The Opinionated Ontologist

This week we are talking with Dr. Mélanie Courtot - the Director of Genome Informatics, a Principal Investigator at the Ontario Institute for Cancer Research in Toronto, and Assistant Professor in the Department of Medical Biophysics and Computer Science at University of Toronto.

Mélanie's work spans multiple biomedical domains, including genomics, cancer, infectious disease, and public health, across many continents and technology stacks.

"What I do best, and enjoy most, is building at these intersections: between ontology and machine learning, across national infrastructure and international consortia, from governance frameworks to their corresponding technical specifications."

Mélanie led the development of the Data Use Ontology (DUO) which is now used in over 200,000 datasets worldwide. We talk about what it takes to successfully implement ontologies at scale and dig in to some of her more recent investigations into the use of LLMs for processing unstructured clinical documents - Benchmarking LLM-based Information Extraction Tools for Medical Documents.

Shortly before recording our conversation, Mélanie's work on the Lancet Commission was published, which looks at ways of creating a more equitable data ecosystems for sharing precision oncology data. (Cancer genomic data systems in precision oncology: from integration to clinical implementation)

"My goal is to use technology and infrastructure to address population health needs at scale, and equitably, so data standards and policies are implemented in the platforms researchers use every day."

We hope you enjoy this conversation as much as we did!

Get in touch and ask us your ontology questions over on Patreon - https://www.patreon.com/OpinionatedOntologist In the meantime, we'll see you in the concept map!

The Ship of Theseus isn’t just a puzzle. It’s a mirror. It reflects back at us all the quiet assumptions we carry about identity, permanence, and change. And in ontology, those assumptions become encoded—solidified into the logic of systems that influence research, healthcare, policy, and more.

Today we’re standing at the river's edge - talking about identity, transformation, and what makes a thing that very thing — from ships to cells to the heart inside your chest. Let’s dive into the philosophical and practical questions of realism, identity over time, and the frameworks we use to describe the world.

Keep in touch over on our patreon channel, where you can bring us your ontological opinions for discussion.

It's been another activating week in the AI doomer news cycle and our friends have been asking us - what's our take? So here it is - our first (O,O) nanopublication, where Jamie and Braeden take a beat to respond to the AI-pocalypse hype and ease us all into a grounded conversation about governance, best practice, open vs. closed models, and the business models that are stoking the frenzy.

01:00 Unpacking the gap between AI doom and reality
04:15 The "bad dog" vs. "the leash" approach to AI safety
10:35 Looking at the structure of the AI market
14:08 OpenAI's "marketing costs"
19:00 Using smaller, open models
23:54 How Jamie uses AI
28:12 What governance looks like
31:54 What does accountability look like
33:36 Making time to ask hard questions
36:00 What will happen to closed-model markets

Connect with us on LinkedIn and let us know what you think. You can bring us your AI and ontology engineering questions for us answer on-air, over on our Patreon. In the meantime, we'll see you in the concept map!

Welcome back to the concept map! It's the start of Season 2 of The Opinionated Ontologist and we're featuring a conversation Jamie had last year with Michel Dumontier.

Michel is the Distinguished Professor of Data Science at Maastricht University and is the inventor & founder of the Semanticscience Integrated Ontology (or SIO as we like to call it). We spend the hour digging into the history and thinking that went into the design of SIO.

Bring us your burning ontology questions for us to answer on-air this season and get early access to our episodes over on patreon.

Announcing Season 2 of The Opinionated Ontologist! This year we kick off with a new addition in the studio: producer Braeden Doane joins Jamie to help bring listener questions to the airwaves, as we dig into upper ontologies, ontology engineering, and real world applications with another round of all-star guests. In this mini episode, we'll hear a bit about Braeden's pathway into ontology and take a peek at what we're looking forward to this next season. For listener questions and early access to feature episodes, connect with us over at patreon.com/opinionatedontologist.

We discuss reification using the W3C draf recommendation RDF 1.2, modeling choices, and how the approach is similar to, and different from, edge properties in Labeled Property Graphs.

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This week I was at the Knowledge Graph Conference, the biggest industry Graph AI conference out there! I spoke with Bob Metcalfe of network effect fame, Peter Crocker of Oxford Semantics, and a huge KGC crew of ontologists, technologists, and knowledge graph experts.

Featuring:

1. Bob Metcalfe

2. Peter Crocker

3. Mara Inglezakis Owens

4. Margaret Warren

5. Pete Rivett

6. Hande McGinty

7. Tom Plasterer

8. Ora Lassila

9. Keith Corbett

10. Elisa Kendall

11. Larry Swanson

12. Deborah McGuinness

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We continue our mini series on upper level ontologies with an episode on the Basic Formal Ontology, or BFO. John Beverley of University at Buffalo joins us. John is the current steward of BFO, and works with its founder Barry Smith on its use in domain applications.

For more information about BFO, visit their github page at https://github.com/BFO-ontology/BFO-2020.

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This week we discuss the upper level ontology gist with its creator, Dave McComb.

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Chime Ogbuji joins me to talk about the role of medical informatics in knowledge graphs and semantics, all the way from MYCIN and GALEN to today.

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