I'm a Senior Research Engineer in the Musen Lab at the Stanford Center for Biomedical Informatics Research, where I lead the BioPortal project and contribute to a range of research and development efforts aimed at improving how biomedical data are described, discovered, and reused.
My work spans ontology engineering, metadata curation, and the development of tools and infrastructure to improve the organization, searchability, and utility of data in support of scientific research.
I’m particularly interested in knowledge representation and reasoning—spanning ontologies, knowledge graphs, and formal semantics in metadata—and in applying artificial intelligence and semantic technologies to make scientific data more structured, interoperable, and reusable in service of open science.
I lead the BioPortal project and oversee a team of software developers and scientists working on various research and development initiatives to enhance the organization, discovery, and reuse of scientific data. My work spans ontology engineering, metadata curation, and the development of methods and tools to improve metadata quality and data infrastructure. I also organize and teach the Protégé Short Course, an intensive hands-on course on building ontologies using OWL and Protégé.
At the Center for Computational Biomedicine (Harvard Medical School), I led the Knowledge Representation team, developing ontology- and knowledge-graph–based solutions that apply knowledge representation and reasoning 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 research labs across HMS.
As a Research Scientist at Stanford's Center for Biomedical Informatics Research (School of Medicine), I was primarily involved in the Protégé project and also contributed to CEDAR. I steered the research activities of the Protégé group; coordinated and led projects to build enterprise knowledge graphs with industrial collaborators—including Pinterest, BASF, and Elsevier; and organized and taught the Protégé Short Course on building, reasoning, and querying ontologies with Protégé and WebProtégé.
As a Senior Software Engineer at Stanford’s Center for Biomedical Informatics Research, I worked on the Protégé and Center for Expanded Data Annotation and Retrieval (CEDAR) projects led by Mark Musen. I designed and implemented Protégé Desktop extensions for collaboratively building OWL ontologies—used in the development of the National Cancer Institute (NCI) Thesaurus; created tools to transform spreadsheet data and web forms into ontology statements and to populate ontologies; built CEDAR extensions to improve metadata authoring; and taught several components of the Protégé Short Course.
As a Research Associate, I worked on an N8 Consortium project to build an intelligent system for browsing and discovering scientific equipment. I developed an OWL ontology to describe equipment available within N8 institutions and a prototype web application for ontology-based, faceted browsing. The 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.
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: