Events and Opportunities

More is Better: How Integrating Multiple Biomedical Ontologies can Unlock Artificial Intelligence Applications

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Presenter: Dr. Catia Pesquita

Date: March 1, 2022 at 11:00AM EDT (click button below to register)

Moderators: Núria Queralt Rosinach, Tiffany Callahan, and Pablo Quinteiro

Abstract

Biomedical AI applications are increasingly multi-domain, with areas such as personalized medicine and systems biology showcasing the increasing need to explore heterogeneous data. Biomedical Ontologies represent an unparalleled opportunity in this area because they add meaning to the underlying data which can be used to support heterogeneous data integration, provide scientific context to the data augmenting AI performance, and afford explanatory mechanisms allowing the contextualization of AI predictions. In this talk I will present our recent work on aligning and integrating multiple ontologies and building knowledge graphs to support both supervised learning and explainable AI approaches for biomedicine. I will highlight lessons learned and chart a path for the coming challenges in biomedical ontology and knowledge graph alignment as AI becomes an integral part of biomedical research.

Biography

Catia Pesquita is an Assistant Professor in Computer Science at Faculdade de Ciências da Universidade de Lisboa and a Senior Researcher at LASIGE where she leads the Health and Bioinformatics Research Line of Excellence. She has a multidisciplinary background in Biology and Computer Science, and she develops her research at the intersection between the areas of Semantic Web and Data Mining, with a focus on biomedical and healthcare applications. She has made internationally recognized contributions, namely in the areas of ontology-based semantic similarity and ontology alignment, winning multiple awards and competitions. She is also active in promoting computer science career paths for young women.

"Fun" facts: After spending a year as lab intern and pipetting more than 100,000 times, Catia announced to her supervisor she was planning a career change and switch to Bioinformatics. On being told "Bioinformatics" was a hype and not a wise move, she still went ahead, because she had learned there were no pipettes in computer labs. Of course, she fell right into a new trap: Bio-Ontologies.

Resolving and Avoiding Design Conflicts in Ontology Development and Deployment

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Presenter: Dr. C. Maria Keet

Date: September 21, 2021 at 11:00AM EDT (click button below to register)

Moderators: Núria Queralt Rosinach, César Bernabé

Abstract

Ontology development avails of science, engineering, and philosophy to represent the subject domain knowledge formally so that it can be used to enhance information systems. This process involves resolving ontological differences and making choices between conflicting axioms, which are due to various reasons. Examples include different foundational ontologies, alternate design patterns for the prospective ontology’s use case, and an ontology language’s expressivity limitations.

Instead of ad hoc decision-making, science and engineering-based modeling guidance with methods and tools can alleviate these issues to assist with the meaning negotiation and conflict resolution in a systematic way. In this talk, I will discuss common conflicts and typical steps toward resolution, including the tool availability for it. A similar situation with trade-offs exist when deploying ontologies for ontology-based data access and integration, which we shall touch upon as well. Use cases, tools, and experiments were in several subject domains, such as avian influenza, horizontal gene transfer, and metabolic pathways.

Biography

C. Maria Keet (PhD, MSc, MA, BSc(hons)) is an Associate Professor with the Department of Computer Science, University of Cape Town. She focuses on ontology engineering, conceptual data modelling, and their interaction with natural language, which has resulted in over 100 peer-reviewed publications at venues including KR, FOIS, K-CAP, EKAW, ESWC, ER, CIKM, Applied Ontology, and the Semantic Web Journal. She is PI on two NRF-funded projects on NLG for Nguni languages, and was PI on an DST/MINCyT-funded bi-lateral project with Argentina on ontology-driven conceptual modelling. She was involved in several EU projects, coordinated the development of several tools, and has written the first textbook on ontology engineering for computer scientists. She has served on many Program Committees of international workshops and conferences and reviewed for numerous journals; recently she has been a (PC or local) chair for EKAW2020, FOIS2018, and the IJCAI 2021 Demo track.

Before her employment at UCT, Maria was Senior lecturer at the University of KwaZulu-Natal, South Africa, and a non-tenured Assistant Professor at the KRDB Research Centre, Free University of Bozen-Bolzano, Italy where she also obtained a PhD in Computer Science in 2008. She also holds a BSc(honours) 1st class in IT & Computing from the Open University UK (2004), an MSc in Food Science (Microbiology) from Wageningen University, the Netherlands (1998), and an MA 1st class in Peace & Development Studies from the University of Limerick, Ireland (2003).