1. LSIDs in a Nutshell Jun Zhao University of Manchester 1 st December, 2005

2. Any idea? 30350027 gi:30350027 THE LSID

3. Outline What is an LSID Why do we need LSIDs How does it work What are available from your LSID comrades How is it working in my Grid Questions

4. LSID: Life Science Identifier Clark T., Martin S., Liefeld T. Globally Distributed Object Identification for Biological Knowledgebases Briefings in Bioinformatics 5.1:59-70, March 1, 2004. http://lsid.sourceforge.net/http://lsid.sourceforge.net/ A URN (Uniform Resource Name) A standard from the OMG LSR group A detailed specification: http://www.omg.org/cgi-bin/doc?lifesci/2003-12-02

5. URN URI –Uniform Resource Identifiers –Can be further classified as URL & URN URL: –Uniform Resource Locators –identifying a place where a resource may reside –a representation of a primary access mechanism URN –required to remain globally unique and persistent even when the resource ceases to exist or becomes unavailable. Tim Berners-Lee. Uniform Resource Identifiers (URI): Generic Syntax http://www.ietf.org/rfc/rfc2396.txt http://www.ietf.org/rfc/rfc2396.txt

6. Five part schema A five-part format: urn:lsid:Authority:Namespace:Object_ID[:Revision-ID] For example: urn:lsid:ncbi.nlm.nih.gov:pubmed:12571434 refers to a PubMed article urn:lsid:ncbi.nlm.nig.gov:genbank:T48601:2 refers to the second version of an entry in GenBank

7. Motivation Making your local publications globally available Persistent Open source –Anyone can become an LSID registration agency –No central third-party registration agency is required, and there are no fees to pay Linking with other database sources: NCBI protein/nucleotide DBs, PubMed, UniProt/SwissProt, GO terms ……

8. How does it work urn:lsid:www.mygrid.org.uk http://hostname:80/authority WSDL script http://hostname:80/authority Operation calls http, ftp and soap Returned results Client Metadata Store Metadata Store Data Store Data Store LSID Authority LSID Authority

9. LSID resources http://lsid.sourceforge.net/ http://lsid.biopathways.org/ http://cvs.sourceforge.net/viewcvs.py/lsid/ Who are using them –BioMOBY(www.biomoby.org)www.biomoby.org –Aventis –BioImage(www.bioimage.org)www.bioimage.org –Haystack, the first Semantic Web browser, based on Eclipse (haystack.lcs.mit.edu)

10. my Grid An e-Science project for bioinformaticians and biologists http://www.mygrid.orghttp://www.mygrid.org A set of middleware services Based on 3 molecular scenarios A successful workflow workbench Taverna http://taverna.sourceforge.net http://taverna.sourceforge.net Hosting 1,800 bio-services We finished but we will continue

11. http://www.mygrid.org.uk/ontology #contains_similar_sequence_to LSIDs in my Grid Motivation –Uniquely and persistently identifying my Grid internal resources –Separating data and metadata –Applying a compatible standard –Integrating with resources in the open world LSIDs and RDF (Resource Description Framework) urn:lsid:taverna.sf.net:datathing:45fg6 urn:lsid:ncbi.nlm.nih.gov.lsid.biopat hways.org:genbank_gi:5851672 report sequence http://www.mygrid.org.uk/ontology#D NA_sequence

12. LSIDs in action Freefluo Enactor Services LSID Assigning Service Store plug-in Metadata plug-in Metadata Store mIR Workflow design User context LSID Metadata Resolver LSID Data Resolver LSID Authority Client application 1. Data sent/ received from services 2. New LSIDs assigned to data 3. Data / Metadata stored 4. Data and metadata retrieved Taverna Workbench

13. View LSIDs

14. LSID ≠ URL An LSID is a URN –Identifying a resource by its name, instead of its location –Persistency (theoretically??) –Legacy support Multiple protocols: http, ftp, file systems, soap…

15. Your responsibility Unique authority id Unique object and revision ids within your namespace Never reassign an LSID Persistently identifying your data

16. What is not working Security Access control LSID synonyms

17. Questions? Thank you!