myExperiment @ Nettab


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Digital Identity is fundamental to collaboration in bioinformatics research and development because it enables attribution, contribution, publication to be recorded and quantified.
However, current models of identity are often obsolete and have problems capturing both small contributions "microattribution" and large contributions "mega-attribution" in Science. Without adequate identity mechanisms, the incentive for collaboration can be reduced, and the utility of collaborative social tools hindered.
Using examples of metabolic pathway analysis with the taverna workbench and, this talk will illustrate problems and solutions to identifying scientists accurately and effectively in collaborative bioinformatics networks on the Web.

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  • myExperiment @ Nettab

    1. 1. Who Are You? Managing collaborative digital identities in bioinformatics with myExperiment Duncan Hull Postdoctoral Research Associate Manchester Biocentre , School of Chemistry University of Manchester, UK NETTAB 2009, Catania, Italy, June 2009
    2. 2. <ul><li>Intro: Collaborative social software on the Web generally </li></ul><ul><ul><li>Scientists and the web </li></ul></ul><ul><ul><li>Publishing </li></ul></ul><ul><ul><li>Digital Identity </li></ul></ul><ul><li>Sets to the scene for in a nutshell </li></ul><ul><ul><li>The What, Who and Why and How of myexperiment </li></ul></ul><ul><ul><li>Building an online community where Scientists share data more efficiently </li></ul></ul><ul><ul><li>Encouraging people to share and re-use data (especially experimental protocols) </li></ul></ul><ul><ul><ul><li>Overcoming publish or perish culture </li></ul></ul></ul><ul><ul><ul><li>Incentives to share data, tooling to make it as easy as possible </li></ul></ul></ul><ul><li>Case Study: REFINE Project </li></ul><ul><ul><li>Refining Pathway models, myExperiment from a personal user point of view ( 40 minutes ) </li></ul></ul><ul><li>Demonstration of myexperiment ( 30 minutes ) </li></ul>@
    3. 3. Social software for collaborating on the Web < 10 yrs old <ul><li>Designed to allow communication by sharing data with friends, colleagues and other people </li></ul> Some people call this “Web 2.0”
    4. 4. Unfortunately <ul><li>Many scientists don’t use these tools for serious work (if at all) </li></ul><ul><li>Why? </li></ul><ul><li>It’s complicated but… </li></ul>
    5. 5. Galileo Galilei (1632) Dialogo sopra i due massimi sistemi del mondo
    6. 6. Scientific publishing has worked this way for centuries <ul><li>Publishing the main (perhaps only) way of sharing data and communicating: </li></ul><ul><li>“ Publish or Perish ” </li></ul>
    7. 7. Digital Data Driven Science <ul><li>Science is increasingly digital and data-driven </li></ul><ul><ul><li>Scientists contributions are increasingly digital </li></ul></ul><ul><ul><li>Not just digital publications in electronic journals… </li></ul></ul><ul><ul><li>wiki edits, software development, workflows, database curation, ontology development, blog posts </li></ul></ul><ul><ul><li>Traditional journal publishing is often inadequate for sharing this kind of data and attributing it to individual people </li></ul></ul>
    8. 8. Burying or Destroying Data and Metadata? <ul><li>Publishing can be inadequte, difficult to mine </li></ul>Barend Mons Wikiproteins Why bury it [data] first and then mine it again? Which gene did you mean? 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 PLoS Computational Biology 2008 Oct;4(10):e1000204
    9. 9. Double Trouble! <ul><li>Scientists reluctant to share data until published in peer-reviewed journals </li></ul><ul><li>When they do publish, data often gets badly damaged or destroyed in the process. Digital Identity of people gets especially mangled… </li></ul>CC licensed double trouble picture by Puck90
    10. 10. Digital Identity is currently a mess (part 1) <ul><li>One person, can be identified by many different URIs </li></ul><ul><li>People who know Paolo can tell the difference </li></ul><ul><ul><li>People who don’t (and software) face a significant challenge to disambiguate </li></ul></ul><ul><li>Digital Identity is a second-class citizen on the Web (see for web e.g.) </li></ul><ul><li> (nettab organiser) </li></ul><ul><li> </li></ul><ul><li> </li></ul><ul><li>en. wikipedia . org/wiki/Paolo_Romano (sculptor) </li></ul><ul><li>it. wikipedia .org/wiki/Paolo_Romano (actor) </li></ul><ul><li> </li></ul><ul><li>[author] </li></ul><ul><li>myspace .com/paoloromano (musician) </li></ul><ul><li> (politician and friend of Berlusconi) </li></ul><ul><li>citeulike . org/tag/paolo-romano </li></ul><ul><li>... uni-trier .de/~ley/db/indices/a-tree/r/Romano_0001:Paolo.html </li></ul>Will the real Paolo Romano please stand up? URI’s are used for identifying people on the web
    11. 11. 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
    12. 12. Misattribution <ul><li>Google Scholar thinks I’m Maurice Wilkins </li></ul>Dr. Duncan Hull Humble Postdoc Article about Authored-by Authored-by Wrong! “ DNA mania” title
    13. 13. Digital identity is currently a mess (part 2) <ul><li>On three levels, the three A ’s: </li></ul><ul><ul><li>Authentication : is Paolo is who he says he is? Or a fake? </li></ul></ul><ul><ul><li>Authorisation : is Paolo authorised to view/operate-on workflow? </li></ul></ul><ul><ul><li>Attribution : Paolo AuthorOf Nettab-Workflow or </li></ul></ul><ul><ul><li>Paolo Reused Workshop-Workflow </li></ul></ul>Currently done through combination of username-and-password Paolo Romano Simon Willison (The Guardian) The average user has [at least] 18 user accounts and 3.49 passwords”
    14. 14. Digital Identity Really Matters <ul><li>Digital Identity is fundamental to collaboration because it enables </li></ul><ul><ul><li>Attribution … </li></ul></ul><ul><ul><li>Contribution… </li></ul></ul><ul><ul><li>Publication … to be recorded and quantified. </li></ul></ul><ul><li>Important decisions made on digital identity </li></ul><ul><ul><li>Hiring, funding, promotion, collaboration </li></ul></ul><ul><ul><li>Selecting appropriate reviewers for grants and publications </li></ul></ul><ul><ul><li>attributing published data </li></ul></ul><ul><li>This is the envionment which myexperiment operates in: </li></ul><ul><ul><li>A “Publish or perish” culture in science </li></ul></ul><ul><ul><li>Encourage workflow sharing before , during & after traditional publication </li></ul></ul><ul><ul><ul><li>Via the website and it’s various API’s </li></ul></ul></ul><ul><ul><li>Get digital attribution done right, with more reliable digital identities </li></ul></ul>
    15. 15. What is myExperiment? <ul><li>Facebook for Scientists? </li></ul><ul><li>Collaborative software for sharing and finding experimental protocols on the web </li></ul>
    16. 16. <ul><li>User Profiles </li></ul><ul><li>Groups </li></ul><ul><li>Friends </li></ul><ul><li>Sharing </li></ul><ul><li>Tags </li></ul><ul><li>Workflows </li></ul><ul><li>Developer interface </li></ul><ul><li>Credits and Attributions </li></ul><ul><li>Fine control over privacy </li></ul><ul><li>Packs </li></ul><ul><li>Federation </li></ul><ul><li>Enactment </li></ul>What is myExperiment? Unique Selling Points, key differentiators to Facebook etc
    17. 17. Taverna Trident BioExtract Kepler Triana BPEL Ptolemy II
    18. 18. Who is involved in myExperiment? <ul><li>Small team of developers (2-3 full time) </li></ul><ul><li>1500 users have uploaded 560 workflows, 150 files and 40 packs in 130 groups </li></ul>Carole Goble David De Roure
    19. 19. Tackling Digital Identity and attribution
    20. 20. Open ID is quickly becoming widespread <ul><li>“ 42,235 sites are now enabled to accept OpenID logins” source </li></ul>
    21. 21. But you can’t force OpenID on people…(yet) [email_address] nettab OR Password handled by third party OpenID provider + 84% 16%
    22. 22. <ul><li>Once logged in, each user gets a profile page identified by a URI </li></ul>
    23. 26. 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
    24. 27. PREFIX rdf: <> PREFIX myexp: <> PREFIX sioc: <> select ?friend1 ?friend2 ?acceptedat where {?z rdf:type <> . ?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
    25. 28. future work Phase 2 <ul><li>Repository integration (institutional: EPrints, Fedora) </li></ul><ul><li>Controlled vocabularies </li></ul><ul><li>Relationships between items (in and between packs) </li></ul><ul><li>Recommendations </li></ul><ul><li>Improved search ranking and faceted browsing </li></ul><ul><li>Indexing of packs </li></ul><ul><li>New contribution types (Meandre, Kepler, e-books) </li></ul><ul><li>Further blog / wiki integration </li></ul><ul><li>Biocatalogue integration </li></ul>Phase 2
    26. 29. R epresenting E vidence F or I nteracting N etwork E lements
    27. 30. Case Study REFINE Project: Improving SBML models Metabolic reconstruction Difficult Document level “tools and resources” - fairly straightforward
    28. 31. Example from Glycolysis in Yeast reactant reactant product product modifier This is just one reaction, there are at least another 1700+ in Yeast
    29. 32. Refine Workflow: <ul><li>Given SBML file, list all reactions </li></ul><ul><li>For each reactant, get synonms (e.g. synonyms of “D-glucose”) </li></ul><ul><li>Construct PubMed queries and execute them </li></ul><ul><li>Rank results </li></ul><ul><li>Display results to user </li></ul>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
    30. 33. <ul><li>Of the 661 workflows, 531 are publicly visible whereas 502 are publicly downloadable. </li></ul><ul><li>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. </li></ul><ul><li>69 workflows (over 10%) have been shared, with the owner granting edit permissions to specific users and groups. </li></ul><ul><li>In addition there are 52 instances where users have noted that a workflow is based on another workflow on the site. </li></ul><ul><li>The most viewed workflow has 1566 views. </li></ul><ul><li>There are 50 packs, ranging from tutorial examples to bundles of materials relating to specific experiments. </li></ul>C Some preliminary data: First few months of use
    31. 34. Conclusions <ul><li>myExperiment experience so far has been </li></ul><ul><li>Scientists do share data but… </li></ul><ul><ul><li>you need to get digital identity right (still an unsolved problem) </li></ul></ul><ul><ul><li>Get digital attribution right </li></ul></ul><ul><li>Allow fine grained control over what is shared and when with who and with what license… </li></ul>
    32. 35. 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
    33. 36. Conclusions: Participation Inequality: Dr. Jakob Nielsen 90% of users in online communities are “lurkers” who never contribute
    34. 37. We need you! <ul><li>It’s all about collaboration </li></ul><ul><li>Sign up for an account at </li></ul><ul><li>Please get in touch if you’d like to join in </li></ul><ul><li>Mailing list [email_address] </li></ul><ul><li>Questions? </li></ul><ul><li>… and now for a live demonstration </li></ul>
    35. 38. Grazie! <ul><li>Paolo Romano, Rosalba Guigno and the organisers / delegates of NETTAB 2009 </li></ul><ul><li>Università degli Studi di Catania (University of Catania) for hosting </li></ul><ul><li>Rete Nazionale de Bioinformatica Oncologica (Italian Network for Oncology Bioinformatics) for funding </li></ul><ul><li>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) </li></ul><ul><li>REFINE project, Sophia Ananiadou, Douglas Kell, Steve Pettifer, Jun'ichi Tsujii, Yoshimasa Tsuruoka funded by BBSRC and at </li></ul>
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