Defrosting the Digital Library: A survey of bibliographic tools for the next generation web

Defrosting the Digital Library A survey of bibliographic tools for the next generation Web Duncan Hull Faculty of Life Sciences (1992-6) BSc. Computer Science (2002-2007) MSc, PhD. Chemistry (2008-date) Postdoc

It’s all Casey’s fault! Dr. Casey Bergman, Lecturer Faculty of Life Sciences I s Citeulike.org! http://ukpmc.ac.uk/

http://pubmed.gov/19060304

Defrosting the Digital Library (in one slide)
There are lots of digital libraries out there for scientists!
ACM, IEEE, PubMed, DBLP, Scopus, ISI-WoK, Google Scholar, arXiv
But they have some fundamental problems with their data
Identity crisis: identifying people accurately
Identity crisis: identifying publications accurately
Keeping data and metadata coupled together
Impersonal, unsociable, difficult to use: “Cold”
Some new tools exist to make things better: “warmer”
Citeulike, Mendeley, Zotero, Papyro, Papers etc
BUT Fundamental problems with identity and data need to be fixed before the tools will get any better

Metawhat? getMetadata getData
From the Greek μετ ά (meta) meaning after
metadata not just data about data
metadata is data after data
data first
metadata second
Reversible reaction (“round-tripping”)
Title: defrosting the digital library Authors: Duncan Hull, Steve Pettifer and Douglas Kell Published: 2008 Journal: PLoS Computational Biology Tell me more? What is it about? Where did it come from?

Metadata in: Chemistry (Science of Matter) Biology (Science of Life) Informatics (Science of Information) Cheminformatics Biochemistry Bioinformatics Science! www.mib.ac.uk nactem.ac.uk/refine www.citeulike.org

R epresenting E vidence F or I nteracting N etwork E lements www.sbml.org from www.biomodels.net database at the EBI.ac.uk

Example from Glycolysis in Yeast reactant reactant product product modifier This is just one reaction, there are at least another 1700+ in Yeast

Synonyms from Pedro Mendes B-Net Database http://www.comp-sys-bio.org/yeastnet/ Robison ester, D-Glucose 6-phosphate Glucose-6-phosphate 5'-adenylphosphoric acid; Adenosine 5'-diphosphate; H3adp ADP Hexokinase-1; Hexokinase-A; Hexokinase PI; YFR053C Hexokinase Adenosine 5'-triphosphate; Adenosine triphosphate; H4atp ATP dextrose; D-Glucose; D-(+)-glucose; D(+)-glucose; grape sugar; Traubenzucker D-Glucose Synonyms Name

Chemistry Biology Informatics Cheminformatics Biochemistry Bioinformatics

For more info. www.nactem.ac.uk/refine One of the biggest challenges is getting hold of accurate metadata from libraries and databases

But first…
Before getting into the paper…
Some lessons I learnt while working in industrial informatics for a small startup company called CSW Informatics Ltd
Ford and BBC
How business and governments manage metadata

Ford Focus (launched 1998)
getMetadata getData 6 million+ “units” sold worldwide to date: america, europe, middle east, africa, australasia Lots of data, metadata and money! Owner’s handbook Tell me more? What is it about?

Final solution: Web XSLT Print

Summary: Lessons from Ford
Data often the tip of the iceberg
If the data doesn’t sink you, the metadata will
Businesses like Ford spent $ £ € keeping data and metadata stay together
Data is often worthless without it
Can’t sell data (cars) without metadata (manuals)
Don’t just “make cars”
DATA METADATA

BBC Spooks?
Open Source Intelligence (OSINT)
Overt not Covert espionage: 370 journalists, 24-7, ~100 languages Caversham, Reading.
Keeping an eye on people around the world since 1939 Winston Churchill “ B ig B ritish C astle” (BBC)

I hate powerpoint Radio MS Word TV

How do they stay in business? Broadcasting House, London Foreign governments, e.g. U.S.A. etc

Word: Not the best way to manage data and metadata

Getting Rid of Word database XML schema Web & Intranet Printed documents XSLT

A solution that worked! getMetadata getData Who is Thabo Mbeki? These documents are all about Thabo Mbeki Thabo Mbeki

Summary: Lessons from the BBC
Important decisions made on the basis metadata
Crucial that metadata is accurate, high quality and trustworthy
Identify people properly is crucial (100%)
You know what data is about (getMetadata)
You know where it came from (getData)
Looked after properly (this can be expensive)
Businesses built on buying/selling metadata:

How have libraries managed metadata?
On paper since 300 B.C.
(Library of Alexandria)
Organised in physical space
In buildings made from bricks and mortar
Expensive and slow distribute
Only ever read by humans
Filled with content bought from publishers, locked up with copyright 
Image via http://en.wikipedia.org/wiki/Library_of_Alexandria

From ~1824 until ~1989 Photos via dpicker http://www.flickr.com/photos/dpicker/3107856991/ and pit yacker http://www.flickr.com/photos/78825653@N00/131611136 JRULM (Main Library) Joule Library Mostly “private” only available to an elite (e.g. University of Manchester Students and Staff)

Metadata (after)
Data Tightly bound (literally) Rarely separated First published 1687, over 300 years old

Data and metadata was like this for centuries!
Until…

+ Tim Berners-Lee 1989

Timeline: Unchanged for centuries but… 20 years ÷ 2309 years = <1%

Everything’s Gone Digital! www.scopus.com www.pubmed.gov http://ukpmc.ac.uk www. isiknowledge .com scholar.google.com

Digital Utopia?
Bits and bytes 1010100101000001101010 (not paper)
In pervasive cyberspace (not physical space)
Databases and/or Web identified by URIs: (not buildings)
Cost of distribution fallen by orders of magnitude
Read and indexed by machines like Googlebot et al (not just humans)
Increasingly public, available to everyone via Open-Access publishing (less private, less restrictive copyright)
Everything is great?
Alexander Griekspoor www.mekentosj.com

Welcome to Digital Dystopia
Isolation
each discipline has its own data silo
Impersonal and unsociable
“ who the hell are you”?
Where are “my” papers? (authored by me, or of interest to me)
What are my friends and colleagues reading?
What are the experts reading? What is popular this week / month / year ?
“ Cold”: Identity of publications and authors is inadequate
Data divorced from its metadata
GetMetadata / GetData unreliable
Therefore can be difficult to tell what data is about, or where metadata came from
Obsolete models of publication, not everything fits publication-sized holes
Micro-attribution
Mega-attribution
Digital contributions (databases, software, wikis/blogs?)

Isolated publication silos Chemistry Informatics Biology impersonal, isolated, unsociable, Generally rubbish

Identity Crisis part 1: Which publication?
http://www.ncbi.nlm.nih.gov/pubmed/18974831
http://ukpmc.ac.uk/articlerender.cgi?accid=pmcA2568856
http://ukpmc.ac.uk/picrender.cgi?artid=1687256&blobtype=pdf
http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000204
http://www.dbkgroup.org/Papers/hull_defrost_ploscb08.pdf
http://dx.doi.org/10.1371/journal.pcbi.1000204
One paper, many URIs. Disambiguation algorithms rely on getting metadata for each
Big problem for libraries is these redundant duplicates
Matching can be done by Digital Object Identifier (DOI) and PubMed ID (PMID);
these are frequently absent < 5% (Kevin Emamy, citeulike)

Identity crisis part 2: Who are you? Who, who … who, who?
Douglas Kell
Doug Kell
Douglas B Kell
Kell, D
Kell, D.B.
Douglas Bruce Kell
Druglas Kell
Neil Smalheiser and Vetle Torvik Typo Attribution would seem to be a simple process and yet it represents a major, unsolved problem for information science. http://tinyurl.com/authorid

Identity crisis part 3: Mistaken Identity
Google Scholar thinks I’m Maurice Wilkins
Dr. Duncan Hull Humble Postdoc Article about Authored-by Authored-by Wrong! “ DNA mania” title http://tinyurl.com/mistakenid

Can’t get metadata (decoupled from data): PDF getMetadata getData Title: defrosting the digital library Authors: Duncan Hull, Steve Pettifer and Douglas Kell Published: 2008 Tell me more Don’t know, Try google Don’t know, Title might be “ defrosting…” Where did this come from?

Can’t get metadata (decoupled from data): PDF
MP3 music file in iTunes
Why can't I manage academic papers like MP3s? http: //tinyurl .com/mp3vpdf James Howison, Carnegie Mellon University Data is tightly coupled to its metadata getMetadata getData Artist: The Who Title: Who Are You? Recorded: 1978 Album: Who Are You

Can’t get metadata (decoupled from data): PDF Peter Murray-Rust Hamburger (unstructured data) PDF is a hamburger, and we're trying to turn it back into a cow. http://tinyurl.com/pdfhamburger Cow (structured data) publishing text-mining

Can’t get metadata (decoupled from data): HTTP
Arbitrary URI (not just pubmed, but any scientific paper) http://www.ncbi.nlm.nih.gov/pubmed/18974831

Can’t get metadata (decoupled from data): HTTP
Fundamental problem with the way the web is built using HTTP, can’t change it now…
Tim Bray, Sun Microsystems One of the Web's distinguishing features is that there's a big gaping hole where the metadata ought to be. http://tinyurl.com/nometadata

I’ll stop moaning now
Isolation
Can’t identify people
Can’t identify publications
Metadata gets divorced from its data
But what are the solutions?

www.citeulike.org Richard Cameron Kevin Emamy Picture from http://network.nature.com/people/mfenner/blog/2009/01/30/interview-with-kevin-emamy and http://www.citeulike.org/faq/faq.adp The reason I wrote the site [citeulike.org] was, after recently coming back to academia, I was slightly shocked by the quality of some of the tools available to help academics do their job. I found it preferable to start writing proper tools for my own use than to use existing software.

Why should you care about citeulike?
Could save you time
But also like Green Fluorescent Protein…

All references in one place

Click Post to Citeulike

Tag it (optional)

Citeulike: Recoupling data and metadata
Wouldn’t be a problem if the publishers hadn’t decoupled it in the first place!

Citegeist = Citeulike + Zeitgeist

allegedly 2,243,177 ~2,000 /day variable 674,076 2,880 /day 2 papers / min Linear growth ~500,000

Where will citeulike break?
The more people that use “social software”, the better they get
Citeulike is one of the leading ones, but there is plenty of competition
Parsers are fragile, easily (and deliberately) broken by publishers
ISI WOK and Scopus
Each publisher has its own parser (euuuggh!)
Privacy and competition
“ I don’t want to share any of my data before publication”
“ It’s nobody’s business but mine” (basic human right to privacy)
Closer integration with Word (and latex tools)
Might go bust? Why put all my precious data in the hands of a commercial company?

Why should you bother with citeulike?
Organisation and time saving
Searching
Browsing
Managing references while writing papers
Quick and efficient sharing of data before publication
e.g. tag “defrost” when writing this paper
http://www.citeulike.org/tag/defrost
Serendipity
Casey Bergman story

Casey Bergman story I was importing papers on solexa and 454 genome assembly and came across the following paper: http://www. citeulike .org/user/cisevol/article/1465689 which was a real find in terms of convincing me that light shotgun sequence data is worth analysing. I nicked this from a phd student's library in Brazil http://www. citeulike . org/profile/GustavoLacerda Wouldn’t have found this any other way e.g (keyword searching or following citation trails)

Many different solutions e.g. Papyro: Steve Pettifer http://utopia.cs.manchester.ac.uk/

And the rest… www.mendeley.com www.zotero.org www.connotea.org www.mekentosj.com www.hubmed.org Re-couple metadata that has be de-coupled from data www.2collab.com www.refworks.com “ iTunes for PDF files”

There is still lots more metadata How many times has http://pubmed.gov/19060304 been cited? Who has cited http://pubmed.gov/19060304 ? Give me all the references that cite this one Give me all the references cited by http://pubmed.gov/19060304 Who the hell is Doug Kell? Steve Pettifer? Duncan Hull? What is Doug Kell’s h-index? Remember: Machines ask these questions, not just humans Notify me whenever Steve Pettifer publishes a paper Notify me whenever someone cites http://pubmed.gov/19060304 Impact factor?

Digital Identity would solve some of these problems Give yourself a URI, you deserve it! Tim Berners-Lee http://www.w3.org/People/Berners-Lee/card#i see http://dig.csail.mit.edu/breadcrumbs/node/71

URI’s for Douglas Kell
http://blogs.bbsrc.ac.uk
http://www.chemistry.manchester.ac.uk/aboutus/staff/showprofile.php?id=194
http://dbkgroup.org/kell.htm
http://douglaskell.myopenid.com
http://dx.doi.org/10.1371/journal.pcbi.1000204
“ Contributor identifier” from
www.myopenid.com www.openid.net (Also Note researcher-id from thomson)

Phil Bourne

John Ziman, Physicist
Science is public knowledge http://tinyurl.com/publicknowledge

Conclusions: What hasn’t changed
The Web has revolutionised libraries in just 20 short years but…
Still takes time for humans to read and digest: We can get more papers but there are still only 24 hours in a day, 7 days in a week, 52 weeks in a year
We need help from machines (and the people that build them)
Need to make metadata more machine-friendly

Conclusions: Publication metadata matters
Managed to convince you metadata matters (and why)
People make important decisions based on metadata
Funding
Hiring (and Firing)
Publishing
Who to collaborate with
Yet our current libraries can’t even accurately identify crucial metadata
Individual people - digital identity needed
Publications - disambiguation
Everything else…

Conclusions: Scientists are too blasé about metadata!
Leave it to stamp collectors, dusty-librarians, informaticians, database administrators (yawn!), “biocurators” http://biocurator.org/
Boring, unscientific, not cutting-edge innovation?
Everyone wants to use good metadata but few people want to spend time curating and cleaning metadata
Like a clean toilet
We ignore metadata at our peril “not my job”
We leave it to publishers, who then mess it up, and charge us for their services, we should be getting better value for money
We waste precious time organising metadata
We waste precious time searching for metadata
Data is more valuable with better metadata
Have a look at citeulike (and other tools)
metadata

Conclusions: Do us a favour!

Acknowledgements
Refine project: Sophia Ananiadou, Jun'ichi Tsujii, Pedro Mendes, Steve Pettifer, Yoshimasa Tsuruoka, Douglas Kell www.nactem.ac.uk/refine
BBSRC grant code BB/E004431/1
CSW Informatics Ltd.: John Chelsom, Mavis Cournane, Niki Dinsey www.csw.co.uk BBC Monitoring, Ford Motor Company
School of Chemistry, MIB (now) www.mib.ac.uk
Faculty of Life Sciences (a long long time ago) and Casey Bergman, Jean-Marc Schwartz (now)
School of Computer Science (not so long ago) Information Management Group http://img.cs.man.ac.uk/
Any Questions?

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Defrosting the Digital Library: A survey of bibliographic tools for the next generation web

by Duncan Hull on Mar 16, 2009

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