My work spans ontology and knowledge graph engineering, and the development of tools to improve how data is structured, discovered, and used in research and production. I focus on knowledge representation and reasoning and applied AI to make data interoperable and analysis-ready.
I led the BioPortal project and a team of software engineers and scientists working on various research and development initiatives. I was involved in the development of methods and tools to automatically improve scientific metadata quality using AI/LLMs. I helped to organize and teach the Protégé Short Course, a hands-on course on building ontologies using OWL and Protégé.
I led the Knowledge Representation group in the development of ontology- and knowledge-graph–based solutions to improve the discovery/search, annotation, integration, and reuse of heterogeneous, evolving biomedical/scientific datasets from multiple sources—including web resources and data generated by HMS labs. I was involved in the development of an LLM-based automatic quiz grader used in medical education.
I worked on the Protégé and CEDAR projects, and wrote multiple research grant poposals. I steered the research activities of the Protégé group; coordinated and led projects to build enterprise knowledge graphs with industry collaborators—including Pinterest, BASF, and Elsevier; and organized and taught the Protégé Short Course on building, reasoning, and querying ontologies with Protégé and WebProtégé.
I worked on the Protégé and Center for Expanded Data Annotation and Retrieval (CEDAR) projects, both led by Mark Musen. I designed and implemented Protégé extensions for collaboratively building OWL ontologies—used in the development of the National Cancer Institute (NCI) Thesaurus; created tools to transform tabular and form data into ontology statements; and taught several components of the Protégé Short Course.
I built an intelligent system for researchers to find scientific equipment owned by institutions across the N8 Consortium. I developed an OWL ontology to describe the different kinds of equipment available within N8 institutions, and a prototype web application for ontology-based, faceted search.
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.
See also: DBLP, Google Scholar, Semantic Scholar.
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: