G. A. Thorisson, A. J. Webb, R. Dalgleish ULEIC / J. Muilu FIMM             Identification of G2P databases -           cha...
Linking	  resources         External	           records	  /	           annotaEons                              c.         ...
URLs	  are	  unstable                        hIp://subdomain.example.com/path/to/resource        • Domain	  names	  /	  su...
1:1                 IDENTIFIER                                                                DATA	  RESOURCE        • Gen...
G. A. Thorisson, A. J. Webb, R. Dalgleish ULEIC / J. Muilu FIMM              Proposal to collaborate with BioDBCore     • ...
G. A. Thorisson, A. J. Webb, R. Dalgleish ULEIC / J. Muilu FIMM GEN2PHEN 8th General Assembly Meeting, Leiden, Jan 24-25 2...
G. A. Thorisson, A. J. Webb, R. Dalgleish ULEIC / J. Muilu FIMM             Persistent resource identifiers in BioDBCore   ...
G. A. Thorisson, A. J. Webb, R. Dalgleish ULEIC / J. Muilu FIMM                                      How might this work? ...
G. A. Thorisson, A. J. Webb, R. Dalgleish ULEIC / J. Muilu FIMM                                              Mututal benefi...
G. A. Thorisson, A. J. Webb, R. Dalgleish ULEIC / J. Muilu FIMM                Open questions, known unknowns etc.        ...
G. A. Thorisson, ULEIC                                      Acknowledgements   GEN2PHEN Consortium                        ...
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GEN2PHEN GAM8 meeting Leiden - Identifiers for LSDBs

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GEN2PHEN GAM8 meeting Leiden - Identifiers for LSDBs

  1. 1. 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
  2. 2. 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
  3. 3. 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
  4. 4. 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
  5. 5. 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
  6. 6. 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
  7. 7. 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
  8. 8. 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
  9. 9. 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
  10. 10. 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
  11. 11. 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
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