COMMIT/VIVO

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This presentation describes the use by Data2Semantics (http://www.data2semantics.org) of the VIVO portal (http://vivoweb.org) for interlinking researchers contributing to projects within the COMMIT programme (http://www.commit-nl.nl).

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COMMIT/VIVO

  1. 1. Rinke Hoekstra and Adianto WibisonoVU University Amsterdam/University of Amsterdam rinke.hoekstra@vu.nl
  2. 2. Rinke Hoekstra and Adianto Wibisono VU University Amsterdam/University of Amsterdam rinke.hoekstra@vu.nlWhat is Data2Semantics?
  3. 3. Rinke Hoekstra and Adianto Wibisono VU University Amsterdam/University of Amsterdam rinke.hoekstra@vu.nlWhat is Data2Semantics? What is
  4. 4. Rinke Hoekstra and Adianto Wibisono VU University Amsterdam/University of Amsterdam rinke.hoekstra@vu.nlWhat is Data2Semantics? What is
  5. 5. Rinke Hoekstra and Adianto Wibisono VU University Amsterdam/University of Amsterdam rinke.hoekstra@vu.nlWhat is Data2Semantics? What is
  6. 6. Next Steps... Rinke Hoekstra and Adianto Wibisono VU University Amsterdam/University of Amsterdam rinke.hoekstra@vu.nl What is Data2Semantics? What is
  7. 7. ... first a bit of background
  8. 8. Data to 2 Semantics From Data Semantics for Scientific Data Publishers http://www.data2semantics.org TabLinker Semi-Automatic RDF Converter for Eccentric Excel Files, February 27, 12 Yasgui Provenance Reconstruction COMPLEXITY vs. INTERESTINGNESS ? Data Analysis PROV-O-MaticTM • HUBBLE Python Wrapper script for shell commands https://github.com/Data2Semantics/data/blob/master/src/d2s/prov.py Linked Data Hub for • Output in PROV-O & W3C Time vocabulary Clinical Decision Support
  9. 9. • HUBBLE Python Wrapper script for shell commands https://github.com/Data2Semantics/data/blob/master/src/d2s/prov.py Linked Data Hub for • Output in PROV-O & W3C Time vocabulary Clinical Decision Support • Timestamped URIs for files/resources Hubble demonstrates three ‘sales pitches’ of • ... integrate with GIT? linked data: inter-operability, interlinking and tool availability. • Provenance trail for conversion, loading and linking AERS-LD serious adverse Monday, February 27, 12 event reports exposed as linked data BioPortal SILK link Mesh, specification Google WebToolkit MedDRA, language SnomedCT, Partial Replication From patient to: - Relevant publications etc. and PROV-O acquiring$data$from$text?$ Cloud$ Analysis/ - Related adverse events Semi8 Metrics$ - Clinical trials BioPortal Automa;c$ Annota;on$ e.g.$GATE$ OpenCalais$ Amalgame$ SILK$ Querying$ - Drug information Annotator LOD Cloud Graph$Rewri;ng$ - Known side effects Papers & Graph$Rewri;ng$ and$Ranking$ RDF$ RDF$ Internal$ Link$to$ with UMLS, DBPedia, Conversion$ Cleaning$ Linking$ Other$Data$ - Statistical analysis Guidelines Annotation Sider, Drugbank,xml2rdf$ d2rq$ Visualiza;on$ sgvizler$rdb2rdf$ $ Provenance$ Ontology LinkedCT and Enrichment$ User$ AIDA$Browser$ Interfaces$ Poseidon$(Pirates/Maps)$ PROV-O Semi8 …$ Automa;c$ Conversion$ “tablinker”$ 4Store RDF$Feedback$ Provenance$
  10. 10. Key Points• Build useful services and tools for data publishers ...• ... that maintain provenance information ...• ... and cater for the entire research cycle ...• ... including a feedback loop to new research
  11. 11. One of our use cases ...
  12. 12. • Public-private research community• Emphasis on applications of IT• Emphasis on knowledge transfer• 15 projects• Collaboration with EIT ICT-Labs http://www.eitictlabs.eu/ http://www.commit-nl.nl
  13. 13. Why VIVO?• Demonstrate collaboration within COMMIT/ between projects (synergy), between organizations• Integrate project results with collaboration network shared publications, deliverables Linked Data Rubik’s Cube by Duncan Hull
  14. 14. Why ?
  15. 15. Why ?Most Dutch universities Large companies Government organizations
  16. 16. The Data• COMMIT Website http://www.commit-nl.nl• All project plans (buzzword mining)• All public deliverables (~200 per year)• All participating persons (not just researchers)
  17. 17. “Pilot” • Scraping • Web Karma http://bit.ly/WebKarma
  18. 18. Future Work• Improve people scraper first name, family name, affiliation• Ingest other content deliverables, plans etc.• Shared ontology amongst Dutch VIVO installations• Shared identifiers for researchers in NL (and VIVO) ORCID, ResearcherID, Digital Author ID
  19. 19. Event• Yearly event for all COMMIT people• Tap into registration process to get detailed info• Wireless sensor networks to capture “synergy”• Prizes whatnot...
  20. 20. VIVO Pitfalls• Very “institutional” perspective• How to actively engage individual researchers? Reward mechanisms, integrate with Web 2.0 practices... http://oreilly.com/web2/archive/what-is-web-20.html (2005)
  21. 21. Web 2.0• Web applications generate your data• Rich user experience• You control your own data• Immediate reward• Quality increases by usage
  22. 22. • Lightweight Web Application• Interface to API of existing data repositories• Enrich metadata by linking to Linked Data resources• Provide annotation services for data files• Plugin based architecture• Publish RDF metadata as new data publication
  23. 23. http://linkitup.data2semantics.org
  24. 24. Where to publish the RDF?http://linkitup.data2semantics.org
  25. 25. Where to publish the RDF?Send me more! http://linkitup.data2semantics.org
  26. 26. Future Work• Improve people scraper first name, family name, affiliation• Ingest other content deliverables, plans etc.• Shared ontology amongst Dutch VIVO installations• Shared identifiers for researchers in NL ORCID, ResearcherID, Digital Author ID• ... reward mechanisms for individual authors! http://www.data2semantics.org
  27. 27. Future Work Next week COMMIT/ Data• Improve people scraper first name, family name, affiliation Early March COMMIT/ VIVO Early April COMMIT/ Days• Ingest other content deliverables, plans etc.• Shared ontology amongst Dutch VIVO installations• Shared identifiers for researchers in NL ORCID, ResearcherID, Digital Author ID• ... reward mechanisms for individual authors! http://www.data2semantics.org
  28. 28. Future Work Next week COMMIT/ Data• Improve people scraper first name, family name, affiliation Early March COMMIT/ VIVO Early April COMMIT/ Days• Ingest other content deliverables, plans etc.• Shared ontology amongst Dutch VIVO installations• Shared identifiers for researchers in NL ORCID, ResearcherID, Digital Author ID• ... reward mechanisms for individual authors! http://www.data2semantics.org
  29. 29. Future Work Next week COMMIT/ Data• Improve people scraper first name, family name, affiliation Early March COMMIT/ VIVO Early April COMMIT/ Days• Ingest other content deliverables, plans etc.• Shared ontology amongst Dutch VIVO installations• Shared identifiers for researchers in NL ORCID, ResearcherID, Digital Author ID• ... reward mechanisms for individual authors! http://www.data2semantics.org

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