Research Remix

May 1, 2007

Open Data at ISMB 2007?

Filed under: conferences, ISMB — Heather Piwowar @ 11:07 am

I was expecting the accepted papers for ISMB 2007 to include a few related to Open Science or Open Data. I suppose ISMB is more about the biology than the science or engineering behind the research. Nonetheless, it could have been a worthwhile mix… many benefits when the users and the builders get together.

My current interest in Open Data is the sharing and reuse of raw clinical trial (specifically cancer, microarray) data. I attended ISMB 2005 and found it fascinating, which led to my plans to attend ISMB 2007. Well, and Vienna is beautiful and has great cycling. So it looks like my focus for the conference will be to hear about state-of-the-art microarray research, and even more, studies which use heterogeneous datasets.

Molecular biology has been a leader in open-access data with its sequence and protein databases, so I’m sure there will be a lot to learn.

A few papers which looked particularly interesting to me, as excerpted from ISMB’s list of accepted papers:

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Accepted Paper Number: 146
Title: Annotating Gene Function by Combining Expression Data with a Modular Gene Network
Author(s): Motoki Shiga, Ichigaku Takigawa and Hiroshi Mamitsuka

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Accepted Paper Number: 184
Title: Biases induced by pooling samples in microarray experiments
Author(s): Tristan Mary-Huard, JeanJacques Daudin, Michela Baccini, Annibale Biggeri and Avner Bar-Hen

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Accepted Paper Number: 220
Title: Kernel-based data fusion for gene prioritization
Author(s): Tijl De Bie, Leon-Charles Tranchevent, Liesbeth van Oeffelen and Yves Moreau

Accepted Paper Number: 264
Title: Information Theory Applied to the Sparse Gene Ontology Annota-tion Network to Predict Novel Gene Function
Author(s): Ying Tao, Lee Sam, Jianrong Li, Carol Friedman and Yves A. Lussier

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Accepted Paper Number: 271
Title: Identification of New Drug Classification Terms in Textual Resources – a Case Study
Author(s): Corinna Kolarik, Martin Hofmann, Marc Zimmermann and Juliane Fluck

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Accepted Paper Number: 282
Title: Comparative analysis of microarray normalization procedures: effects on reverse engineering gene networks
Author(s): Wei Keat Lim, Kai Wang, Celine Lefebvre and Andrea Califano

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Accepted Paper Number: 342
Title: Using genome context data to identify specific types of functional associations in pathway/genome databases
Author(s): Michelle Green and Peter Karp

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Accepted Paper Number: 363
Title: Bayesian association of haplotypes and non-genetic factors to regulatory and phenotypic variation in human populations
Author(s): Jim Huang, Anitha Kannan and John Winn

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Accepted Paper Number: 436
Title: Manual curation is not sufficient for annotation of genomic databases
Author(s): William Baumgartner, Lynne Fox, George Acquaah-Mensah, K. Bretonnel Cohen and Lawrence Hunter

If anyone else is planning to attend ISMB 2007, please let me know — it would be fun to meet up. A data sharing/reuse birds-of-a-feather session, perhaps?

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