Bibliography 2.0: A citeulike case study from the Wellcome Trust Genome Campus

Bibliography 2.0: A case study from the Wellcome Trust Genome Campus Dr. Duncan Hull http://twitter.com/dullhunk European Bioinformatics Institute, EBI.ac.uk e-Science workshop: The influence and impact of Web 2.0 on various applications 11th-12th May 2010, Edinburgh

Overview
Introduction: Wellcome Trust Genome Campus
The European Bioinformatics Institute ( ebi.ac.uk )
The Wellcome Trust Sanger Institute ( sanger.ac.uk )
The Library
Problem: economics and “freakonomics” of publishing
The unintended consequences of “publish or perish”
Burying data in publication silos
Obscuring identities and obstructing social applications
Solution? Bibliography 2.0 with citeulike
Incentives
Disincentives
Case study: What we’ve learnt
Conclusions and future work
21.05.10

Wellcome to the Genome Campus
Home of
The European Bioinformatics Institute
The Sanger Institute
Just outside Cambridge, UK

EBI: a data hub for bioinformatics in Europe Literature ebi.ac.uk/citexplore DNA +RNA sequences ebi.ac.uk/ena Genomes: ensembl.org Transcriptomes e.g. ArrayExpress Protein structure ebi.ac.uk/pdbe Protein domains, families ebi.ac.uk/interpro Pathways reactome.org Systems biomodels.net Small molecules ebi.ac.uk/chebi and ebi.ac.uk/chembl Protein sequence uniprot.org Protein protein interactions ebi.ac.uk/intact ~400 staff (research/services), publishing data on the web

21.05.10 e.g. Chemical Entities of Biological Interest (ChEBI) Free database /ontology of 500,000 small molecules (many drugs)

The Wellcome Trust Sanger Institute 21.05.10 Alex Bateman ~900 Sanger staff (total)

Shared Library 21.05.10 Annual Journal subscription budget £500,000 (modest compared to multi million pound journal budgets of university libraries) More later

)
21.05.10 “ People respond to incentives, although not necessarily in ways that are predictable and manifest. Therefore, one of the most powerful laws in the universe is the law of unintended consequences. This applies to schoolteachers and Realtors and crack dealers as well as expectant mothers, sumo wrestlers, bible salesman, and the Ku Klux Klan…” … and scientists too…

Unintended consequences, an example
Incentive: “ publish or perish ”
Publications are rewarded with recognition, hiring, promotion, tenure, fame, funding, fortune, prizes, job satisfaction etc
Unintended consequences :
Valuable data gets damaged, destroyed or “buried” (see later)
Inaccessible to data and text mining on the Web
Copyright and toll-access journals
Luddite scientists
Minimal exploitation of social software for sharing data
Minimal exploitation of Web 2.0 for sharing data
21.05.10

Gene names: e.g. Hexokinase, HK1, HK2, HK3
Protein names: e.g. Hexokinase, HK1, HK2, HK3
Chemical names: e.g. Glucose-6-phosphate, G6P, Glu, Gluc
Author names: e.g. Mark Baker (see next slide)
Poor precision and recall
21.05.10 Why bury it [data] first and then mine it again? Barend Mons, Wikiproteins http://proteins.wikiprofessional.org Which gene did you mean? BMC Bioinformatics. 2005 Jun 7;6:142 DOI:10.1186/1471-2105-6-142

Identity crisis: Mark Baker
http://pubmed.gov?term=Baker+M[author]
http://pubmed.gov?term=Mark+Baker[author]
etc
21.05.10 Until we have unique author identifiers, it is difficult or impossible to reliably find the papers published by a particular person Open Researcher and Contributor ID http://orcid.org “ Tell me whenever Mark Baker publishes a paper”

Social information (need identity for this)
Socialisation: (e-science > “we-science”)
How many other people have read this paper?
What are my friends / enemies reading?
What other papers did they also read?
Personalisation (e-science > “me-science”)
These are my publications
This is my bibliography (stuff I’m reading / have read)
Digital libraries “ document-centred ” rather than “ people-centred ” Author name disambiguation in MEDLINE by: Vetle I. Torvik, Neil R. Smalheiser ACM Trans. Knowl. Discov. Data, Vol. 3, No. 3. (2009), pp. 1-29. DOI:10.1145/1552303.1552304
21.05.10

A solution, citeulike.org?
http://www.citeulike.org
Lack of personalisation of library data
Lack of socialisation of library data
Works a lot like http://www.delicious.com
21.05.10

Click Post to Citeulike 21.05.10

Tag it (optional) e.g. author tags 21.05.10

Journal picks is a group of 40+ invited users on campus, who select interesting papers 21.05.10

21.05.10 2,016 unique articles in journal picks (less than one year) 3,880,055 unique articles total

Citeulike + ZeitGeist = CiteGeist http://www.citeulike.org/citegeist 21.05.10

Citeulike incentives
Selfish scientist (just organise my reference mess)
What’s popular (interesting stuff CiteGeist)
Serendipity (find papers you wouldn’t find normally)
Increase visibility and PageRank of papers?
Person-centred access points into first / second page of Google results
e.g. http://www.google.com/search?q=carole+goble
Has result below fairly high up list,
http://www.citeulike.org/group/10570/tag/carole-goble
21.05.10

Citeulike disincentives
Privacy, don’t want to share with rivals
(but can make collections private)
Citeulike might go bust?
But Springer sponsored
Parsers are fragile
easily (and deliberately) broken by publishers
Valuable data in the hands of a commercial company?
But Facebook? LinkedIn? Twitter etc?
No academic reward for using it
publication = “finished”
Social software works best with network effects
There are LOTS of other tools that do this…
21.05.10

And the rest… 21.05.10 www.mendeley.com www.zotero.org www.connotea.org www.mekentosj.com www.hubmed.org www.refworks.com “ iTunes for PDF files” “ Last.fm of research”

Giant corporate commercial competitors
With significant vested financial interests
Scopus http://www.scopus.com/
ISI WOK http://isiknowledge.com Wrote a review of these systems: Hull, D., S. R. Pettifer, and D. B. Kell (2008). Defrosting the digital library: Bibliographic tools for the next generation web. PLoS Comput Biol 4 (10), e1000204+. DOI:10.1371/journal.pcbi.1000204
21.05.10

Conclusions
“ Publish or perish” has some unfortunate and unintended consequences in science
Citeulike is an interesting Web 2.0 tool
We’ve had some success using it (typical “long tail”)
Weak incentives for use by many cultural barriers to adoption
Technical barriers to adoption, many tools, messy data
Future work
Social network analysis, clickthroughs, tag analysis
Any other ideas…
But the times they are a changin’
Citeulike or something like it will work much better if/when “publishing” incentives change over time…
21.05.10

Acknowledgements
Mark Baker for organising this workshop
EBI, Christoph Steinbeck (laboratory head)
Carole Goble, University of Manchester
The Sanger, Alex Bateman, Frances Martin, Tim Hubbard and all the contributors to the Journal Picks group
Richard Cameron, Kevin Emamy and the rest of the citeulike team
BBSRC for funding
Any questions?
21.05.10

Bibliography 2.0: A citeulike case study from the Wellcome Trust Genome Campus

by Duncan Hull

Accessibility

Categories

Upload Details

Usage Rights

2 Embeds 120

Statistics