myExperiment @ Nettab

Who Are You? Managing collaborative digital identities in bioinformatics with myExperiment Duncan Hull Postdoctoral Research Associate Manchester Biocentre mib.ac.uk , School of Chemistry University of Manchester, UK NETTAB 2009, Catania, Italy, June 2009

Intro: Collaborative social software on the Web generally
Scientists and the web
Publishing
Digital Identity
Sets to the scene for http://www.myexperiment.org in a nutshell
The What, Who and Why and How of myexperiment
Building an online community where Scientists share data more efficiently
Encouraging people to share and re-use data (especially experimental protocols)
Overcoming publish or perish culture
Incentives to share data, tooling to make it as easy as possible
Case Study: REFINE Project http://www.nactem.ac.uk/refine
Refining Pathway models, myExperiment from a personal user point of view ( 40 minutes )
Demonstration of myexperiment ( 30 minutes )
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Social software for collaborating on the Web < 10 yrs old
Designed to allow communication by sharing data with friends, colleagues and other people
http://tinyurl.com/myscience Some people call this “Web 2.0”

Unfortunately
Many scientists don’t use these tools for serious work (if at all)
Why?
It’s complicated but…

Galileo Galilei (1632) Dialogo sopra i due massimi sistemi del mondo

Scientific publishing has worked this way for centuries
Publishing the main (perhaps only) way of sharing data and communicating:
“ Publish or Perish ”

Digital Data Driven Science
Science is increasingly digital and data-driven
Scientists contributions are increasingly digital
Not just digital publications in electronic journals…
wiki edits, software development, workflows, database curation, ontology development, blog posts
Traditional journal publishing is often inadequate for sharing this kind of data and attributing it to individual people

Burying or Destroying Data and Metadata?
Publishing can be inadequte, difficult to mine
Barend Mons Wikiproteins Why bury it [data] first and then mine it again? Which gene did you mean? http://pubmed.gov/15941477 BMC Bioinformatics. 2005 Jun 7;6:142. In other cases important data and metadata gets destroyed completely (author, title, gene, protein, chemical names etc) Make digital libraries difficult to use Defrosting the Digital Library Hull, Pettifer and Kell http://www.pubmed.gov/18974831 PLoS Computational Biology 2008 Oct;4(10):e1000204

Double Trouble!
Scientists reluctant to share data until published in peer-reviewed journals
When they do publish, data often gets badly damaged or destroyed in the process. Digital Identity of people gets especially mangled…
CC licensed double trouble picture by Puck90 http://www.flickr.com/photos/puck90/2480833393/

Digital Identity is currently a mess (part 1)
One person, can be identified by many different URIs
People who know Paolo can tell the difference
People who don’t (and software) face a significant challenge to disambiguate
Digital Identity is a second-class citizen on the Web (see http://www.flickr.com/photos/dullhunk/3618998907/ for web e.g.)
http://www.nettab.org/promano/ (nettab organiser)
mailto:paolo.rmano@istge.it
http://www.paoloromano.it/
en. wikipedia . org/wiki/Paolo_Romano (sculptor)
it. wikipedia .org/wiki/Paolo_Romano (actor)
www.linkedin.com/in/paoloromano
http://pubmed.gov?Term=Paolo+Romano[author]
myspace .com/paoloromano (musician)
www.paoloromano.net/ (politician and friend of Berlusconi)
citeulike . org/tag/paolo-romano
... uni-trier .de/~ley/db/indices/a-tree/r/Romano_0001:Paolo.html
Will the real Paolo Romano please stand up? URI’s are used for identifying people on the web

Digital attribution Neil Smalheiser and Vetle Torvik Attribution would seem to be a simple process and yet it represents a major, unsolved problem for information science. Author name disambiguation Chapter published in Volume 43 (2009) of the Annual Review of Information Science and Technology (ARIST) (edited by B. Cronin) which is available from the publisher Information Today, Inc http://www.hbs.edu/units/tom/seminars/2007/docs/Author%20Name%20Disambiguation.pdf

Misattribution
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

Digital identity is currently a mess (part 2)
On three levels, the three A ’s:
Authentication : is Paolo is who he says he is? Or a fake?
Authorisation : is Paolo authorised to view/operate-on workflow?
Attribution : Paolo AuthorOf Nettab-Workflow or
Paolo Reused Workshop-Workflow
Currently done through combination of username-and-password http://tinyurl.com/too-many-passwords Paolo Romano Simon Willison (The Guardian) The average user has [at least] 18 user accounts and 3.49 passwords”

Digital Identity Really Matters
Digital Identity is fundamental to collaboration because it enables
Attribution …
Contribution…
Publication … to be recorded and quantified.
Important decisions made on digital identity
Hiring, funding, promotion, collaboration
Selecting appropriate reviewers for grants and publications
attributing published data
This is the envionment which myexperiment operates in:
A “Publish or perish” culture in science
Encourage workflow sharing before , during & after traditional publication
Via the website www.myexperiment.org and it’s various API’s
Get digital attribution done right, with more reliable digital identities

What is myExperiment?
Facebook for Scientists?
Collaborative software for sharing and finding experimental protocols on the web

User Profiles
Groups
Friends
Sharing
Tags
Workflows
Developer interface
Credits and Attributions
Fine control over privacy
Packs
Federation
Enactment
What is myExperiment? Unique Selling Points, key differentiators to Facebook etc

Taverna Trident BioExtract Kepler Triana BPEL Ptolemy II

Who is involved in myExperiment?
Small team of developers (2-3 full time)
1500 users have uploaded 560 workflows, 150 files and 40 packs in 130 groups
Carole Goble David De Roure

http://openid.net/ Tackling Digital Identity and attribution

Open ID is quickly becoming widespread
“ 42,235 sites are now enabled to accept OpenID logins” source http://blog.janrain.com/2009/05/relying-party-stats-as-of-may-1-2009.html

But you can’t force OpenID on people…(yet) http://romano.myopenid.com/ [email_address] nettab OR Password handled by third party OpenID provider + 84% 16%

Once logged in, each user gets a profile page identified by a URI

HTML For Developers mySQL Search Engine reviews ratings groups friendships tags Enactor files workflows ` RDF Store SPARQL endpoint Managed REST API facebook iGoogle android XML API config profiles packs credits

PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX myexp: <http://rdf.myexperiment.org/ontology#> PREFIX sioc: <http://rdfs.org/sioc/ns#> select ?friend1 ?friend2 ?acceptedat where {?z rdf:type <http://rdf.myexperiment.org/ontology#Friendship> . ?z myexp:has-requester ?x . ?x sioc:name ?friend1 . ?z myexp:has-accepter ?y . ?y sioc:name ?friend2 . ?z myexp:accepted-at ?acceptedat } All accepted Friendships including accepted-at time Semantically-Interlinked Online Communities SPARQL endpoint: maximises data re-use

future work Phase 2
Repository integration (institutional: EPrints, Fedora)
Controlled vocabularies
Relationships between items (in and between packs)
Recommendations
Improved search ranking and faceted browsing
Indexing of packs
New contribution types (Meandre, Kepler, e-books)
Further blog / wiki integration
Biocatalogue integration
Phase 2

R epresenting E vidence F or I nteracting N etwork E lements

http://www.biomodels.net http://www.sbml.org http://pubmed.gov Case Study REFINE Project: Improving SBML models Metabolic reconstruction Difficult Document level “tools and resources” - fairly straightforward

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

Refine Workflow:
Given SBML file, list all reactions
For each reactant, get synonms (e.g. synonyms of “D-glucose”)
Construct PubMed queries and execute them
Rank results
Display results to user
Workflow itself not rocket science (just a tool that needed to be built) Services 2 and 4 have been based on other people’s workflows saved lots of effort re-inventing the wheel Services 1, 3 and 5 are “private” during prototyping

Of the 661 workflows, 531 are publicly visible whereas 502 are publicly downloadable.
3% of the workflows with restricted access are entirely private to the contributor and for the remaining they elected to share with individual users and groups.
69 workflows (over 10%) have been shared, with the owner granting edit permissions to specific users and groups.
In addition there are 52 instances where users have noted that a workflow is based on another workflow on the site.
The most viewed workflow has 1566 views.
There are 50 packs, ranging from tutorial examples to bundles of materials relating to specific experiments.
C Some preliminary data: First few months of use

Conclusions
myExperiment experience so far has been
Scientists do share data but…
you need to get digital identity right (still an unsolved problem)
Get digital attribution right
Allow fine grained control over what is shared and when with who and with what license…

Conclusions: Aristocracy 2.0 or Democracy 2.0? What will Science 2.0 look like once scientists start sharing more data on the web? We live in exciting times! High barrier to entry, exclusive Low barrier to entry, inclusive Artistocratic ? (program committees, editorial boards, funding panels, academic faculty staff etc) Democratic (“a link is a vote”) and Technocratic (“The geeks shall inherit the earth”) Heavily filtered information (peer review) Lightly filtered information (or not filtered at all) Wisdom of experts Wisdom of Crowds Science 1.0 ? Web 2.0

Conclusions: Participation Inequality: http://www.useit.com/alertbox/participation_inequality.html Dr. Jakob Nielsen 90% of users in online communities are “lurkers” who never contribute

We need you!
It’s all about collaboration
Sign up for an account at http://www.myexperiment.org
Please get in touch if you’d like to join in
Mailing list [email_address]
Questions?
… and now for a live demonstration

Grazie!
Paolo Romano, Rosalba Guigno and the organisers / delegates of NETTAB 2009
Università degli Studi di Catania (University of Catania) for hosting
Rete Nazionale de Bioinformatica Oncologica (Italian Network for Oncology Bioinformatics) http://www.rnbio.it for funding
myExperiment team, led by Dave De Roure, Carole Goble, also Jiten Bhagat, Danius Michaelides, Don Cruickshank, Sergejs Aleksejevs, Paul Fisher, ( Also Kell Group lab members, Paul Dobson and Neil Swainston)
REFINE project, Sophia Ananiadou, Douglas Kell, Steve Pettifer, Jun'ichi Tsujii, Yoshimasa Tsuruoka funded by BBSRC and at http://www.nactem.ac.uk

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myExperiment @ Nettab

by Duncan Hull

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