Rafael Gonçalves

Associate Director · Center for Computational Biomedicine · Harvard Medical School

I'm the Associate Director of Knowledge Representation at the Center for Computational Biomedicine, Harvard Medical School.

My interests revolve around the theory and applications of knowledge representation and reasoning, natural language processing and semantic web technologies to facilitate the discovery, analysis and integration of heterogeneous, evolving datasets.

Before moving to Boston I was a Research Scientist in the Protégé group at Stanford University.


Experience

Associate Director

Harvard Medical School · Center for Computational Biomedicine

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.

2021 - Present

Research Scientist

Stanford University · Center for Biomedical Informatics Research

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.

2018 - 2021

Research Software Engineer

Stanford University · Center for Biomedical Informatics Research

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.

2014 - 2018

Research Associate

The University of Manchester · School of Computer Science

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.

2012 - 2013

Teaching Assistant

The University of Manchester · School of Computer Science

I was a Teaching Assistant on the following courses:

  • Object-Oriented Programming with Java (B.S. 1st year course)
  • Ontology Engineering for the Semantic Web (M.S. course)
  • Knowledge Representation and Reasoning (B.S. 3rd year course)
  • Semi-Structured Data and the Web (M.S. course)
2009 - 2012

Education

PhD in Computer Science

The University of Manchester

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.

2009 - 2014

MSc in Software Engineering

The University of Manchester

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.

2008 - 2009

BSc in Computer Science

University of Liverpool

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.

2005 - 2008

Publications

2023

2022

2021

2020

2019

New Features for Biomedical Ontology Editing in Protégé [Demo]
Int. Conference on Biomedical Ontology

2018

Protégé 5.5 – Improvements for Editing Biomedical Ontologies
Int. Conference on Biomedical Ontology
Using Ontologies to Drive the Creation of High-Quality Metadata in CEDAR [Demo]
Int. Semantic Web Conference
WebProtégé 3.0 – Collaborative OWL Ontology Engineering in the Cloud [Demo]
Int. Semantic Web Conference

2017

2016

2015

Structured Data Acquisition with Ontology-Based Web Forms
Int. Conference on Biomedical Ontology
The OWL Reasoner Evaluation (ORE) 2015 Competition Report
Workshop on Scalabale Semantic Web Knowledge Base Systems
NCBO BioPortal version 4 [Demo]
Int. Conference on Biomedical Ontology
OWL-based form generation and structured data acquisition [Demo]
Int. Conference on Biomedical Ontology

2014

2013

The empirical robustness of description logic classification [Poster]
Int. Semantic Web Conference
Comparing ontologies with ecco [Demo]
Int. Semantic Web Conference
OWL Reasoner Evaluation (ORE) Workshop 2013 Results: Short Report
OWL Reasoner Evaluation Workshop
The empirical robustness of description logic classification
Int. Workshop on Description Logics

2012

FishMark: A linked data application benchmark
Workshop on Scalabale Semantic Web Knowledge Base Systems
Concept-based semantic difference in expressive description logics
Int. Workshop on Description Logics
ecco: A hybrid diff tool for OWL 2 ontologies
OWL: Experiences and Directions Workshop

2011

ACM Conference on Information and Knowledge Management
Analysing multiple versions of an ontology: A study of the NCI Thesaurus
Int. Workshop on Description Logics
Facilitating the analysis of ontology differences
Workshop on Knowledge Evolution and Ontology Dynamics
IEEE Symposium on Computer-Based Medical Systems

See also: DBLP, Google Scholar, Semantic Scholar.


Reviewing Activities

Conference Program Committees

I frequently review papers for multiple conferences and workshops:

  • WWWThe Web Conference
  • ISWCInternational Semantic Web Conference
  • AAAISymposia/Conference on Artificial Intelligence
  • ESWCEuropean Semantic Web Conference
  • AMIAAmerican Medical Informatics Association Annual Symposium
  • CBMSIEEE International Symposium on Computer-Based Medical Systems
  • CIKMACM International Conference on Information and Knowledge Management
  • ICSCIEEE International Conference on Semantic Computing
  • SIMBigInternational Conference on Information Management and Big Data
  • KESWConference on Knowledge Engineering and Semantic Web
  • OWLEDOWL: Experiences and Directions Workshop
  • OREOWL Reasoner Evaluation Workshop
Journal Reviews

I am a member of the editorial board for the Semantic Web Journal. I also review for the following journals:


Organization Activities

  • Program Chair11th International Conference on Knowledge Capture (K-CAP), 2021
  • Research Track Chair - Science Data and Scholarly Communication18th European Semantic Web Conference (ESWC), 2021
  • Sponsorship & Publicity Chair20th International Semantic Web Conference (ISWC), 2021
  • Publicity Chair22nd International Conference on Knowledge Engineering and Knowledge Management (EKAW), 2020
  • Posters & Demos Track Chair19th International Semantic Web Conference (ISWC), 2020
  • Session Organizer"Fostering an awesome tool ecosystem for the semantic web" at U.S. Semantic Technologies Symposium (US2TS), 2020
  • Local Chair17th International Semantic Web Conference (ISWC), 2018
  • Program Chair12th OWL: Experiences and Directions Workshop (OWLED), 2015
  • Program Chair4th OWL Reasoner Evaluation Workshop (ORE), 2015
  • Program Chair2nd OWL Reasoner Evaluation Workshop (ORE), 2013

Awards

  • Best In-Use Paper Award International Semantic Web Conference, 2019
  • Best Reviewer Award (honorable mention, In-Use track) International Semantic Web Conference, 2019
  • Outstanding Reviewer Award The Web Conference, 2017
  • Best Resource Paper Award International Semantic Web Conference, 2016
  • PhD Scholarship Fundação para a Ciência e a Tecnologia, 2012
  • Best Student Paper Award (runner-up) The University of Manchester, 2012
  • Doctoral Training Award Engineering and Physical Sciences Research Council, 2009
  • PhD Scholarship Fundação para a Ciência e a Tecnologia, 2009
  • Kilburn Scholarship The University of Manchester, 2008
  • Best Achievement in the Field of Computational Biology University of Liverpool, 2008