Thursday, October 7, 2010

Gene Wiki talk saved at NCBO

A webex recording of our webinar "The Gene Wiki: Cultivating and mining community intelligence in biology" is now available on the NCBO website. It was a little weird talking to myself - in particular it was totally impossible to know if any attempt at humor was successful.. Overall I think it went pretty well though since we had a good number of relevant questions from the audience. I imagine it would probably be a good idea from a learning and improving perspective but I have yet to bring myself to actually listen to myself speak.. Thankfully the webcam was not in effect so I'll never have to watch myself. (Andrew had the first half and I had the second.)


Andrew McKnight said...

Hey Ben, I just you and Andrew Su's presentation and it was really interesting. I think the 3d spiral feedback image was simple but powerful. It sounds like a great way to prioritize candidate annotations for human curators.

I was wondering how you implemented most of the steps you took. Is it an automatically repeatable process? I mean, could you run the whole setup again tomorrow if you wanted to? Could some sort of generalized and pluggable process be set up so that if I wanted to set up something similar for, say, astronomical data I could get it going in just a couple of weeks?

Benjamin Good said...

Hi Andrew (not my boss Andrew),

I agree, Andrew (my boss)'s spiral picture is clear and compelling. I am very glad to hear you found the talk interesting!

Funny you should ask about the code.. I was just starting to refactor things a bit today to make it easier to repeat the process. As far as Wikipedia API/parsing goes you could apply this strategy to any content you like immediately. The domain specific challenges will be in identifying ontologies to map to and in devising strategies for classifying/ranking your predictions. The simpler ontology-related elements could certainly be generalized in the code (ie plugin OWL ontology x here..). If you are interested in this, let me know and I will show you how to get to and run the code as it stands. Its open source, maybe you can even help me out with it if you get inspired!

Andrew McKnight said...

I'm at least interested in taking a look. I have a few other projects I'm also trying to work on but if I'm in the right mood at the right time I might use it to do something similar.

Benjamin Good said...

Your enthusiasm is overwhelming...
The code is here,
but it depends on projects that aren't there so you will have some challenges building it. It also has no ant build file or really any specific entry point - so buyer beware. If you do get interested, let me know and I'll get you set up.
Perhaps more useful from a generic perspective is this java project for working with Wikipedia
I use some pieces of it.