LSIDs in a Nutshell

Jun Zhao

University of Manchester

1st December, 2005

Any idea?

• 30350027• 30350027

• gi:30350027 THE LSID

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 myGrid• Questions

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/

• 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

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

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

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 ……

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 soapReturned results

ClientClient

MetadataStore

MetadataStore

DataStoreDataStore

LSIDAuthority

LSIDAuthority

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)– Aventis– BioImage(www.bioimage.org)– Haystack, the first Semantic Web browser, based on

Eclipse (haystack.lcs.mit.edu)

myGrid

• An e-Science project for bioinformaticians and biologists http://www.mygrid.org

• A set of middleware services• Based on 3 molecular scenarios• A successful workflow workbench Taverna

http://taverna.sourceforge.net• Hosting 1,800 bio-services• We finished but we will continue

http://www.mygrid.org.uk/ontology

#contains_similar_sequence_to

LSIDs in myGrid

• Motivation– Uniquely and persistently

identifying myGrid 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.biopathways.org:genbank_gi:5851672

reportsequence

http://www.mygrid.org.uk/ontology#DNA_sequence

LSIDs in action

FreefluoEnactor

Services

LSID Assigning Service

Store plug-in

Metadata plug-in MetadataStore

mIR

Workflow design User

context

LSID Metadata Resolver

LSID Data Resolver

LSIDAuthority

Client application

1. Data sent/ received from services

2. New LSIDs assigned to data

3. Data / Metadata stored

4. Data and metadata retrieved

TavernaWorkbench

View LSIDs

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…

Your responsibility

• Unique authority id

• Unique object and revision ids within your namespace

• Never reassign an LSID

• Persistently identifying your data

What is not working

• Security

• Access control

• LSID synonyms

Questions?

Thank you!