Globally Unique Identifiers and Life Science Identifiers

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Globally Unique IdentifiersandLife Science
Identifiers

• Dave Thau
• thau_at_learningsite.com
• University of Kansas
• California Academy of Sciences
• www.learningsite.com

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Outline

• Describe Global Unique Identifiers
• Show how theyre relevant
• Describe one GUID system (LSIDs)
• Outline some issues around using GUIDs for
  TDWG-related activities
• Provide some resources
• Open discussion

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GUID Is Not An Ugly Word
It s guid to be merry and wise, It s guid to
be honest and true,        Robert Burns Heres a
Health to Them that s Awa.
Pteroptochos tarnii AKA Guidguid
Image From animaldiversity.ummz.umich.edu
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GUID Globally Unique Identifier

• A short name for a complex entity
• Useful for locating information about the entity
• Each name identifies only one entity
• There is some sense of permanence

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Some things which fit this description

• GenBank accession numbers AP006480.1
• US Patent numbers 5443036 (laser guided cat
  exercise)
• Digital Object Identifier 10.121/3212

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In Our Domain
SDD Document Representing some data
set. ltClassName id"1"gt ltLabelgt
ltRepresentation language"en"gt  
ltTextgtCypselurus heterurus (Rafinesque,
1810)lt/Textgt   lt/Representationgt   lt/Labelgt
ltLinkgt   ltLSIDgtlsid.gbif.netwww.fishbase.org10
29lt/LSIDgt   lt/Linkgt   ltRankgtsplt/Rankgt
lt/ClassNamegt
Napier Schema Document Representing some
taxon. ltTaxonConcept idurnlsidbioguid.orgsee
k121212
type"original"gt
ltName type"scientific"gt   ltNameSimplegtCanis
lupuslt/NameSimplegt lt/Namegt
ltRelationshipsgt ltRelationship typeis child
of"gt   ltToTaxonConcept refurnlsidbioguid.o
rgseek5743" /gt lt/Relationshipgt
lt/Relationshipsgt lt/TaxonConceptgt
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Features of a GUID system

• Global uniqueness scoped to Internet
• Should be easily resolvable by a computer or
  human
• Should identify things down to whatever level of
  granularity necessary
• Should not be limited to proprietary systems
• Should serve up all sorts of data
• Database records
• Text files
• Images
• It would be nice if the identifier had associated
  metadata

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Life Science Identifiers

• Official standard of the Object Management Group
  (OMG)
• Support for metadata and authentication
• Supports multiple protocols (e.g. HTTP, SOAP)
• Can serve up data in any format
• Decentralized anyone can issue an LSID
• LSID code available in Java and Perl.
• A young standard, but increasingly used.

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Organizations Using LSIDs

• National Center for Biotech Information (NCBI)
• Pubmed
• Genbank
• European Bioinformatics Institute (EBI)
• US Long Term Ecological Research Network (LTER)
• BioMOBY an biological database interoperability
  program (biomoby.org)
• Open Bioinformatics Foundation (open-bio.org)
• myGrid a BioGRID project (mygrid.org.uk)

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A Small Pause For More Squid Humor
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LSID Format
urnlsidbioguid.orgseek117866v1

• urn indicates that this is a URN
• lsid indicates that its an LSID-type urn
• bioguid.org the authority who issued the LSID
• Doesnt have to be a domain name but for now
  probably should be.
• bioguid.org does not necessarily have the data or
  metadata.
• There may not even be a machine called
  bioguid.org.
• seek a name space id internal to that authority
• The name space is meaningless to systems outside
  that authority.
• 117866 the local identifier within that
  authority
• Also internal to the authority
• v1 an optional version number
• If no version, no trailing colon either.

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Data and Metadata

• An LSID has data
• Examples
• The gene sequence in GenBank
• The actual LTER data set, maybe in excel, or in a
  text file
• The data should never change
• An LSID also has metadata
• Example metadata
• The format of the data
• A display title for clients displaying the LSID
• Dublin core metadata
• Anything you want
• The metadata can change

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Example LSIDs

• An LTER fish abundance data set
• urnlsidlimnology.wisc.edudatasetntlfi02
• A PubMed reference
• urnlsidncbi.nlm.nih.gov.lsid.biopathways.orgpub
  med12441808
• A GenBank sequence
• urnlsidncbi.nlm.nih.gov.lsid.biopathways.orggen
  bank_gi30350027

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How LSIDs work
LSID Client Maybe Launchpad Maybe Haystack Maybe
BioFerret Maybe myGRID Maybe Yours!
DNS Find DNS record Resolve it to get Address of
Authority

• Find the authority for this LSID

Returns the LSID Authority Server
LSID Authority
2. Query authority for available services
Returns WSDL for this LSID
3. Chose a service, get the goods
Data Store
Metadata Store
HTTP, SOAP, FTP, others
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LSID Promises

• I promise to never change the data behind an
  LSID.
• I will make sure my LSIDs are being served, or
  give them to someone who can do it.
• I will give my LSIDs metadata at least give
  them a title and a format

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Other GUID systems

• URLs
• Files move
• The data change
• Unstructured metadata
• UUIDs 128 bit string, guaranteed unique
• 58f202ac-22cf-11d1-b12d-002035b29092
• No resolution
• No metadata
• Handle System / DOIs (10.12/2312)
• Non standard protocol
• Centralized resolution
• Unstructured metadata (for Handle System)
• High costs (for DOI)

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Issues For This Community

• What gets a GUID?
• For each of those things, whats the data, whats
  the metadata?
• One GUID per item?
• Centralization who issues GUIDs?

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What Gets a GUID?

• These things probably should get GUIDs
• Taxonomic concepts
• Specimens
• Publications
• People
• These things might get GUIDs
• Taxonomic names
• Journals
• Data providers
• Observations

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Specimen Data? Metadata?

• If specimens get a GUID what does it identify?
• The physical specimen?
• A collections database record of the specimen?
• What about multiple labels?
• Main question what doesnt change about a
  specimen?
• Other main question how should the data be
  represented?
• Darwin core includes current institution
  location. Not a good idea for the data of a GUID
  since that may change.

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One GUID Per Item?

• No GUID system inherently enforces a 11 mapping
  between GUID and data.
• Everyone should TRY to limit the number of GUIDs
  per item.
• Should there be any centralization to help
  achieve this?

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Degrees of Centralization

• An index
• List your GUID authority in an index so your
  GUIDs are easy to find.
• A central authority
• One authority could be responsible for issuing
  GUIDs to the community for specific types of
  information youd have to get one from here.
• GBIF?
• The IC_Ns? (ICZN, ICBN.)
• lsidauthority.org?
• This would help enforce a 11 mapping of GUIDs
  and data items
• It would also alleviate data providers from the
  need to maintain their own authorities
• It MAY also reduce the likelihood of GUIDs
  becoming unresolvable
• It may also be infeasible technically, or
  socially.
• A respected authority
• With LSIDs, an authority can be set up to serve
  its own GUIDs and proxy other authorities.
• This would help enforce a 11 mapping for those
  who use the authority
• It may also be more feasible.

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LSID Resources

• LSID Articles and code from IBM
• http//www-124.ibm.com/developerworks/oss/lsid/wh
  atislsid
• Current LSID specification
• http//www.omg.org/cgi-bin/doc?dtc/04-05-01
• Launchpad An LSID resolver for Windows IE
• available from first link
• A website which resolves LSIDs
• http//lsid.biopathways.org/resolver/
• URN specification
• http//www.ietf.org/rfc/rfc2141.txt

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Acknowledgements

• My work on GUIDs has been funded by the SEEK
  project seek.ecoinformatics.org.
• SEEK is funded by National Science Foundation
  award 0225676.
• Thanks to Ben Szekely at IBM for his LSID
  articles, his LSID java code, and for answering
  all my questions.

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Questions for Discussion

• Do we need GUIDs?
• What gets a GUID?
• One GUID per item?
• Centralization?