1 / 10

Life Science Identifiers

Life Science Identifiers. Chris Wroe (based on material from myGrid team and IBM Life Sciences). The Issue. Each database on the web has: Different policies for assigning and maintaining identifiers, dealing with versioning etc. Different mechanism for retrieving an item given an ID.

glenys
Download Presentation

Life Science Identifiers

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. Life Science Identifiers Chris Wroe (based on material from myGrid team and IBM Life Sciences)

  2. The Issue • Each database on the web has: • Different policies for assigning and maintaining identifiers, dealing with versioning etc. • Different mechanism for retrieving an item given an ID. • LSID designed to harmonise the retrieval of data.

  3. What is an LSID? • An OMG standard: urn:lsid:AuthorityID:NamespaceID:ObjectID:RevisionID urn:lsid:ncbi.nlm.nig.gov:GenBank:T48601:2 • LSID Designator: A mandatory preface that notes that the item being identified is a life science-specific resource • Authority Identifier: An Internet domain owned by the organization that assigns an LSID to a resource • Namespace Identifier: The name of the resource (e.g., a database) chosen by the assigning organization • Object Identifier: The unique name of an item (e.g., a gene name or a publication tracking number) as defined within the context of a given database • Revision Identifier: An optional parameter to keep track of different versions of the same item

  4. How is data retrieved? 2. Where can I get data and metadata for urn:lsid:pdb.org.1AFT Application PDB Authority @ pdb.org 1. Get me info for:urn:lsid:pdb.org:1AFT LSID client PDB Data resolver PDB database PDB Metadata resolver 2. Get me the data and metadata for:urn:lsid:pdb.org:1AFT

  5. Authority Commitments • Data returned for a given LSID must always be the same • Must always maintain an authority at e.g. pdb.org that can point to data and metadata resolvers.

  6. LSID Components • IBM built client and server implementations in Perl, Java, C++http://www-124.ibm.com/developerworks/oss/lsid/ • Fairly simple to wrap an existing database as a source of data or metadata • Client also simple to use • LSID Launchpad adds LSID resolution to Internet Explorer

  7. LSID Launchpad

  8. Use within myGrid • Needed an identifier for things such as workflows, experiments, new data results etc • Everything identified with LSIDs ! • LSID saves us having to invent our own conventions and code. • Can pass references to data around and be reassured the other party will know how to resolve that reference

  9. Haystack demonstrator GenBank record Provenance of results Managing collection of sequences for review

  10. Caveats • To be successful across the community, it will require widespread adoption by data providers such as Genbank, UniProt etc • Status of such adoption unclear

More Related