1. IBM Watson Research © 2004 IBM Corporation BioHaystack: Gateway to the Biological Semantic Web Dennis Quan dennisq@us.ibm.com

2. IBM Watson Research © 2004 IBM Corporation Problems in bioinformatics  Myriad of public databases have specific facets of information about biological objects of interest (e.g., proteins, genes, etc.)  Databases have their own access protocols, data formats, naming conventions, and means of describing relationships between objects in different databases  Different software required to view information from different databases –User must be keenly aware of which tool or site to use –Relevant information comes in fragments –Exploration process is discontinuous

3. IBM Watson Research © 2004 IBM Corporation A common naming convention: LSID URNs  Life Sciences Identifiers (LSIDs) are URNs for biological objects that are backed by RDF metadata: –E.g., urn:lsid:ncbi.nlm.nih.gov.lsid.i3c.org:genbank:nm_001240  LSID and LSID protocol (SOAP-based) specification sponsored by I3C and undergoing standardization by OMG  Most of the publicly available bioinformatics databases available via LSID today –PDB LSID authority online; “proxy” LSID authorities for databases such as NIH databases, SwissProt hosted by I3C  Really easy to set up LSID clients and servers –IBM Internet Technology group provides Open Source LSID client and server software for a variety of languages and platforms

4. IBM Watson Research © 2004 IBM Corporation RDF/XML: on demand data integration human hemoglobin LSID oxygen transport protein atagccgta cctgcgagt ctagaagct derives from is a human hemoglobin LSID has 3D structure GenBank Gene Ontology PDB human hemoglobin LSID atagccgta cctgcgagt ctagaagct derives from oxygen transport protein is a has 3D structure Unified view + +

5. IBM Watson Research © 2004 IBM Corporation Haystack: letting users interact with their data  Haystack is a tool for creating, exploring, and organizing information: –Personal information: e-mails, contacts, documents, etc. –Bioinformatics: proteins, publications, genes, etc.  Research project originating from MIT CSAIL  Uses RDF as an underlying data model  Built on Java and Eclipse, IBM’s Open Source rich client platform http://haystack.lcs.mit.edu/

6. IBM Watson Research © 2004 IBM Corporation Browsing highly interconnected information  Single screen presents multiple facets of a single object originating from separate databases  Users navigate space like a Web browser: hyperlinking, drag and drop, etc.

7. IBM Watson Research © 2004 IBM Corporation Personalization  People keep track of their information by personalizing their workspaces: –Grouping paperwork into folders –Highlighting important text in documents –Attaching sticky notes as reminders –Jotting down lists of related items  Haystack has pervasive support for annotation and allows users to group related objects together arbitrarily for their own purposes

8. IBM Watson Research © 2004 IBM Corporation BioHaystack  BioHaystack: application of Haystack technologies to bioinformatics problem –Integrated environment for working with biological data –Intended for end users, i.e., non-programmers –Builds on LSID, RDF, and Haystack  Integration offers the promise of lowering barriers to access to different backend systems (e.g., LSID servers, Grids, Web Services, relational databases, annotation servers)  Just as the Web browser acts as a client for Web content, BioHaystack can act as a client for biological Semantic content and services

9. IBM Watson Research © 2004 IBM Corporation Real world collaboration: myGrid  UK-funded joint project with the University of Manchester and other UK research institutions  RDF-based platform for supporting e-Science experiments  Real use cases; developed in collaboration with bioinformaticians  myGrid creates LSIDs and RDF metadata in the process of enacting experiments for scientists  Using BioHaystack as a browser for metadata

10. IBM Watson Research © 2004 IBM Corporation Registry mIR Discovery View Haystack Provenance Browser FreeFluo Enactor Taverna WF Builder Pedro Annotation tool Ontology Store Others WSDL Soap- lab Interface Description Annotation/description Annotation providers Query & Retrieve Workflow Execution Store data/ knowledge Scientists Bioinformaticians invoking Query & register Service Providers Data descriptions Vocabulary myGrid Architecture Courtesy of Professor Carole Goble, University of Manchester

11. IBM Watson Research © 2004 IBM Corporation BioHaystack + myGrid Courtesy of Professor Carole Goble, University of Manchester

12. IBM Watson Research © 2004 IBM Corporation Thank you for your attention  Dennis Quan, dennisq@us.ibm.com (IBM Watson Research)  Haystack project home page (download available May 24) –http://haystack.lcs.mit.edu/  IBM LSID home page –http://www.ibm.com/developerworks/oss/lsid/  myGrid home page –http://www.mygrid.org.uk/  See also our session on constructing Haystack applications: –Developer’s Day, Saturday, 4:30pm