commit/vivo
Post on 12-Sep-2014
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DESCRIPTION
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).TRANSCRIPT
Rinke Hoekstra and Adianto WibisonoVU University Amsterdam/University of Amsterdam
Rinke Hoekstra and Adianto WibisonoVU University Amsterdam/University of Amsterdam
What is Data2Semantics?
Rinke Hoekstra and Adianto WibisonoVU University Amsterdam/University of Amsterdam
What is Data2Semantics? What is
Rinke Hoekstra and Adianto WibisonoVU University Amsterdam/University of Amsterdam
What is Data2Semantics? What is
Rinke Hoekstra and Adianto WibisonoVU University Amsterdam/University of Amsterdam
What is Data2Semantics? What is
Rinke Hoekstra and Adianto WibisonoVU University Amsterdam/University of Amsterdam
What is Data2Semantics?
Next Steps...
What is
... first a bit of background
to2Data Semantics
Semantics for Scientific Data PublishersFrom Data
HUBBLE Linked Data Hub for Clinical Decision Support
PROV-O-MaticTM
• Python Wrapper script for shell commandshttps://github.com/Data2Semantics/data/blob/master/src/d2s/prov.py
• Output in PROV-O & W3C Time vocabulary
• Timestamped URIs for files/resources
• ... integrate with GIT?
• Provenance trail for conversion, loading and linking
Monday, February 27, 12
TabLinkerSemi-Automatic RDF Converter for Eccentric Excel Files
Monday, February 27, 12
Partial Replication
Yasgui
COMPLEXITY vs. INTERESTINGNESS
?
Data Analysis
Provenance Reconstruction
http://www.data2semantics.org
RDF$Conversion$
RDF$Cleaning$
Internal$Linking$
Link$to$Other$Data$
Semi8Automa;c$Annota;on$
Cloud$
Provenance$Enrichment$
acquiring$data$from$text?$
xml2rdf$d2rq$
rdb2rdf$$
e.g.$GATE$OpenCalais$
AIDA$Browser$Poseidon$(Pirates/Maps)$
…$
SILK$Amalgame$Graph$Rewri;ng$Graph$Rewri;ng$
Provenance$
Analysis/Metrics$
Querying$and$Ranking$
Visualiza;on$
User$Interfaces$
sgvizler$
RDF$Feedback$
Semi8Automa;c$Conversion$
“tablinker”$
to2Data Semantics
Semantics for Scientific Data PublishersFrom Data
AERS-LDserious adverse
event reportsexposed as linked data
Papers & Guidelines
BioPortalMesh,
MedDRA,SnomedCT,
etc.
LOD CloudUMLS, DBPedia,Sider, Drugbank,
LinkedCT
SILK linkspeci!cation
languageand
PROV-O
BioPortalAnnotator
withAnnotationOntology
andPROV-O
4Store
Google WebToolkit
Hubble demonstrates three ‘sales pitches’ of linked data: inter-operability, interlinking and tool availability.
From patient to:- Relevant publications- Related adverse events- Clinical trials- Drug information- Known side e"ects- Statistical analysis
HUBBLE Linked Data Hub for Clinical Decision Support
PROV-O-MaticTM
• Python Wrapper script for shell commandshttps://github.com/Data2Semantics/data/blob/master/src/d2s/prov.py
• Output in PROV-O & W3C Time vocabulary
• Timestamped URIs for files/resources
• ... integrate with GIT?
• Provenance trail for conversion, loading and linking
Monday, February 27, 12
TabLinkerSemi-Automatic RDF Converter for Eccentric Excel Files
Monday, February 27, 12
Partial Replication
Yasgui
COMPLEXITY vs. INTERESTINGNESS
?
Data Analysis
Provenance Reconstruction
http://www.data2semantics.org
RDF$Conversion$
RDF$Cleaning$
Internal$Linking$
Link$to$Other$Data$
Semi8Automa;c$Annota;on$
Cloud$
Provenance$Enrichment$
acquiring$data$from$text?$
xml2rdf$d2rq$
rdb2rdf$$
e.g.$GATE$OpenCalais$
AIDA$Browser$Poseidon$(Pirates/Maps)$
…$
SILK$Amalgame$Graph$Rewri;ng$Graph$Rewri;ng$
Provenance$
Analysis/Metrics$
Querying$and$Ranking$
Visualiza;on$
User$Interfaces$
sgvizler$
RDF$Feedback$
Semi8Automa;c$Conversion$
“tablinker”$
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
One of our use cases ...
• Public-private research community
• Emphasis on applications of IT
• Emphasis on knowledge transfer
• 15 projects
• Collaboration with EIT ICT-Labshttp://www.eitictlabs.eu/
http://www.commit-nl.nl
Why VIVO?• Demonstrate collaboration within COMMIT/
between projects (synergy), between organizations
• Integrate project results with collaboration networkshared publications, deliverables
Linked Data Rubik’s Cube by Duncan Hull
Why ?
Why ?Most Dutch universities
Large companies
Government organizations
The Data
• COMMIT Websitehttp://www.commit-nl.nl
• All project plans (buzzword mining)
• All public deliverables (~200 per year)
• All participating persons (not just researchers)
Future Work
• Improve people scraperfirst name, family name, affiliation
• Ingest other contentdeliverables, plans etc.
• Shared ontology amongst Dutch VIVO installations
• Shared identifiers for researchers in NL (and VIVO)ORCID, ResearcherID, Digital Author ID
Event
• Yearly event for all COMMIT people
• Tap into registration process to get detailed info
• Wireless sensor networks to capture “synergy”
• Prizes whatnot...
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)
Web 2.0
• Web applications generate your data
• Rich user experience
• You control your own data
• Immediate reward
• Quality increases by usage
• 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
http://linkitup.data2semantics.org
http://linkitup.data2semantics.org
Where to publish the RDF?
http://linkitup.data2semantics.org
Send me more!
Where to publish the RDF?
Future Work• Improve people scraper
first name, family name, affiliation
• Ingest other contentdeliverables, plans etc.
• Shared ontology amongst Dutch VIVO installations
• Shared identifiers for researchers in NLORCID, ResearcherID, Digital Author ID
• ... reward mechanisms for individual authors!
http://www.data2semantics.org
Future Work• Improve people scraper
first name, family name, affiliation
• Ingest other contentdeliverables, plans etc.
• Shared ontology amongst Dutch VIVO installations
• Shared identifiers for researchers in NLORCID, ResearcherID, Digital Author ID
• ... reward mechanisms for individual authors!
http://www.data2semantics.org
Next week COMMIT/ Data
Early March COMMIT/ VIVO
Early April COMMIT/ Days
Future Work• Improve people scraper
first name, family name, affiliation
• Ingest other contentdeliverables, plans etc.
• Shared ontology amongst Dutch VIVO installations
• Shared identifiers for researchers in NLORCID, ResearcherID, Digital Author ID
• ... reward mechanisms for individual authors!
http://www.data2semantics.org
Next week COMMIT/ Data
Early March COMMIT/ VIVO
Early April COMMIT/ Days
Future Work• Improve people scraper
first name, family name, affiliation
• Ingest other contentdeliverables, plans etc.
• Shared ontology amongst Dutch VIVO installations
• Shared identifiers for researchers in NLORCID, ResearcherID, Digital Author ID
• ... reward mechanisms for individual authors!
http://www.data2semantics.org
Next week COMMIT/ Data
Early March COMMIT/ VIVO
Early April COMMIT/ Days