Geek Speak: Melanie Courtot, organizer of the Vancouver Semantic Web Meetup Group

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Mélanie Courtot is helping build the Semantic Web through her work on ontologies. On April 8, Courtot cofounded the Vancouver Semantic Web Meetup Group with Mark Wilkinson, an assistant professor of medical genetics at the University of British Columbia. Eleven people attended the group’s first meeting on April 23.

Born in Strasbourg, France, the 32-year-old Courtot is a bioinformatics specialist at the Terry Fox Laboratory in the B.C. Cancer Research Centre in Vancouver. Her main project is the Ontology for Biomedical Investigations. She’s also helping develop the Information Artifact Ontology. According to the World Wide Web Consortium’s Web site, “Ontologies define the concepts and relationships used to describe and represent an area of knowledge.”

Courtot studied biochemistry and computer science at the University of Strasbourg, before working at the European Bioinformatics Institute in Cambridge, England. At the institute, she developed her first ontology—the Systems Biology Ontology. Now, she hopes to pursue a PhD in the bioinformatics graduate program at UBC.

The Georgia Straight interviewed Courtot in a coffee shop at West Broadway and Granville Street.


Mélanie Courtot, organizer of the Vancouver Semantic Web Meetup Group, talks about how the Semantic Web will help people in general. Stephen Hui video.

Why did you and Mark Wilkinson found the Vancouver Semantic Web Meetup Group?

We are both academics. We thought there must be a lot of people around here—either academics or not—who are interested in the Semantic Web. It would make sense to come together and exchange ideas, and see what we can bring, what they can bring, and how we can link it all together.

What’s the best way to describe the Semantic Web to a newbie?

For me, it’s just a way of linking data on the Web and integrating data. People put data on the Web. They get integrated...linked together on the Web, and then computers can actually parse that and use that to hopefully build something bigger.

What is bioinformatics?

For me, bioinformatics is everything that you can do with computers—so every kind of software you can develop, every kind of database, user interface—that could have an application in biology.

What is the Ontology for Biomedical Investigations?

The Ontology for Biomedical Investigations is a large collaborative project. We have more than 40 people working on that across the world, mostly in the U.K., in the U.S., and a few other places. What we are trying to do is represent knowledge associated with biomedical investigation, which is every kind of experiment that as a biologist you would do in your lab, every type of analysis that as a bioinformatician you would do on data produced by biologists. We are trying to formalize that. So, it’s pretty large, and it’s still in development. So, we don’t have a first official release yet. But we’re getting there.

How do you think the Semantic Web or linked data might change our lives?

I think you’ll have access to more structured information that will connect you with what you really, really want.

Why should people who are interested in the Semantic Web come out to the Meetup group?

Because they’re interested in the Semantic Web. What I would like to find is I really want to make connections between different kinds of people. The side of things I know more about is really the academic side. But what I would like to see is more industrial application—people who are really using it today to make commercial products....

I’ve worked on this project, which is developing a repository for flow-cytometry data. What I would like to do is take this database and put it as linked data on the Web, and have it integrate with other things. But, as of today, I don’t know what is the best way. So, I want to find people who have been actually developing tools or have been doing the work, and who can help me and tell me “That’s the right way of doing it” and “That’s not the right way of doing it.” I want to get a different perspective. When you’re an academic, you’re reading lots of papers. You’re reading more on the research side of things. I really want to see the real applicative side.

How might linked data help scientists?

I think linked data will help scientists in the sense that it will allow them to integrate their information with other resources....So, you’ll be able to get a bigger view of what you are actually doing.

Every Friday, Geek Speak catches up with someone in Vancouver’s technology sector, video-game industry, or social-media scene. Who should we interview next? Tell Stephen Hui on Twitter at twitter.com/stephenhui.

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Ben Stein
For those newbies who want to try Semantic Web - check out this great tool - http://www.urlclassifier.com - for extracting the main topics from URLs.
Using a ContextIn Semantic Advertising algorithm
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