Rafael Goncalves, PhD

Rafael Goncalves, PhD

Associate Director of Knowledge Representation

Center for Computational Biomedicine

Harvard Medical School

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Rafael Gonçalves is the Associate Director of Knowledge Representation at the Center for Computational Biomedicine, Harvard Medical School. He has a PhD in Computer Science from The University of Manchester, where he investigated methods and tools to compute the logical and (reasoning) performance impact of changes in description logic ontologies. He is interested in applying knowledge representation and reasoning, natural language processing and semantic web techniques to biomedical informatics research. In his current role at CCB, he investigates methods and tools to facilitate the discovery, analysis, and integration of heterogeneous, evolving biomedical datasets originating from multiple sources.

Prior to his role at Harvard, Dr. Gonçalves was a Research Scientist at the Stanford Center for Biomedical Informatics Research, where he contributed to projects related to ontology development and knowledge graph construction. He was involved in the development of Protégé, WebProtégé and CEDAR—tools for building ontologies and for creating and semantically annotating metadata. He has also taught courses on ontology engineering, knowledge representation and reasoning, and software development.

  • Visualising the effects of ontology changes and studying their understanding with ChImp

    Authors: Romana Pernisch, Daniele Dell’Aglio, Mirko Serbak, Rafael S. Gonçalves, Abraham Bernstein

    Journal of Web Semantics, Volume 74, October 2022, 100715

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  • Obstacles to the reuse of study metadata in ClinicalTrials.gov

    Authors: Laura Miron, Rafael S. Gonçalves, Mark A. Musen

    Scientific Data, 2020

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  • The variable quality of metadata about biological samples used in biomedical experiments.

    Authors: Rafael S. Gonçalves, Mark A. Musen

    Scientific Data, 2019

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  • Use of OWL and Semantic Web Technologies at Pinterest

    Authors: Rafael S. Gonçalves, Matthew Horridge, Rui Li, Yu Liu, Mark A. Musen, Csongor I. Nyulas, Evelyn Obamos, Dhananjay Shrouty, David Temple

    The Semantic Web – ISWC 2019. Lecture Notes in Computer Science, vol. 11779, 2019

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  • WebProtégé: A Cloud-Based Ontology Editor

    Authors: Matthew Horridge, Rafael S. Gonçalves, Csongor I. Nyulas, Tania Tudorache, Mark A. Musen

    Companion Proceedings of The 2019 World Wide Web Conference, 2019

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  • Aligning Biomedical Metadata with Ontologies Using Clustering and Embeddings

    Authors: Rafael S. Gonçalves, Maulik R. Kamdar, Mark A. Musen

    The Semantic Web – ESWC 2019. Lecture Notes in Computer Science, vol. 11503, 2019

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  • Protégé 5.5-Improvements for Editing Biomedical Ontologies.

    Authors: Matthew Horridge, Rafael S. Gonçalves, Csongor I. Nyulas, Tania Tudorache, Mark A. Musen

    Proc. of the 9th International Conference on Biological Ontology (ICBO), 2018.

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  • The CEDAR Workbench: An Ontology-Assisted Environment for Authoring Metadata that Describe Scientific Experiments.

    Authors: Rafael S. Gonçalves, Martin J. O’Connor, Marcos Martínez-Romero, Attila L. Egyedi, Debra Willrett, John Graybeal, Mark A. Musen

    The Semantic Web – ISWC 2017. Lecture Notes in Computer Science, vol. 10588, 2017

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  • The OWL Reasoner Evaluation (ORE) 2015 Competition Report

    Authors: Bijan Parsia, Nicolas Matentzoglu, Rafael S. Gonçalves, Birte Glimm, Andreas Steigmiller

    Journal of Automated Reasoning, 2017

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  • An ontology-driven tool for structured data acquisition using Web forms

    Authors: Rafael S. Gonçalves, Samson W. Tu, Csongor I. Nyulas, Michael J. Tierney, Mark A. Musen

    Journal of Biomedical Semantics, 2017

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  • The OWL Reasoner Evaluation (ORE) 2015 Resources

    Authors: Bijan Parsia, Nicolas Matentzoglu, Rafael S. Gonçalves, Birte Glimm, Andreas Steigmiller

    The Semantic Web – ISWC 2016. Lecture Notes in Computer Science, vol. 9982, 2016

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  • Finding Fault: Detecting Issues in a Versioned Ontology.

    Authors: Maria Copeland, Rafael S. Gonçalves, Bijan Parsia, Uli Sattler & Robert Stevens

    The Semantic Web – ESWC 2013. Lecture Notes in Computer Science, vol. 7955, 2013

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  • The Empirical Robustness of Description Logic Classification.

    Authors: Rafael S Gonçalves, Nicolas Matentzoglu, Bijan Parsia, Uli Sattler

    Proc. of the 26th International Workshop on Description Logics (DL), 2013

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  • Performance heterogeneity and approximate reasoning in description logic ontologies

    Authors: Rafael S. Gonçalves, Bijan Parsia, Ulrike Sattler

    The Semantic Web – ISWC 2012. Lecture Notes in Computer Science, vol. 7649, 2012

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  • Concept-Based Semantic Difference in Expressive Description Logics

    Authors: Rafael S. Gonçalves, Bijan Parsia, Ulrike Sattler

    The Semantic Web – ISWC 2012. Lecture Notes in Computer Science, vol. 7649, 2012

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  • Analysing the evolution of the NCI thesaurus.

    Authors: Rafael S. Gonçalves, Bijan Parsia, Uli Sattler

    Proc. of the 24th IEEE International Symposium on Computer-Based Medical Systems (CBMS), 2011

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