HCLSIG/LODD/Meetings/2010-09-15 Conference Call

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Conference Details

  • Date of Call: Wednesday September 15, 2010
  • Time of Call: 11:00am Eastern Daylight Time (EDT), 16:00 British Summer Time (BST), 17:00 Central European Time (CET)
  • Dial-In #: +1.617.761.6200 (Cambridge, MA)
  • Dial-In #: + (Paris, France)
  • Dial-In #: +44.203.318.0479 (London, UK)
  • Participant Access Code: 4257 ("HCLS").
  • IRC Channel: irc.w3.org port 6665 channel #HCLS (see W3C IRC page for details, or see Web IRC)
  • LiveMeeting URL: https://www.livemeeting.com/cc/jnjamericas/join?id=G7PP87&role=present&pw=5K%5BDH%7Bp
  • Duration: ~1h
  • Convener: Susie


  • TripleMap demo - Chris
  • Mapping experimental data - Susie
  • Data updates - Egon, Matthias, Anja, Oktie, Janos
  • AOB


Date: September 15, 2010

Attendees: Bosse, Julia, Susie, Chris Bouton, Claus, Egon, Jun, Scott

Chris presenting TripleMap Demo (Entagen, LLC)

* Entagen is a Semantic Tech company, building a system called TripleMap and using LODD data for a demo.
* Aim to provide “dynamic knowledge maps”
* 16 software engineers and informaticians
* Large pharma clients
* Web app for navigating triple stores via standard web browser
* Rich graphics
* SPARQL queries
* RDF triple store 
* D2R to map to relational
* SharePoint interface to Team Sites and ERooms
* Less “graph-based” view of data and more of a “mind map” view
* Users can build dynamic maps (as new info is generated, it’s added dynamically) for ongoing projects
* Constant back-end literature scanning
* Entities (proteins, compounds, essays, pathways) have properties and include hyperlinks to other web-based systems
* To avoid “visual hairballs”, data can be presented in a sortable table or as “visual collections”
* Services-based with API, to connect to tools such as rendering, analytics, modeling, virtual screening
* Inferencing and network connectivity analysis
* Maps can be shared based on group authentication and searched using network analytics
* Can print out reports and summaries in PDF or Powerpoint
* Question: how to deal with refutation in Pubmed articles? Can it be represented? Answer: users have access to original data sources.  A link’s validity is based on the number of sources.
* Question: is there chemistry development? Answer: yes
* Question: did you convert any of the data? Answer: used LODD sets
* Question: how to represent inferred connections and distinguish them from other types? Answer: no, only provided triples are currently used via SPARQL endpoint of the original source. 
* Demo: 
* Interface is based on the “master list” of entity types
* Once entity is selected, all the properties are visible
* SPARQL call then runs to identify all the relationships
* Related entities can be dragged to workspace on demand (either as table or a visual collection – all compounds are rendered on the fly)
* The system avoids duplicates on any given map
* Information can come from different sources behind the scenes and be displayed together
* The interface can be “touchable”
* Question: how does the system decide if two entities are the same?
* Answer: for a any given data source, the users have an interface to map entities and create a “master index”
* For any two entities, the system traverses the tree on the fly to identify all potential connections
* Maps can be integrated (links between canonical maps for two different diseases, for example)
* Working on visualizing images and plate-based data
* Susie: it would be good for LODD to use this software to demonstrate value
* Chris: there is interest in adding patient data for personalized medicine analysis
* Susie: to get a demo acct, send email to Susie and she will pass it on to Chris to get a “trial code” for testing
* Chris: keep in mind that the system is still being heavily developed, so it might be down occasionally.