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WP3 – Information Platform

WP3 – Information Platform. Mário J. Silva Universidade de Lisboa, Faculdade de Ciências, Departamento de Informática mjs@di.fc.ul.pt. What will be necessary to predict epidemics precisely ?. Data of many different types and many unrelated sources .

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WP3 – Information Platform

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  1. WP3 – Information Platform Mário J. Silva Universidade de Lisboa, Faculdade de Ciências, Departamento de Informática mjs@di.fc.ul.pt

  2. Whatwillbenecessary to predictepidemicsprecisely? • Dataofmanydifferenttypesandmanyunrelatedsources. • Improvedaccuracymakesrequired data a never-endingstory • Weallwant to seerealisticandtimelyplotsofepidemicspropagation. • Available, buthard to find, collectandmaintain! 15 Mar 2011 - 2nd Epiwork Review Brussels

  3. Epiwork 15 Mar 2011 - 2nd Epiwork Review Brussels

  4. http://www.gripenet.pt/ 15 Mar 2011 - 2nd Epiwork Review Brussels

  5. Other Internet MonitoringSources 15 Mar 2011 - 2nd Epiwork Review Brussels

  6. Social Media Sources 15 Mar 2011 - 2nd Epiwork Review Brussels

  7. Data.gov.uk, keyword=epidemiology 15 Mar 2011 - 2nd Epiwork Review Brussels

  8. data.gov, epidemiology 15 Mar 2011 - 2nd Epiwork Review Brussels

  9. http://linkeddata.org/ Linked Data 15 Mar 2011 - 2nd Epiwork Review Brussels

  10. Data inEpiwork ClassicSources ModernSources [NationalBureauofStatistics] demographics, transportation data, .. [PublicHealthauthorities] surveillance data (maybe?) [Internet MonitoringSources] [Social Media]behavioural data To besharedbyepidemicmodellersin a digital library, dubbedtheEpidemicMarketplace 15 Mar 2011 - 2nd Epiwork Review Brussels

  11. Epiwork 15 Mar 2011 - 2nd Epiwork Review Brussels

  12. Outline • The need for anEpidemicMarketplace • EpidemicMarketplace 1.0 • D3.3 Public Release of the Epidemic Marketplace Platform • Where we stand and plans for work ahead 15 Mar 2011 - 2nd Epiwork Review Brussels

  13. Steps for Creating the EM • Elaborate meta-model for describing datasets used by epidemic modellers. • Provide query services over the meta-data to discover resources. • Select ontologies for characterizing data and develop an ontology of epidemic concepts. • Ingest, harmonize and cross-link data. • Provide query services to select epidemic data using the EM meta-data and ontologies. 15 Mar 2011 - 2nd Epiwork Review Brussels

  14. CommonReferenceModel • Open domain: detailed description of the datasets used in the models of all sorts of epidemics would require describing virtually every kind of information, given the diversity of factors and the interdisciplinary of epidemiologic studies. • Data model needs to support interlinked data. 15 Mar 2011 - 2nd Epiwork Review Brussels

  15. Meta-dataand Ontologies • The information model of the EM is directly defined as metadata and ontologies. • Ontology and Meta-data standards, the Pros and Cons of using them, annotation and deployment strategies, and the steps for creating an metamodel for epidemic data were the subject of D3.1 reviewed last year. 15 Mar 2011 - 2nd Epiwork Review Brussels

  16. EM: MainComponents 15 Mar 2011 - 2nd Epiwork Review Brussels

  17. EM 1.0 Software Components • Fedora Commons 2.X for the implementation of the main features of the repository. • Access control in the platform • XACML (OASIS 2010), • LDAP (Tuttle et al. 2004) • Shibolleth (identity management). • Front-end based in Muradora • Forum based on phpBB (+ Muradora) 15 Mar 2011 - 2nd Epiwork Review Brussels

  18. Outline • The need for anEpidemicMarketplace • EpidemicMarketplace 1.0 • D3.3 Public Release of the Epidemic Marketplace Platform • Where we stand and plans for work ahead 15 Mar 2011 - 2nd Epiwork Review Brussels

  19. Whatisnewsince Mar 2010? • Improvedreliability • MEDCollector – automatic data collector • Meta-data policies and editor • Web services API + SimpleEM Client • Improveduser interface • Public: anyonecanbrowseandregister(required for upload) 15 Mar 2011 - 2nd Epiwork Review Brussels

  20. ImprovedReliability • Reorganizationsandback-endServicesBeforePublicDeployment • Virtualizedenvironment: every major componentrunningontwoseparate virtual machines - production + developmentenvironments (Xen+CentOS) • Monitoringandalerts for allservices (Nagios) • LoggingandAnalysis (Google Analytics) 15 Mar 2011 - 2nd Epiwork Review Brussels

  21. MEDCollector • Web Services • Workflow Processes • Local Storage • Dashboard for Workflow Design 15 Mar 2011 - 2nd Epiwork Review Brussels

  22. MEDCollector Data Model UMLS: twitter searched ion subset of 89 terms related to “Disease or Syndrome” Geonames.org: All Countries and Capitals 15 Mar 2011 - 2nd Epiwork Review Brussels

  23. MEDCollector Services • Data Collection Services • Query Selection Services • Data Harvesting Services • XML Transformation Services • Database Loading Service • Data Packaging Services • To CSV 15 Mar 2011 - 2nd Epiwork Review Brussels

  24. MEDCollector - BPEL • Language to define how Web-Services Communicate Standard graphical notation – BPMN → Complex! 15 Mar 2011 - 2nd Epiwork Review Brussels

  25. MEDCollector: Dashboard 15 Mar 2011 - 2nd Epiwork Review Brussels • WireIt! - http://javascript.neyric.com/wireit/

  26. MEDCollector: Dashboard Watchthe Demo! 15 Mar 2011 - 2nd Epiwork Review Brussels

  27. AutomaticallyCollected Data 15 Mar 2011 - 2nd Epiwork Review Brussels • Twitter: 89 diseases,world-coverage • ProMed-mail • Google FluTrends • CDC RSS Feeds • Fluupdates • TravelNotices • ... Periodicallypackedanduploaded to the EM repository

  28. Whatisnewsince Mar 2010? • Improvedreliability • MEDCollector – automatic data collector • Meta-data policies and editor • Web services API + Simple EM Client • Improveduser interface • Public: anyonecanbrowseandregister (for upload) 15 Mar 2011 - 2nd Epiwork Review Brussels

  29. Meta-data Policies and Editor • Meta-data introduction simplified • Editor that pops-up on upload now fills most of the entries with appropriate defaults. • EM Repository Meta-data Vocabulary • Generic DCTERMSadopted for datasets characterisation • Epidemics-specific DCTERMS defined for epidemic datasets characterisation 15 Mar 2011 - 2nd Epiwork Review Brussels

  30. DC TermExample: RightsHolder 15 Mar 2011 - 2nd Epiwork Review Brussels

  31. EM TermExample: HostGroup 15 Mar 2011 - 2nd Epiwork Review Brussels

  32. Mediator Web Services Mediator FedoraCommons Repository Client Fetch/Search RESTful Interface OAI-PMH Upload OAI-ORE OpenLDAP 15 Mar 2011 - 2nd Epiwork Review Brussels

  33. Simple EM Client Download from http://epimarketplace.net/mediator/ • Mappingofclientfilenames to EM resources(FC data streamsandCollections) • Operations:Check-out, check-in Watchthe Demo! 15 Mar 2011 - 2nd Epiwork Review Brussels

  34. EM OldGraphicStyle 15 Mar 2011 - 2nd Epiwork Review Brussels

  35. Tryitat:http://epimarketplace.net 15 Mar 2011 - 2nd Epiwork Review Brussels

  36. Outline • The need for anEpidemicMarketplace • The EpidemicMarketplace • D3.3 Public Release of the Epidemic Marketplace Platform • Where we stand and plans for work ahead 15 Mar 2011 - 2nd Epiwork Review Brussels

  37. WP3: status (whatwehavedone) • Deliverable D3.1 (meta-model) released • Deliverable D3.2 (prototype) released • Hardware and base software deployed; • Initialprototypeof EM withinitialsetofcharacterizeddatasets • Deliverable D3.3 (publicversion) released • Data-collector • EM DCAP andmeta-datahandling • Web Services 15 Mar 2011 - 2nd Epiwork Review Brussels

  38. Events 2nd year London, Delhi, Bilbao, ERCIM News 15 Mar 2011 - 2nd Epiwork Review Brussels

  39. EM-relatedPublications(2nd year) • Mário J. Silva, Fabrício A.B. Silva, Luís Filipe Lopes, Francisco M Couto, Building a Digital Library for Epidemic Modelling. Proceedings of ICDL 2010 - The International Conference on Digital Libraries 1, p. 447–459, New Delhi, India, 23–27 February, 2010. TERI Press–New Delhi, India. Invited Paper. • Fabrício A.B. Silva, Mário J. Silva, Francisco M Couto, Epidemic Marketplace: an e-Science Platform for Epidemic Modelling and Analysis. ERCIM News 82 – Special Theme: Computational Biology. July, 2010. • Luis Filipe Lopes, Fabrício A.B. Silva, Francisco M Couto, João Zamite, Hugo Ferreira, Carla Sousa, Mário J. Silva, EpidemicMarketplace: AnInformationManagementSystem for Epidemiological Data. Proceedings of ITBAM'10 - 1st International Conference on Information Technology in Bio- and Medical Informatics - DEXA 2010 August, 2010. • João Zamite, Fabrício A.B. Silva, Francisco M Couto, Mário J. Silva, MEDCollector: MultisourceEpidemic Data Collector. Proceedings of ITBAM'10 - 1st International Conference on Information Technology in Bio- and Medical Informatics - DEXA 2010 August, 2010. • JoãoZamite, Multisource Epidemic Data Collector, Master Dissertation, University of Lisbon, Faculty of Sciences, September 2010. • Luis Filipe Lopes, A Metadata Model for the Annotation of Epidemiological Data, Master Dissertation, University of Lisbon, Faculty of Sciences, September 2010. • Hugo Ferreira, O Mediador do Epidemic Marketplace. Master Dissertation, University of Lisbon, Faculty of Sciences, September, 2010; (in Portuguese). 15 Mar 2011 - 2nd Epiwork Review Brussels

  40. WP3: status (whatwewill do) • Overcomingtheinitialdifficultiesinhiringtheplannedresources • Refreshed team with competencies required for the 2nd and 3rd year; Hiring1 sweng for pushinreleaseof EM 2.0 • Working on Epidemic Marketplace 2.0 • D3.4 and D3.5 due Feb 2012 • site analytics • interlinking • Peekingonhow to addresschallengesfor the 4th year • negotiatingaccess to content 15 Mar 2011 - 2nd Epiwork Review Brussels

  41. In Changesin UL WP3 Team Out Fabrício Silva Luis F. Lopes (meta-data) Hugo Ferreira (mediator) Dulce Domingos (accesscontrol) Juliana Duque (informationarchitecture, graphics) João Ferreira (ontologies) + (alwaysin) Mário Francisco João Zamite 15 Mar 2011 - 2nd Epiwork Review Brussels

  42. ScheduledDeliverables 15 Mar 2011 15 Mar 2011 - 2nd Epiwork Review Brussels

  43. Todo ListandPlanning(Brussels, Mar 2011) • Evolve Simple EM Client and GleamViz to become showcase for tight integration with Computational Platform • Refine and populatethe catalogue of epidemic resources: enrichment, interlinking and semantification of epidemic data • Release second version of the EM.Re-implemented Web Services (no more Muradora)New information architecture, new front-end designNew social network access control 15 Mar 2011 - 2nd Epiwork Review Brussels

  44. OnthenatureofSocIntelligentSystems • Who should learn behaviours about individuals from the network? • No Silver Bullet • “Classic” Engineering approaches too slow for 21st century pace • We are now all part of a huge Living Lab • How much longer will the fact that your cat sneezed be relevant?...we might have to ask again. • Are we still under control? • We may need more flexible ways to control access to sensitive data.. 2 Aug 2010 - Assyst, London

  45. Classical Approaches • Role Based Access Control (RBAC): • Advantages: • Roles are intuitive concepts in organizations • Users can easily be reassigned from one role to another • Disadvantages: • Central Administration has to manage roles • Does not take into account collaborative/social dynamics

  46. Access Control Based on Social Networks • Objects have owners (or publishers) • Owners are part of a social network and define access policies based on the network information

  47. EM 2.0 Software Components • Fedora Commons 3.4 - main features of the repository. • Mediator services reimplemented. Webservicesprovided by FC invoked directly. • Access control in the platform • XACML + LDAP (Tuttle et al. 2004) • Shibolleth (identity management). • Access Control Based on Social Networks • Front-end based in the Drupal CMS • Integrated forum 15 Mar 2011 - 2nd Epiwork Review Brussels

  48. EM 2.0 Mock-up interface http://v2.epimarketplace.net/mockup 15 Mar 2011 - 2nd Epiwork Review Brussels

  49. Weaknesses WP3 SWOT Analysis Strengths Epiwork-driven EM Standards-based OpenSource modules Supported (until 2012) Unchanged ! Unpopulated EM Looking for theright policies What are the incentives? Interfaces to WP4 and WP5? 15 Mar 2011 - 2nd Epiwork Review Brussels

  50. Threats WP3 SWOT Analysis Opportunities Epiworktestbed Creationof a baseline for epidemicmodelling Showcase for partners’ outputs Unchanged ! Consortiumenters “everyone for himself” mode. “Somebodywilltakecareofthat” attitude EM perceived as a veryexpensive, complexanduseless cache 15 Mar 2011 - 2nd Epiwork Review Brussels

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