well as HuBMAP. My research interests revolve around knowledge representation, automated reasoning, and linguistics. I research methods to build, maintain, deploy and use knowledge bases, mainly represented in the Web Ontology Language (OWL). I coordinate and teach the Protégé Short Course (at Stanford and off-site), which covers the OWL, RDF and SPARQL languages, and building, reasoning, and querying ontologies with the Protégé and WebProtégé tools.
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 Desktop. These extensions are used in the development of the National Cancer Institute Thesaurus. In collaboration with industry partners, I developed ontologies used in enterprise knowledge graphs. I also 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:
I grew up in a small town in the south coast of Portugal, where I spent many weekends sailing. Nowadays, scuba diving has become my main hobby, and I've dived a bit all over the world: the Red Sea in Egypt, the Great Barrier Reef in Australia, around the Caribbean Sea, the cenotes in Mexico, the Blue Hole in Belize, French Polynesia, and Hawaii. I swam with whale sharks off of Honduras, for a few seconds. Diving through a halocline in a cenote was incredible too!