SHARQ

Executive Summary

Over the past decade, biological research has been transformed from a science of the "small" to a science of the "large". Fueled by novel technologies capable of producing massive amounts of data for a single experiment, scientists are faced with an explosion of information which must be rapidly analyzed and combined with other data to form hypotheses and create knowledge. Thus a number of new research challenges have arisen in data modeling and data integration that must be solved to further biological as well as other scientific research.
A major challenge lies in effective sharing of information among collaborating, yet autonomous, parties. They are characterized by having a diversity of perspectives (and hence heterogeneous schemas), dynamic data, and the possibility of intermittent connectivity or participation. The parties are peers in the sense that they are fully autonomous, they contribute and use resources as they choose, and they may join or leave at any point.

SHARQ (Sharing Heterogenous and Autonomous Resources and Queries) aims to develop generic tools and technologies for creating and maintaining confederations whose purpose is distributed data sharing that is, data cooperatives. In response to the difficulties outlined, our solution emphasizes

• (1) decentralization for both scalability and flexibility,
• (2) incremental development of resources such as schemas, mappings between different schemas, and queries,
• (3) rapid discovery mechanisms for finding the resources relevant to a topic, and
• (4) tolerance for intermittent participation of members and for approximate consistency of mappings.

• (i) Representing biological entities and relationships as a graph, following the approach of BioGuide (Cohen-Boulakia et al, 2005) (http://bioguide-project.net). This graph can be extended in a collaborative way by the peer administrators.
• (ii) Expressing queries (a) without having to know/cite the schemas to use for querying (transparent queries) and (b) using query schema templates.
• (iii) Proposing new features to maximize the amount of data returned to the user, by allowing some fields in the query to be optional.
• (iv) Helping administrators of peers to register their schema.

Some references

• BioGuideSRS: Querying Multiple Sources with a user-centric perspective [.pdf] 
  BioInformatics (2007)
  Sarah Cohen Boulakia   Olivier Biton   Susan Davidson   Christine Froidevaux   
  

• Materialization and update translation for collaborative data sharing
  In progress (2006)
  Todd J. Green   Zachary Ives   Grigoris Karvounarakis   Val Tannen   
  

• Reconciling while tolerating disagreement in collaborative data sharing [.pdf] 
  Proceedings of ACM SIGMOD International Conference on Management of Data (2006)
  Nicholas Taylor   Zachary Ives   
  

• Path-based systems to guide life scientists in the maze of biological data sources. [.pdf] 
  Journal of Bioinformatics and Computational Biology 4:5 (October 2006), pp. 1069-1095 (2006)
  Sarah Cohen Boulakia   Susan Davidson   Christine Froidevaux   Zoe Lacroix   Maria-Esther Vidal   
  

• SHARQ Guide: Finding relevant biological data and queries in a peer data management system [.pdf] 
  DILS'06, Data Integration for the Life Sciences, Poster proceedings (Selected for oral presentation). (2006)
  Sarah Cohen Boulakia   Olivier Biton   Shirley Cohen   Zachary Ives   Val Tannen   Susan Davidson   
  

• Orchestra: Rapid, collaborative sharing of dynamic data [.pdf] 
  Biennial Conference on Innovative Data Systems Research (CIDR) (2005)
  Zachary Ives   Nitin Khandelwal   Aneesh Kapur   Murat Cakir   
  

• Schema mediation for large-scale data sharing [.pdf] 
  International Conference on Very Large Databases (VLDB) (2005)
  Alon Halevy   Zachary Ives   Dan Suciu   Igor Tatarinov   
  

• A User-centric Framework for Accessing Biological Sources and Tools. [.pdf] 
  DILS'05, Data Integration for the Life sciences, Lecture Notes in Bioinformatics (LNBI), Num. 3615, pp. 3-18. (2005)
  Sarah Cohen Boulakia   Christine Froidevaux   Susan Davidson   
  

• Schema Mediation in Peer Data Management Systems [.pdf] 
  ICDE 2003 (2003)
  Alon Halevy   Zachary Ives   Dan Suciu   Igor Tatarinov   
  

Project Members

Funding