SHARQ Guide: SHARQ Guide: Finding relevant biological data Finding - PowerPoint PPT Presentation

Nov 14, 2022 •216 likes •305 views

SHARQ Guide: SHARQ Guide: Finding relevant biological data Finding relevant biological data and queries in a and queries in a Peer Data Management System Peer Data Management System Sarah Cohen-Boulakia , Olivier Biton, Shirley Cohen,

SHARQ Guide: SHARQ Guide: Finding relevant biological data Finding relevant biological data and queries in a and queries in a Peer Data Management System Peer Data Management System Sarah Cohen-Boulakia , Olivier Biton, Shirley Cohen, Zachary Ives, Val Tannen, Susan Davidson Database Group, University of Pennsylvania 07/ 20/ 2006 DILS 2006 - SHARQ Guide 1
Biological peer data sharing Biological peer data sharing I would like to share part of my data I want to be free to leave the network at any time Human disease information 3D-structures Data related to Malaria Proteomic domains Sequencing data (Genes, BACs, Contigs) I wish to integrate RefSeq and Microarray data UniGene data in my local � Collaboration: Peer Collaboration: Peer network � database but when these sources disagree I always trust RefSeq! � Mappings between data sources o I nterm ittent I nterm ittent participation is possible o o Peers may disagree disagree 07/ 20/ 2006 DILS 2006 - SHARQ Guide 2
Biological queries Biological queries SwissProt and PFAM are my preferred resources! Which proteins contain an erythrocyte domain? Give me the name of these proteins, any annotations, and, if available , their sequence. � Explorative Explorative � � Composed of biological entities, keywords � Unspecified schema � Posed over a netw ork netw ork of resources � Intricate and highly complementary 07/ 20/ 2006 DILS 2006 - SHARQ Guide 3
Solutions for Peer networks Solutions for Peer networks � Querying with Piazza Piazza [ Halevy et al, 04] � Queries asked to a given peer and rew ritten rew ritten over the schema of other peers � Certain answers are provided � Querying and Updating with Orchestra Orchestra [ Ives et al, 06] � Builds upon concepts from Piazza Piazza � Allows data exchange exchange / updates propagation among peers � Uses policies to quickly and automatically m anage m anage disagreem ent (conflicting data) disagreem ent 07/ 20/ 2006 DILS 2006 - SHARQ Guide 4
Remaining Problems… Remaining Problems… What kind of information can I found in this network? How to express my queries? Had anybody ever asked a similar query? I want to join the peer network: What should I do? How do I specify links between my data and the data of other peers? How can my data be found by users? Need for a Guide! Need for a Guide! 07/ 20/ 2006 DILS 2006 - SHARQ Guide 5
SHARQ - - Overview Overview SHARQ � S S haring H H eterogeneous and A A utonomous � R esources and Q Q ueries R � Collaborative Collaborative project � � Database group at the University of Pennsylvania � Penn Center for Bioinformatics � Children's Hospital of Philadelphia � Goal � Develop generic generic tools and technologies � creating / maintaining confederations of peers confederations of peers � SHARQ is composed of two main modules � Orchestra Orchestra : Core engine � � SHARQ Guide SHARQ Guide : Help in querying and administrating � the biological peer network 07/ 20/ 2006 DILS 2006 - SHARQ Guide 6
More about SHARQ Guide? More about SHARQ Guide? Visit Poster # 14! 07/ 20/ 2006 DILS 2006 - SHARQ Guide 7

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