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G. A. Thorisson www.gen2phen.org
3rd Human Variome Project Meeting, Paris, 10-14 May, 2010
Who’s who on the Web?Digital identity for tracking contributions
and managing data access
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Gudmundur A. Thorisson <[email protected]>Brookes lab
Department of GeneticsUniversity of Leicester, UK
-- Outline --• The author name problem and the challenge of attribution
• Unique identifiers for authors - the ORCID initiative
• A digital identity on the Internet - IDs for researchers?
• Introduce several identity-based projects in our group
• Attribution for data publications
• Access control for sensitive data
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G. A. Thorisson www.gen2phen.org
3rd Human Variome Project Meeting, Paris, 10-14 May, 2010
Non-unique names are a majorproblem in the scholarly literature
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How about these?
Are these authors all the same person?G. Thorisson, Univ. LeicesterG. A. Thorisson, Univ. LeicesterG. A. Thorisson, Cold Spring Harbor Laboratory
J. SmithJ. SmithJ. SmithJ. SmithJ. Smith [etc.]
Or these?
∼2/3 of the ∼6 million authors in MEDLINE share a last name and first initial with at least one other author, and an ambiguous name refers to ∼8 persons on average.Torvik and Smalheiser. Author name disambiguation in MEDLINE. ACM Transactions on Knowledge Discovery from Data (2009) vol. 3 (3)
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G. A. Thorisson www.gen2phen.org
3rd Human Variome Project Meeting, Paris, 10-14 May, 2010
Unique identifiers for authors contributors
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Dec’09: launch of the Open Researcher Contributor Identification Initiative - ORCID
ORCID ID: B-1242-2010G. Thorisson, Univ. LeicesterG. A. Thorisson, Univ. LeicesterG. A. Thorisson, Cold Spring Harbor Lab.
automated author disambiguation+
author involvement
ORCID ID: G-1442-2009J. Smith, Univ. North Pole
ORCID ID: D-2400-2010J. Smith, Luthor Corporation
Informatics infrastructure:i) for researchers to manage profilei) interaction with other systems
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G. A. Thorisson www.gen2phen.org
3rd Human Variome Project Meeting, Paris, 10-14 May, 2010
• =
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G. A. Thorisson www.gen2phen.org
3rd Human Variome Project Meeting, Paris, 10-14 May, 2010
Digital identity - an online ‘presence’
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Problem: the Web ‘me’ is fragmentedacross many identity silos
Self-asserted
Identity = The collective aspect of the set of characteristics by which a thing is definitively recognizable or known (dictionary.com)
Many usernames/passwords- password fatigue -
Asserted by others
Nature Rev Genet G. A. Thorisson <authored> Nat Biotechnol (2009) vol. 27 (11)Nature Biotech G. A. Thorisson <authored> Nat Rev Genet (2009) vol. 10 (1) [...]
Nature Rev Genet B-1242-2010 <authored> Nat Biotechnol (2009) vol. 27 (11)Nature Biotech B-1242-2010 <authored> Nat Rev Genet (2009) vol. 10 (1) [...]
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G. A. Thorisson www.gen2phen.org
3rd Human Variome Project Meeting, Paris, 10-14 May, 2010
Bridging the silos - distributed identity systems
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Open, lightweight decentralised
authentication protocol
Web 2.0social networking
-Federated authentication-
Closed-world: Single sign-on (SSO) across the federation
-reuse profile information- username/pwd problem
Institution-centricidentityuser gt50 at University of Leicester
User-centric identity
Open-world: SSOacross the entire Web
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G. A. Thorisson www.gen2phen.org
3rd Human Variome Project Meeting, Paris, 10-14 May, 2010 7
>50,000 websites now accepting 3rd party IDs (from www.janrain.com)
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G. A. Thorisson www.gen2phen.org
3rd Human Variome Project Meeting, Paris, 10-14 May, 2010 8
ORCID ID: B-1242-2010G. Thorisson, Univ. LeicesterG. A. Thorisson, Univ. LeicesterG. A. Thorisson, Cold Spring Harbor Lab.
http://mummi.myopenid.com
A digital identity for researchers centred on
scholarly profile?
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G. A. Thorisson www.gen2phen.org
3rd Human Variome Project Meeting, Paris, 10-14 May, 2010
• Identity-enabled access management– Controlling access to protected resources on the Web
• Tracking contributions– data submissions to central repositores
– data curation / micro-attribution
– crucial to bio-resource impact factor + nanopublications
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Data-related applications for digitalidentity (a.k.a ‘researcher IDs’)
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G. A. Thorisson www.gen2phen.org
3rd Human Variome Project Meeting, Paris, 10-14 May, 2010
Cafe RouGE for mutation data exchange
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1. Diagnostic laboratories
2. Central mutation
depot
3. End-users (e.g. LSDB curators)
Publish data
Owen Lancaster, Session 10, Thu 10:10am
Retrieve RSS feeds
•Security•Log in via OpenID and other 3rd party identity (aka ‘outsourced’ security)•Identity-based management of access to non-open data
•Attribution•Link ORCID ID with variation data submissions => publication credit •B-1242-2010 <authored> doi:10.9354/caferouge0005 (Cafe RouGE entry 0005, 19/12/2009)
DOIs for scholarly publications vs DOIs for datasets
http://www.datacite.org
“Our long term vision is to support researchers by providing methods for them to locate, identify, and cite research datasets with confidence.”
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G. A. Thorisson www.gen2phen.org
3rd Human Variome Project Meeting, Paris, 10-14 May, 2010
HGVbaseG2P - a centralgenetic association database
• Controlled access to aggregate GWAS datasets
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http://www.hgvbaseg2p.org Robert Free, Session 10, Thu 11:30am
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G. A. Thorisson www.gen2phen.org
3rd Human Variome Project Meeting, Paris, 10-14 May, 2010
Molgenis-based distributedG2P data infrastructure
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• Identity-based access control + attribution
http://www.molgenis.org Morris Swertz, Session 10, Thu 9:40am
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G. A. Thorisson www.gen2phen.org
3rd Human Variome Project Meeting, Paris, 10-14 May, 2010 13
The GEN2PHEN Strategy
A federated network of databases, not a central database
Data import systems
Data standards
Database solutions
Locus-specific databases
‘Genomics’ G2P databases
Data exchange mechanisms
The GEN2PHEN Knowledge Centre will fully leverage this network
GEN2PHENKnowledge
Centre
http://www.gen2phen.org Adam Webb, Session 10, Thu 9:40am
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G. A. Thorisson www.gen2phen.org
3rd Human Variome Project Meeting, Paris, 10-14 May, 2010 14
GEN2PHEN Consortiumhttp://www.gen2phen.org/about-gen2phen/partners
University of Leicester
-Anthony J. Brookes Bioinformatics Group
Tim Beck
Rob Free
Sirisha Gollapudi
Rob Hastings
Owen Lancaster
Adam Webb
-Raymond Dalgleish
This work has received funding from the European Community's Seventh Framework Programme (FP7/2007-2013)under grant agreement number 200754 - the GEN2PHEN project.
Acknowledgements
Contact me! Gudmundur A. Thorisson <[email protected]>