Transcript BioHaystack
IBM Watson Research BioHaystack: Gateway to the Biological Semantic Web Dennis Quan [email protected] © 2004 IBM Corporation IBM Watson Research 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 © 2004 IBM Corporation IBM Watson Research 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 © 2004 IBM Corporation IBM Watson Research RDF/XML: on demand data integration human hemoglobin LSID atagccgta cctgcgagt ctagaagct derives from GenBank derives from atagccgta cctgcgagt ctagaagct + human hemoglobin LSID is a oxygen transport protein human hemoglobin LSID is a oxygen transport protein Gene Ontology + has 3D structure human hemoglobin LSID has 3D structure Unified view PDB © 2004 IBM Corporation IBM Watson Research 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/ © 2004 IBM Corporation IBM Watson Research 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. © 2004 IBM Corporation IBM Watson Research 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 © 2004 IBM Corporation IBM Watson Research 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 © 2004 IBM Corporation IBM Watson Research 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 © 2004 IBM Corporation IBM Watson Research myGrid Architecture Bioinformaticians Registry Query & register Annotation/description Discovery View Query & Retrieve invoking Annotation providers Pedro Annotation tool Interface Description Others Vocabulary Ontology Store Service WSDL SoapProviders lab Taverna WF Builder Workflow Execution FreeFluo Enactor Store data/ knowledge mIR Haystack Provenance Browser Data descriptions Courtesy of Professor Carole Goble, University of Manchester Scientists © 2004 IBM Corporation IBM Watson Research BioHaystack + myGrid Courtesy of Professor Carole Goble, University of Manchester © 2004 IBM Corporation IBM Watson Research Thank you for your attention Dennis Quan, [email protected] (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 © 2004 IBM Corporation