Recent trends in biological data integration

cse590q: Database Seminar (Winter 2008)
Wednesdays 4:30-5:20 in CSE 605 (database lab)

This winter quarter, the database seminar will focus on data management issues in life sciences. Primary organizer is Wolfgang Gatterbauer (gatter@cs).

Background

Biological research is becoming increasingly data intensive. The outcome of individual experiments are generally large and diverse data sets. In order to build upon existing work and infer new insights, researchers want to integrate these heterogeneous data sets in some efficient way. This task, however, creates some serious data management issues such as how to ideally represent biological data and how to link different existing representations together in a way that scales.

Procedure

Each class, a pair of two students presents either one longer or two shorter and related papers. Everyone reads the papers. One day before class, the presenters prepare and send out a one-slide graphical summary of their paper (Examples). Before last class, each pair prepares a one-slide graphical big picture summary of their view on the discussed papers at the end of the term (Examples). Hand drawings instead of computer drawings are fine and even encouraged.

Preliminary agenda

Date Paper(s) Presenters Jan 9 Introduction to topic and organization of seminar Wolfgang Jan 16 BioNavigation, BioGuide: University of Pennsylvania, Université Paris-Sud 11 Path-based systems to guide life scientists in the maze of biological data sources, Sarah Cohen Boulakia, Susan Davidson, Christine Froidevaux, Zoe Lacroix, Maria-Esther Vidal, Journal of Bioinformatics and Computational Biology 4(5):1069-1095, 2006. [GS] BioGuideSRS: Querying Multiple Sources with a user-centric perspective, Sarah Cohen-Boulakia, Olivier Biton, Susan Davidson, Christine Froidevaux, Bioinformatics 23(10):1301-1303, 2007. [offcampus] [GS] Casey, Michal Jan 23 Michigan Molecular Interactions: University of Michigan, Ann Arbor Michigan Molecular Interactions (MiMI): putting the jigsaw puzzle together, Magesh Jayapandian, Adriane Chapman, V. Glenn Tarcea, Cong Yu, Aaron Elkiss, Angela Ianni, Bin Liu, Arnab Nandi, Carlos Santos, Philip Andrews, Brian Athey, David States and H. V. Jagadish, Nucleic Acids Research 35(Database-Issue): 566-571, 2007. [GS] (OPTIONAL Provenance Management in Curated Databases, Peter Buneman, Adriane Chapman, James Cheney, SIGMOD 2006. [offcampus] [GS]) Julie Jan 30 Aladin: Humboldt University Berlin (Almost) Hands-Off Information Integration for the Life Sciences, Ulf Leser, Felix Naumann, CIDR 2005. [GS] Efficiently Computing Inclusion Dependencies for Schema Discovery, Jana Bauckmann, Ulf Leser, Felix Naumann, InterDB at ICDE 2006. [offcampus] [GS] Vibhor, YongChul Feb 6 BIOZON: Cornell BIOZON: a system for unification, management and analysis of heterogeneous biological data, Aaron Birkland, Golan Yona, BMC Bioinformatics, 7:70, 2006. [GS] Lynn Feb 13 Gaggle: Institue for Systems Biology The Gaggle: An open-source software system for integrating bioinformatics software and data sources, Paul T Shannon, David J Reiss, Richard Bonneau, Nitin S Baliga, BMC Bioinformatics, 7:176, 2006. [GS] The Firegoose: two-way integration of diverse data from different bioinformatics web resources with desktop applications, J Christopher Bare, Paul T Shannon, Amy K Schmid, Nitin S Baliga, BMC Bioinformatics, 8:456, 2007. [GS] Marianne, Bob Feb 20 Bioverse: University of Washington Bioverse: functional, structural and contextual annotation of proteins and proteomes, Jason McDermott, Ram Samudrala, Nucleic Acids Research, 31(13):3736-3737, 2003 [GS] Computational representation of biological systems (UW internal access only), Zach Frazier, Jason McDermott, Michal Guerquin, Ram Samudrala4, Computational Systems Biology: Methods in Molecular biology (ed Jason McDermott, Ram Samudrala, Roger Bumgarner, Kristina Montgomery, Renee Ireton), (in press), 2008. Michal Feb 27 Biomediator (U2): University of Washington The BioMediator system as a tool for integrating biologic databases on the Web, Ron Shaker, Peter Mork, J. Scott Brockenbrough, Loren Donelson, Peter Tarczy-Hornoch, IIWeb 2004 (at VLDB 2004). [GS] Incorporating uncertainty metrics into a general-purpose data integration system, Brenton Louie, Landon Detwiler, Nilesh N. Dalvi, Ron Shaker, Peter Tarczy-Hornoch, Dan Suciu, SSDBM 2007. [offcampus] [GS] Wolfgang Mar 5 One-page summary slides and discussion All Mar 12 no class -

Overview on biological data integration

• Data integration and genomic medicine,
  Brent Louie, Peter Mork, Fernando Martin-Sanchez, Alon Halevy, Peter Tarczy-Hornoch,
  Journal of Biomedical Informatics, 40:5-16, 2007. [offcampus] [GS]
• Addressing the problems with life-science databases for traditional uses and systems biology,
  Stephan Philippi, Jacob Köhler,
  Nature Reviews Genetics, 7(6):482-8, 2006. [offcampus] [GS]
• Integration of biological sources: current systems and challenges ahead,
  Thomas Hernandez, Subbarao Kambhampati,
  SIGMOD Record, 33:51-60, 2004. [offcampus] [GS]

More

Intro to biology

• Bioinformatics - An Introduction for Computer Scientists,
  Jacques Cohen,
  ACM Computing Surveys, 36(2):122-158, 2004. [offcampus] [GS]
• Life and Its Molecules: A Brief Introduction,
  Lawrence Hunter,
  AI Magazine, 25(1):9-22, 2004. [GS]

Why graphics

Infographics
Graphicacy

Contact

Standard contact form
Anonymous contact form
Class email list

Version: March 2008, Contact