ISMB 2022 Meeting

Encoding Biases’ Influences on Development and Use of Ontologies in the Life Sciences

Maria Keet, University of Cape Town

Abstract:

Ontology authoring, sometimes referred to as the ‘implementation’ stage of representing the knowledge, may seem like a just-do-it task, but even when experts agree on what to represent, there are a myriad of ways how to represent it. Consistently adhered to, they lead to transformable modelling styles. Different representation choices may clash with other ontologies to reuse, however, and with some of the purposes that an ontology may have been built for. Cognizance of such differences may facilitate smoother deployment of ontologies in applications with different requirements. They also pose challenges on methods and tools, such as for competency questions and verification with them, test-driven development, and various bottom-up ontology development approaches, such as knowledge extraction from biological diagrams. In this talk we take a tour through new insights into such factors that slow down or speed up development of bio-ontologies and their use in tools for the life sciences.

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, and bio-ontologies intermittently, which has resulted in some 150 peer-reviewed publications. She is PI on an NRF-funded  project on NLG for Nguni languages, and was PI on an DST/MINCyT-funded project on ontology-driven conceptual modelling, and was involved in several EU projects. She coordinated the development of several tools and has written the first textbook on ontology engineering for computer scientists. She has served on many conference and workshop program committees and reviewed for numerous journals; recently she was PC (co-)chair of the IJCAI 2021 Demo track and EKAW 2020, and is for the ISWC 2022 resources track. Before her employment at UCT, Maria has worked at the University of KwaZulu-Natal, South Africa, and 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).

The Open Data Highway: Turbo-Boosting Translational Traffic with Ontologies

Melissa Haendel, University of Colorado Anschutz Medical Campus

Keynote shared with BOSC

Biography: 

Melissa Haendel is the Chief Research Informatics Officer and Marsico Chair in Data Science at University of Colorado Anschutz Medical Campus, and the Director of the Center for Data to Health (CD2H). Her background is molecular genetics and developmental biology as well as translational informatics, with a focus over the past decade on open science and semantic engineering. Dr. Haendel’s vision is to weave together healthcare systems, basic science research, and patient-generated data through development of data-integration technologies and innovative data capture strategies. Dr. Haendel’s research has focused on integration of genotype-phenotype data to improve rare-disease diagnosis and mechanism discovery. She also leads and participates in international standards organizations to support improved data sharing and utility worldwide.