VIVO conference Aug 2011: The VIVO platform and ORCID in the scholarly identity ecosystem

http://www.orcid.org
G. A. Thorisson, University of Leicester

The VIVO platform and ORCID in the
scholarly identity ecosystem
Gudmundur A. Thorisson <gt50@le.ac.uk>
University of Leicester, United Kingdom
On behalf of the Open Researcher and Contributor ID initiative (http://www.orcid.org)

-- Outline --
• Background (or, how did we get sucked into this identity business?)
• ORCID - Unique IDs for authors/contributors
• Introduction to the initiative
• Update on technical development
• Mini-grant collaborative project
• Thoughts on ORCID & VIVO interop going forward

This work can be freely copied, redistributed and
adapted, as long as proper attribution is given

2nd Annual VIVO Conference, Washington, 24-26 August 2011 1
Friday, 26 August 2011


Prologue



Prof Anthony J Brookes
GEN2PHEN coordinator
Chair, Bioinformatics and Genomics
Department of Genetics
University of Leicester, UK



Cataloguing genome-wide association studies
http://www.gwascentral.org



The data sharing problem in the biosciences



Lack of incentives for sharing research data

• Effort required to prepare, package and submit datasets to public
repositories
• Time better spent writing papers & grants
• All sticks (funders, journals) - no carrots
• Need incentives - treat data as publications and credit creators

“[...] Many of the issues regarding data availability can be
addressed if the principles of “publication” rather than
“sharing” are applied. However, online data publication systems
also need to develop mechanisms for data citation and indices of
data access comparable to those for citation systems in print
journals”

Costello, M. Motivating Online Publication of Data. BioScience (2009) vol. 59 (5) pp. 418-427

7


The identiﬁcation requirement



• Identifying published scholarly works
– Why? So we can..
• ..cite the work unambiguously (‘..we used the method described in Thorisson et al (2009)’)
• ..locate the work (retrieve Nature article as PDF from journal website)
• ..give credit to those persons who contributed to the work (G. Thorisson authored paper X)
– What kind of scholarly works?
• journal articles, books, dataset, blog entries, Wikipedia articles, scientiﬁc software [..]



• Identifying published scholarly works
• ..cite the work unambiguously (‘..we used the method described in Thorisson et al (2009)’)
• ..locate the work (retrieve Nature article as PDF from journal website)
• ..give credit to those persons who contributed to the work (G. Thorisson authored paper X)
– What kind of scholarly works?
• journal articles, books, dataset, blog entries, Wikipedia articles, scientiﬁc software [..]

• Identifying scholarly contributors
• ..link content creators with their works - attribute credit
• ..ﬁgure out: who contributed to publication X?
which publications has Y contributed to?
– What kind of contributions? Characterizing ‘contributorship’
• author, creator, analyst, reviewer, ‘conceived of study & designed experiment’ etc.



Tackling the author name ambiguity problem
(aka ‘Who’s Who?’)

How about these? Or these?
J. Smith
Are these authors all the same person? J. Smith
G. Thorisson, University of Leicester J. Smith
G. A. Thorisson, University of Leicester J. Smith
G. A. Thorisson, Cold Spring Harbor Laboratory J. Smith
[etc.]

∼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)



Introducing the ORCID initiative



The ORCID mission
ORCID will work to support the creation of
a permanent, clear and unambiguous
record of scholarly communication by
enabling reliable attribution of authors and
contributors through unique identifiers



ORCID will add value for scholars and
the organizations that they are
interacting with, including universities,
scholarly societies, funding
organizations and publishers

•Joins faculty or student body
•Joins scholarly society
•Applies for grant
•Submits manuscript



Example use cases for contributor IDs
• Scholar
– I need a list of my publications (and other scholarly output) for this job application.
– What other papers were published by the authors of this interesting paper?

• University
– What was the research output of our institution (departments, individual researchers) last year?
– What open access papers did we publish?

• Scholarly Society
– We want to offer better user proﬁles in our membership database.

– What was the research output of our members last year?

• Funding Agency
– What papers were written by this grant applicant?
– What papers were published as a result of our funding?
– What datasets were made available by this research project?

• Publisher
– We want to better track authors and reviewers in our journal submission system.

– Tell us more about this author, including other papers that he published.
– What potential reviewers have collaborated with this author?


The organization
ORCID transcends discipline, geographic,
national and institutional boundaries



The organization
ORCID is open to any organization with
an interest in scholarly communication



The organization
The Board of Directors represents a
broad cross-section of stakeholders



The infrastructure

?

ORCID

F67572010
ORCID ID: 1242-2010-24
G. Thorisson, Univ. Leicester
G. A. Thorisson, Univ. Leicester
G. A. Thorisson, Cold Spring Harbor Lab.

ORCID ID: 1442-2009-42
J. Smith, Univ. North Pole
ORCID ID: 2400-2010-91
J. Smith, Luthor Corporation

Centralized contributor identification service will:
i) enable researchers to manage & use their ORCID ID
ii) facilitating linking content creators with their published works
iii) interact with other systems (publishers, digital libraries, universities etc)


The infrastructure
ORCID will interact with other scholarly
author identification systems



The infrastructure
Researchers will be able to create and
maintain an ORCID ID and profile free of
charge, and will control their privacy settings



ORCID is serious about being open

Data - all profile data contributed to ORCID by
researchers or claimed by them will be released
under the CC0 waiver

Sourcecode - all software developed by ORCID will
be publicly released under an Open Source
Software license approved by the Open Source
Initiative

Services - mix of free and non-free, but any fees
will be used to ensure the long- term sustainability
of the ORCID system


ORCID technical development



Development Approach

Geoff Bilder, CrossRef
ORCID’s Interim Technical Director 5


Phase I devevelopment - planned beta features

Core ResearcherID.com functionality plus:
• Institutional seeding of profiles (i.e. batch upload, alerting)
• Delegated management of profiles
• Profile exchange into grant/manuscript submission systems
• Fine-grained control of privacy settings at the claim level
– public=”share with anybody”
– protected=”share with parties authorized via OAuth”
– private=”do not share”

• ORCID identifier resolution (both via GUI and REST API)
• Metadata search (both GUI and REST API)



Phase I development - status update
• ResearcherID.com sourcecode donated by Thomson Reuters has
been delivered to ORCID

• Oxford development team hired & Phase I work commenced
– Initial code ‘cleansing’ & de-branding - decouple core s/w from TR’s proprietary stuff
– Current codebase passes core regression tests for core functionality
– Will be released as Open Source (as per Principles!!)

• Timeline for beta ORCID service
– Prospect good for a spring 2012 go-live date for ﬁrst public release
– Developer API access to a test sandbox probably well before this

• API documentation being drafted & discussed by the TWG



Phase I prototype screenshots

2nd Annual VIVO Conference, Washington, 24-26 August 2011


Phase I prototype screenshots



Collaborative development with VIVO



ORCID vs. VIVO: similarities/differences



Mini-grant project outline

• Broad aim = technology evalutation for ORCID
– Get hands-on experience w/ VIVO platform
– analogy: take a radio / sewing machine apart, see how it works (and maybe not be
able to put it together!)
– Can/should ORCID reuse VIVO technology? Lessons learned? Etc.

• Implementation objectives: extend VIVO system to enable
– #1 Searching for and adding publications from external bibliographic system
– #2 Identiﬁcation & exchange of proﬁle information with external system

• Other objectives
– investigate ontological approach (e.g. what can ORCID reuse/repurpose/learn?)
– engage with VIVO community on technical level and build relationships



Hacking VIVO #1

• Objective: enabling VIVO user to interactively search for &
retrieve records from external bibliographic system and add to
their proﬁle
• Implementation stuff:
– JRuby apps running alongside VIVO servlets inside Tomcat
• *very* simple Sinatra app <-- 2x RESTful web service endpoints
• Wrapper API around CrossRef’s SIGG metadata search
– <200 lines of client-side jQuery JavaScript
• Interactive UI bits
• Process biblio-RDF retrieved from DOI metadata service
– JSP hacking
• Modify VIVO UI forms + deal with biblio-RDF
– Freemarker hacking
• More useful reference listing in proﬁle + other UI tweaks



Screenshots from hack #1



Hacking VIVO #2
• Objective: enabling VIVO user to identify him/herself to &
exchange proﬁle data with external service
• Implementation stuff - some more JRuby:
– #1: Embedded Rails app - runs alongside VIVO servlets
• Turns VIVO into OAuth provider <-- works with existing VIVO authentication
• Hooks into VIVO via JRuby-Rack servlet integration (e.g. is user logged in?)
• Reuses existing Rails components, incl. oauth-plugin for most of the OAuth API
– #2: Standalone Rails app
• Demo OAuth consumer app <-- mockup manuscript tracking system
• Reuses existing Rails components, incl. devise for user registration/login/etc.

• Standard API - can in principle point any app to an OAuth-
enabled VIVO instance



Hacking VIVO #2 cont.

• Utility of this proof-of-principle work?
i) User registering his ORCID profile with a journal when submitting manuscript
[and vice versa]
ii) ORCID user linking his VIVO profile with his institutional VIVO profile

• OAuth-based authn/authz will be at the core of ORCID API



• Key next steps to complete mini-grant project

– In OAuth routine, fetch profile as RDF & fish out E-mail, name, affiliation etc.
• use new rich export feature?
• dig back into the ontology and have proper look

– Get hacks work with new VIVO v1.3 release [bonus: will be useful for testing how
easy/hard extensions are to install]

– write report and, erm, write documentation



Sourcecode, docs & community
Code: https://github.com/gthorisson/vivo-orcidextensions
Sandbox: http://vivo.crossref.org

– Disclaimer!! not complete, don’t use yet
– WIMH status ( as in ‘works in my hands’)



Challenges
• Java!
– Documentation - Java codebase largely undocumented

• Ruby!
– learning language+Rails framework, debugging JRuby-rack etc.

• Getting data out of VIVO triplestore - crash course in SPARQL
• Getting data into VIVO triplestore
• Freemarker templates - non-trivial, but fairly logical
• Hacking JSP templates - non-trivial, PITA
• Community participation been tricky
– Other projects / travel / summer vacation / family move between countries
– Timing of weekly VIVO dev calls (am 4-5 hours ahead of Eastern time)



VIVO + ORCID interop



VIVO + ORCID interop

• How can VIVO take advantage of ORCID (2012 beta & beyond)
– Leverage ORCID IDs for integrating with global services (journals, data
repositories)
• NB not nearly all institutions will adopt VIVO
– Retrieve publication claims for researchers from central ORCID registry

• How can ORCID take advantage of VIVO
– VIVO-iﬁed institution could bulk-deposit proﬁle information into ORCID
• pre-registration of research staff
• VIVO could provide set of tools to help inst. implementers with this?
– Explore semantic approach
• how should ORCID interoperate on the semantic level? Ontologies / URIs
• Example utility: nanopub a la Mons et al



Acknowledgements
ORCID Technical Working Group This work has received funding from the
European Community's Seventh
GEN2PHEN Consortium
Framework Programme (FP7/2007-2013)
http://www.gen2phen.org/about-gen2phen/partners under grant agreement number 200754 -
the GEN2PHEN project.

Anthony J. Brookes Bioinformatics Group, Leicester

Contact me!

<gt50@le.ac.uk> |<gthorisson@gmail.com>
http://www.linkedin.com/in/mummi
http://www.twitter.com/gthorisson
http://www.gthorisson.name


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