LSIDs

1
LSIDs

• Background on GUIDs
• What is a GUID?
• Globally Unique IDentifier
• Persistent
• Opaque transparent
• Resolvable?
• Examples UUID, DOI, Handle, LSID, PURL

2
LSIDs

• What is an LSID?
• Life Science IDentifier
• Developed by OMG W3C
• Implementations by the team at IBM
• Structure urnlsidauthoritynamespaceobjectre
  vision
• Eg urnlsidindexfungorum.orgnames213649
• Used for data objects, databases, images, files
  etc?
• Versioning
• Deprecation must maintain LSID, but can point
  to new ID

3
LSIDs

• Data fixed, immutable
• Allows caching
• Very little data in biodiversity domain
• Eg image, document
• Metadata can be changed
• Most biodiversity data is LSID metadata

4
TDWG GUID subgroup

• Subgroup decisions
• To use LSIDs for identifying biodiversity data,
  but not exclude use of other GUIDs
• Reuse GUIDs where they already exist, eg some
  DOIs for literature (assuming no commercial
  restrictions)
• Use RDF for metadata of objects identified by
  LSIDs
• Implement as a minimum the HTTP GET metadata
  service for each LSID server/resolver
• See GUID Reports - http//wiki.gbif.org/guidwiki/w
  ikka.php?wakkaGUID2Reportshow_comments1

5
Pros and Cons of LSIDs
URL

• Tied to physical addresses
• Inspection required to determine identical
  contents
• Brittle (broken links)

LSID

• Same Id same content
• Location independent
• Enables transparent caching
• Formalized, rich metadata

• Requires specialised software to resolve an LSID
  (not built in to most software)

but
6
Pros and Cons of LSIDs

• LSIDs do not require any central registration
  before they can be used (c.f. DOI)
• Allow quick adoption of a GUID technology by
  using LSID namespaces and appending existing IDs
  (including integer PKs)
• Eg urnlsidexample.orgnamespace of
  choiceexisting ID
• LSIDs do not rely on the availability of any
  central service
• LSIDs (unlike HTTP URIs) do not assume that the
  Internet as we know it will persist forever
• LSIDs (unlike HTTP URIs) require some thought and
  planning before they are allocated

7
LSID Tools and Services

• IBM LSID Launchpad
• Firefox LSID Browser
• LSID Tester (Rod Page)
• Web based resolver http//lsid.biopathways.org/r
  esolver/
• Example LSID servers
• Index Fungorum - urnlsidindexfungorum.orgnames
  213649
• IPNI urnlsidipni.orgnames30000959-21.1.2.1
• uBio - urnlsidubio.orgnamebank11815
• Bio Pathways http//lsid.biopathways.org/resolve
  r/urnlsidgene.ucl.ac.uk.lsid.biopathways.orghug
  oMVP

8
An LSID is resolved using a three-part resolution
1 Resolve LSID Authority
Client
DNS HTTP
Query Authority
2 Get Available Services
WSDL
Data via
3 Retrieve Data
SOAP, HTTP, FTP, NFS, AFS, DFS
9
DNS

• LSIDs use DNS for resolver lookup
• Eg for LSID urnlsidindexfungorum.orgnames21364
  5
• DNS lookup for SRV record_lsid._tcp.indexfungoru
  m.org
• Returns
• 194.131.255.4 the IP address of the Index
  Fungorum LSID resolver server
• So then http//194.131.255.4/authority/metadata/?l
  sidurnlsidindexfungorum.orgnames213645will
  return the metadata for that LSID

10
LSID Code

• Current Code Stacks
• Open Source (sourceforge.net)
• Java, C, Perl (IBM)
• Microsoft .NET (Myself)

11
LSIDs and RDF

• The standard for LSIDs is to return RDF Data and
  Metadata
• Only metadata is required for TDWG domain, no
  data
• LSID vocabularies used for RDF ontologies (TDWG
  TAG group)

12
RDF

• What is RDF
• Resource Description Framework
• w3C
• Describes resources on the web
• Putting data on the web
• Intended for machine processing
• Has a defined xml syntax

13
Basic RDF

• lt?xml version"1.0"?gt
• ltrdfRDF xmlnsrdf"http//www.w3.org/1999/02/22-r
  df-syntax-ns"
• xmlnsdc"http//purl.org/dc/elements/1.1
  /"gt
• ltrdfDescription rdfabout"http//www.example.or
  g/index.html"gt
• ltdclanguagegtenlt/dclanguagegt
• lt/rdfDescriptiongt
• lt/rdfRDFgt
• rdfDescription basic description xml node
• Every xml node must be namespaced and the
  namespace must be resolvable
• DublinCore handy set of basic descriptive
  elements, such as title, creator, language, etc

14
Issues to think about

• Who assigns new LSIDs
• Who maintains LSID resolvers
• What to assign LSIDs to
• Granularity?
• Only objects that need to be resolved /
  identified externally
• Is there any data, or only metadata
• Versioning
• Best not to use LSID version

15
Issues to think about

• When to resolve LSIDs
• Every time an LSID is encountered, or only when a
  client requests it?
• Requires LSID client software to resolve them
• What metadata format to use (which RDF ontology
  objects)
• How to map objects in your domain to this
  metadata format (in a consistent way)

16
LSID References

• LSID RDF Vocabularies http//wiki.tdwg.org/twiki
  /bin/view/TAG/LsidVocs
• LSID Source Forge - http//lsid.sourceforge.net/
• LSID .NET Source Forge - http//sourceforge.net/pr
  ojects/lsid-dotnet
• LSID Tutorial - http//www-128.ibm.com/developerwo
  rks/opensource/library/os-lsid/
• LSID Specification - http//www.omg.org/cgi-bin/do
  c?dtc/04-05-01
• LSID Tester - http//linnaeus.zoology.gla.ac.uk/r
  page/lsid/tester/
• LSID Launchpad - http//www-124.ibm.com/developerw
  orks/downloads/detail.php?group_id124whatrelei
  d553
• GUID Subgroup - http//wiki.tdwg.org/GUID
• GUID Subgroup Reports
• http//wiki.gbif.org/guidwiki/wikka.php?wakkaGUID
  2Reportshow_comments1
• http//wiki.tdwg.org/twiki/pub/TIP/TipDocuments/GU
  ID1Report.pdf
• Firefox LSID developer site - http//lsid.mozdev.o
  rg/, http//lsid.biopathways.org/lsid_browser/
• TDWG Presentation - http//tdwg2006.tdwg.org/filea
  dmin/2006meeting/slides/Richards_LsidAndRdfTutoria
  l_abs0026.ppt
• Documents - http//www.tdwg.org/activities/guid/do
  cuments