Rafael Gonçalves

Research Scientist · Center for Biomedical Informatics Research · Stanford University · rafael.goncalves@stanford.edu

I'm a Research Scientist in the Protégé project. I research methods to build, maintain, and reason over knowledge bases represented in the Web Ontology Language (OWL). I coordinate and teach the Protégé Short Course, which covers the OWL language, and building, reasoning, and querying OWL ontologies with Protégé. I also investigate methods to standardize metadata that describe scientific data with ontologies, in an effort to make data findable and reusable. My research interests revolve around artificial intelligence, knowledge representation and reasoning, and ontology engineering.


Experience

Research Software Engineer

Stanford University

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.

2014 - 2018

Research Associate

The University of Manchester

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.

2013 - 2014

Teaching Assistant

The University of Manchester

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)
2013 - 2014

Education

PhD in Computer Science

The University of Manchester

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.

2009 - 2014

MSc in Software Engineering

The University of Manchester

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.

2008 - 2009

BSc in Computer Science

University of Liverpool

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.

2005 - 2008

Publications

2019

The variable quality of metadata about biological samples used in biomedical experiments
Scientific Data
Use of OWL and Semantic Web Technologies at Pinterest
Int. Semantic Web Conference
Aligning Biomedical Metadata with Ontologies Using Clustering and Embeddings
European Semantic Web Conference
New Features for Biomedical Ontology Editing in Protégé [Demo]
Int. Conference on Biomedical Ontology
WebProtégé: A Cloud-Based Ontology Editor
Workshop on Knowledge Graph Technology and Applications

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

The OWL Reasoner Evaluation (ORE) 2015 Competition Report
Journal of Automated Reasoning
An ontology-driven tool for structured data acquisition using Web forms
Journal of Biomedical Semantics
The CEDAR Workbench: An Ontology-Assisted Environment for Authoring Metadata
Int. Semantic Web Conference
Metadata in the BioSample Online Repository are Impaired by Numerous Anomalies
Workshop on Enabling Open Semantic Science

2016

The OWL Reasoner Evaluation (ORE) 2015 Resources
Int. Semantic Web Conference

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

Impact analysis in description logic ontologies
PhD Thesis

2013

Finding fault: Detecting issues in a versioned ontology
European Semantic Web Conference
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

Performance heterogeneity and approximate reasoning in description logic ontologies
Int. Semantic Web Conference
Concept-based semantic difference in expressive description logics
Int. Semantic Web Conference
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

Categorising logical differences between OWL ontologies
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
Analysing the evolution of the NCI Thesaurus
IEEE Symposium on Computer-Based Medical Systems

DBLP and Google Scholar are likely more up to date.


Reviewing Activities

Conference Program Committees

I frequently review papers for multiple conferences and workshops:

  • WWWThe Web Conference
  • ISWCInternational Semantic Web Conference (Research, Resource, In-Use, Industry, and Poster & Demo tracks)
  • ESWCEuropean Semantic Web Conference (Resource, and Poster & Demo tracks)
  • AMIAAmerican Medical Informatics Association Annual Symposium
  • CBMSIEEE International Symposium on Computer-Based Medical Systems
  • ICSCIEEE International Conference on Semantic Computing
  • 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

  • Publicity Chair22nd International Conference on Knowledge Engineering and Knowledge Management, 2020
  • Poster & Demo Track Chair19th International Semantic Web Conference, 2020
  • Local Chair17th International Semantic Web Conference, 2018
  • Program Chair12th OWL: Experiences and Directions Workshop, 2015
  • Program Chair4th OWL Reasoner Evaluation Workshop, 2015
  • Program Chair2nd OWL Reasoner Evaluation Workshop, 2013

Awards

  • Best In-Use Track Paper Award International Semantic Web Conference, 2019
  • In-Use Track Best Reviewer Award (honorable mention) International Semantic Web Conference, 2019
  • Outstanding Reviewer Award The Web Conference, 2017
  • Best Resource Track 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 (declined) 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

Interests

I grew up in a coastal town in south Portugal, where I spent most of my free time sailing. I became an avid Laser-class sailor and competed around the country and in Spain. More recenty I've taken up surfing, skiing, and scuba diving.

Scuba diving has become my main hobby (I'm a PADI instructor). I've logged over 200 dives, including in the Red Sea in Egypt, the Great Barrier Reef in Australia, the Caribbean Sea, the cenotes in Mexico, the Blue Hole in Belize, and Hawaii. I swam with whale sharks in Honduras, for brief seconds!