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

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

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

The VIVO platform and ORCID in the scholarly identity ecosystem

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Gudmundur A. Thorisson <[email protected]>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

Friday, 26 August 2011

mailto:[email protected]


http://www.orcid.org

http://www.orcid.org



Prologue

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Prof Anthony J Brookes GEN2PHEN coordinatorChair, Bioinformatics and GenomicsDepartment of GeneticsUniversity of Leicester, UK




Cataloguing genome-wide association studieshttp://www.gwascentral.org

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http://www.gwascentral.org/

http://www.gwascentral.org/



The data sharing problem in the biosciences

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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

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“[...] 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




The identification requirement

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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 [..]

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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 scholarly contributors– Why? So we can..

• ..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.

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

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Are these authors all the same person?G. Thorisson, University of LeicesterG. A. Thorisson, University of 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)

How about these?




Introducing the ORCID initiative

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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

The ORCID mission




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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?

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The organization

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ORCID transcends discipline, geographic,national and institutional boundaries




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

The organization




The organization

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




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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)

ORCID

F67572010

?

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

ORCID ID: 1442-2009-42J. Smith, Univ. North Pole

ORCID ID: 2400-2010-91J. Smith, Luthor Corporation

The infrastructure




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ORCID will interact with other scholarly author identification systems

The infrastructure




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

The infrastructure




ORCID is serious about being open

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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

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Development Approach

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Geoff Bilder, CrossRefORCID’s Interim Technical Director




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)

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• 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

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Phase I development - status update




Phase I prototype screenshots





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Collaborative development with VIVO

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ORCID vs. VIVO: similarities/differences

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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

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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

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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

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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

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• 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

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Sourcecode, docs & community

– Disclaimer!! not complete, don’t use yet

– WIMH status ( as in ‘works in my hands’)

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Code: https://github.com/gthorisson/vivo-orcidextensionsSandbox: http://vivo.crossref.org


https://github.com/gthorisson/vivo-orcidextensions

https://github.com/gthorisson/vivo-orcidextensions

http://vivo.crossref.org/

http://vivo.crossref.org/



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)

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VIVO + ORCID interop

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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

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ORCID Technical Working Group

GEN2PHEN Consortium

http://www.gen2phen.org/about-gen2phen/partners

Prof Anthony J. Brookes Bioinformatics Group, Leicester

This work has received funding from the European Community's Seventh Framework Programme (FP7/2007-2013)under grant agreement number 200754 - the GEN2PHEN project.

Contact me!

<[email protected]> |<[email protected]>http://www.linkedin.com/in/mummihttp://www.twitter.com/gthorisson

http://www.gthorisson.name

Acknowledgements








http://www.linkedin.com/in/mummi

http://www.linkedin.com/in/mummi

http://www.twitter.com/gthorisson




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