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2011 VIVO Hackathon
May 4th - 7th 2011, Health Science Center Library, University of Florida, Gainesville, Florida, USA http://www.vivoweb.org/blog/2011/05/2011-vivo-hackathon-report
TitanPad Collaborative Document: http://titanpad.com/HsdYySMQHL
|Nick Benik||Harvard University|
|Jiten Bhagat||University of Manchester|
|Kees Burger||Maastricht University|
|Brian Caruso||Cornell University|
|Nicholas Skaggs||University of Florida|
|Chintan Tank||Indiana University|
|Andra Waagmeester||Maastricht University|
|Stephen Williams||University of Florida|
|Rebecca Younes||Cornell University|
- Taverna (http://www.taverna.org.uk/ )
- Wiki people (http://conceptwiki.org/index.php/%20WikiPeople )
- LOGD (http://logd.tw.rpi.edu )
- myExperiment (http://www.myexperiment.org )
- BioCatalogue (http://www.biocatalogue.org )
- ConceptWiki (http://conceptwiki.org/ )
- Text mining tool (http://www.acknowledgeconnect.eu/linker/default.py?url=nph-proxy.cgi/010000A/http/www.google.com/search?q=malaria not the production site, but that seems to be down. Sysadmin is looking into it)
- Wikipathways (http://www.wikipathways.org )
- Pathvisio (http://www.pathvisio.org )
- Citedin (http://www.citedin.org )
- VIVO (http://www.vivoweb.org )
- Saffron (http://saffron.deri.ie/ )
- Harvard Profiles (Example profile http://connects.catalyst.harvard.edu/profiles/profile/person/32213 )
The attendees self-organized and identified projects of interest. Brief notes below.
A game platform for connecting people and things. Have fun. People, things, events, challenges, levels, badges, gamer points. Data driven. QR codes to link real world to virtual. Linked in Sabaku. Organizers of a conference can determine the badge based on rules. VIVO, wikipeople, mendeley. Aggregator -- Sabaku gator. Vivo and wikipeople working, profiles, mendeley, my experiment can be aggregated. Mobile app to come. Qr builder. On github. A few bits working. Google doc. A skype chat.
- Expose visualization data in VIVO as a Data cube (DERI RDF format for statistical purposes). Data extraction from visualization. Added a data cube link. Observation.
- VIVO UF, VIVO WUSTL, Harvard Profiles, bio2rdf. Dimension property. http://sameas.org. Web service. Crawled articles from harvard, wustl, UF. Pubmed IDs to reconcile. Created a new web service for identifying VIVO same as. Common identified, pubmedid. Can infer "stub" identities via common publications. Infer the same as between the authors via scoring related to common publications. NCBI has pubmedid to geneid.
Interlinking People and Concepts
Use info from outside the organizations. Using blogs, social connections, home pages, forums. http://sindice.com/ http://sig.ma Dealing with the digital dinosaur -- some people do not leave many tracks on the web. Disambiguate names. Stubs attached to publications. Match keywords from pubs to DBPedia resources. Move up the category scale. User topic visualization, http://vis.stanford.edu/protovis/ Concepts from DBPedia via Wikipedia categories -- shown to be more useful than some hand curated ontologies and across a much broader array of concepts than UMLS. able to use VIVO keywords to match to DBPedia concepts and move up a concept heirarchy.
Views can query Sparql endpoints such as VIVO. Standalone use of Drupal Views to show data in VIVO. Miles Worthington a strong contributor. http://drupal.org/project/views Demo of Drupal Views slide show of faculty members in a department with grant dollar total for each. Click on change view to see histogram, or other visualizations in views.
- Working on adding RDFA to the HTML of VIVO display pages, providing semantic content in the HTML -- useful for search engines.
- Adding SPARQL query via URL extension for every VIVO.
- Using Taverna http://www.taverna.org.uk/ to link VIVO Harvester command line calls as components in a graphical workflow, creating a graphical user interface for Harvester. Taverna could be used to automate the production of graphics using R functions.