GEN2PHEN GAM8 meeting Leiden - Identifiers for LSDBs
Upcoming SlideShare
Loading in...5
×
 

GEN2PHEN GAM8 meeting Leiden - Identifiers for LSDBs

on

  • 576 views

 

Statistics

Views

Total Views
576
Views on SlideShare
576
Embed Views
0

Actions

Likes
0
Downloads
0
Comments
0

0 Embeds 0

No embeds

Accessibility

Upload Details

Uploaded via as Adobe PDF

Usage Rights

CC Attribution License

Report content

Flagged as inappropriate Flag as inappropriate
Flag as inappropriate

Select your reason for flagging this presentation as inappropriate.

Cancel
  • Full Name Full Name Comment goes here.
    Are you sure you want to
    Your message goes here
    Processing…
Post Comment
Edit your comment

GEN2PHEN GAM8 meeting Leiden - Identifiers for LSDBs GEN2PHEN GAM8 meeting Leiden - Identifiers for LSDBs Presentation Transcript

  • G. A. Thorisson, A. J. Webb, R. Dalgleish ULEIC / J. Muilu FIMM Identification of G2P databases - challenges and proposal for a solution Gudmundur A. Thorisson <gt50@leicester.ac.uk> ULEIC Adam J. Webb <ajw51@leicester.ac.uk> ULEIC Raymond Dalgleish <ray@leicester.ac.uk> ULEIC Juha Muilu <juha.muilu@helsinki.fi> FIMM -- Overview -- ✴ Identification difficulties - the Knowledge Centre perspective ✴ Or, why we need persistent identifiers for database resources ✴ Proposal to collaborate with the BioDBCore initiative ✴ standardizing registration & description of bio-databases This work is published under the Creative Commons Attribution license (CC BY: http://creativecommons.org/licenses/by/3.0/) which means that it can be freely copied, redistributed and adapted, as long as proper attribution is given. GEN2PHEN 8th General Assembly Meeting, Leiden, Jan 24-25 2012 1Friday, 27 January 12
  • Linking  resources External   records  /   annotaEons c. c. c. c. c. Databases 301C> 465A 555G> 103C> 321G> T >G T T T DB  maintainer SubmiIer SubmiIer DB  maintainerFriday, 27 January 12
  • URLs  are  unstable hIp://subdomain.example.com/path/to/resource • Domain  names  /  subdomains  can  change – hgvbaseg2p.org  -­‐>  gwascentral.org – server1.example.com  -­‐>  server2.example.com • Paths  can  change – e.g  /LOVD2/  change  to  /LOVD3/ • LSDB  genes  can  move   – e.g  gene  ADAM19  moves  from  one  LOVD  install  to  another • Databases  can  merge – i.e  gene  ADAM19  on  two  different  installs  are  reconciled  into  a   single  installFriday, 27 January 12
  • 1:1 IDENTIFIER DATA  RESOURCE • Gene  name  not  suitable – >  1  database  for  a  given  gene • gene.lovd.nl  -­‐>  returns  list  of  databases  (or  redirects  if  only  1  is   known) – 1  to  many • lovd.nl/gene  -­‐>  redirects  to  *one*  database – 1  to  one,  but  many  resource  do  not  receive  idenEfiers • These  are  locators,  not  idenEfiers • Non-­‐gene  based  resources • Ideally  the  idenEfier  should  also  operate  as  the   locator  (like  DOIs  via  a  DOI  resoluEon  service) – hIp://dx.doi.org/10.19192  resolves  DOI  10.19192Friday, 27 January 12
  • G. A. Thorisson, A. J. Webb, R. Dalgleish ULEIC / J. Muilu FIMM Proposal to collaborate with BioDBCore • BioDBCore aims – annotation - organize the bio-database ‘resourceome’ – discovery - e.g. which protein sequence databases are available? • Who’s behind it? – International Society for Biocuration – Resource catalogues: Bioinformatics Links, BioSiteMaps, NAR db-issue etc – Working group includes reps from NAR and DATABASE journals, MIBBI, Model organism db’s, CASIMIR mouse informatics consortium, others GEN2PHEN 8th General Assembly Meeting, Leiden, Jan 24-25 2012 5Friday, 27 January 12
  • G. A. Thorisson, A. J. Webb, R. Dalgleish ULEIC / J. Muilu FIMM GEN2PHEN 8th General Assembly Meeting, Leiden, Jan 24-25 2012 6Friday, 27 January 12
  • G. A. Thorisson, A. J. Webb, R. Dalgleish ULEIC / J. Muilu FIMM Persistent resource identifiers in BioDBCore • They plan to use MIRIAM registry / ID resolution service – unique, persistent and unambiguous identification of various kind of concepts. • http://identifiers.org/ec-code/1.1.1.1 • http://identifiers.org/pubmed/16333295 • http://identifiers.org/doi/10.1038/nbt1156 • Decouples identification from location • Many resourcesa are already registered with MIRIAM • Operated by EBI <-- long-term sustainability prospect • Adoption by players LS Semantic Web comunity – URIs for identifying entities in biological information represented in RDF – http://lsrn.org, Shared Names, Bio2RDF, others GEN2PHEN 8th General Assembly Meeting, Leiden, Jan 24-25 2012 7Friday, 27 January 12
  • G. A. Thorisson, A. J. Webb, R. Dalgleish ULEIC / J. Muilu FIMM How might this work? • Using database URIs - plausible scenario – Persistent canonical URI: http://identifiers.org/biodbcore/10235900 – Click URL, browser redirects to http://biodbcore.org/resource/10235900 – BioDBCore metadata record for the database (akin to “landing page” online journal site) • BioDBCore “landing page” presents database metadata – Information *about* the “thing” – Name: Ehlers-Danlos Syndrome Variant Database Main resource URL: https://eds.gene.le.ac.uk <-- the “thing” itself [scope, data standards, other metadata] • Location of database = the “thing” itself GEN2PHEN 8th General Assembly Meeting, Leiden, Jan 24-25 2012 8Friday, 27 January 12
  • G. A. Thorisson, A. J. Webb, R. Dalgleish ULEIC / J. Muilu FIMM Mututal benefits • To GEN2PHEN / G2P community – Identification - slot into resource identifier scheme for bio-databases globally, build more detailed catalogues & annotation systems around this – Discovery - finding relevant LSDB and other G2P resources via range of search/ query tools outside the KC or LSDB lists – BioDBCore could possibly evolve into a sort of live “database publishing platform” , instead of the static “snapshot” conventional papers. • To BioDBCore initiative – Acquire an entire category’s worth of metadata records & link to community – Extra pairs of eyes on what they’re doing, alternative perspective – Potential for further collaboration on contrib. tracking tools & ORCID integration GEN2PHEN 8th General Assembly Meeting, Leiden, Jan 24-25 2012 9Friday, 27 January 12
  • G. A. Thorisson, A. J. Webb, R. Dalgleish ULEIC / J. Muilu FIMM Open questions, known unknowns etc. • BioDBCore quite new, many things remain in flux – e.g. the MIRIAM / identifiers.org technical details are vague • DOIs for BioDBCore records - register database DOIs for fuller integration into publishing process? • How will this work with existing LSDB lists? GEN2PHEN 8th General Assembly Meeting, Leiden, Jan 24-25 2012 10Friday, 27 January 12
  • G. A. Thorisson, ULEIC Acknowledgements GEN2PHEN Consortium This work has received funding from the http://www.gen2phen.org/about-gen2phen/partners European Communitys Seventh Framework Programme (FP7/2007-2013) under grant agreement number 200754 - Prof Anthony J. Brookes Bioinformatics Group, Leicester the GEN2PHEN project. Contact me! <gt50@le.ac.uk> |<gthorisson@gmail.com> http://www.linkedin.com/in/mummi http://www.twitter.com/gthorisson Published under the CC BY license (http:// http://www.gthorisson.name creativecommons.org/licenses/by/3.0/) GEN2PHEN 8th General Assembly Meeting, Leiden, Jan 24-25 2012 11Friday, 27 January 12