HCLSIG/PharmaOntology/Meetings/2010-02-02 Conference Call

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Conference Details

  • Date of Call: Tuesday, February 2 2010
  • Time of Call: 10-11am EST
  • Duration: 1h
  • Convener: Elgar

Agenda

  • next steps for TMO development
  • tighter integration of TMO with your triplestore
  • visualizations
  • drug code mappings

Minutes

Attendees: Colin Batchelor (C), Michel Dumontier (M), Joanne Luciano (J), Elgar Pichler (E)

Apologies: Susie Stephens

  • E:
  • intro referring to agenda;
  • interested in catching up on triple store work, coordinating next steps &
  • efforts, preparing presentation of TMO work for CSHALS2010;
  • M:
  • problem we face: no ontology & data connect;
  • reconcile what we actually have [in triplestore];
  • interesting patient record data;
  • unfortunately for other data no actual linking;
  • queries so far based mostly on regexp matching;
  • added NDC (National Drug Code) codes to triplestore;
  • E:
  • can try RxNorm matching to NDC based on mapping in UMLS;
  • J:
  • at Partners/Dana Farber have colleague [name?] who has experience with ontologies/mapping exercises - could contact him for help
  • E:
  • can spend some time on UMLS based mappings;
  • M:
  • if we have matches, then we can move away from (queries based on) matching on labels;
  • inclusion/exclusion criteria: would be interesting to look at formalized criteria if they exist; otherwise create ontology to define propositions for in/exclusion criteria; see, e.g., emailed ontology;
  • problem for ClinicalTrials.gov;
  • can we extract propositions from other systems and align/normalize those;
  • this is a difficult/hard problem because of different encoding, criteria used in different systems
  • C:
  • agreed, combinatorial problem, similar case for [?]
  • M:
  • prefer finding people who have done some of this;
  • verify with those experts if on the right track;
  • J:
  • have done similar work in [what?]
  • M:
  • difficulties in these exercises have been highlighted by others; see paper by Patau (@IBM Watson) [add link?];
  • SNOMED-BFO notation differences exist - how to align the two?
  • C:
  • SNOMED people are working on this;
  • could talk to Kent Spackman at SNOMED;
  • M:
  • would be good to start a dialogue with SNOMED folks;
  • C:
  • see paper by Stefan Schultz [add link?] on topic;
  • E:
  • would be interesting to talk about mapping problems at CSHALS, and how efficient various approaches are in getting mappings;
  • M:
  • access to anonymized patient data would be nice;
  • NW eHealth, partnering with UK eLab [correct names?, add links to what they are doing?]
  • J:
  • will contact MITRE contacts on anonymized data, see if some are available;
  • M:
  • will meet with CTO [of ?] to discuss which access to patient data is available and under what conditions these data would be available;
  • general comment: paper was focussed on patient; also have opportunity to look at basic reasearch questions;
  • other aspect is visualization: no good visualization interfaces exist for linked data; might have to build customized webapp for that;
  • E:
  • try to stay away from developing webapps unless we have resources for that;
  • would prefer getting (potentially large size) dumps of multidim data sets based on certain queries from triplestore and then do multifaceted visual browsing/querying/display of data with standard visualization tools;
  • description of visualization tools;
  • problem: what happens if query result tables are very large? need further discussion on that;
  • M:
  • should also get input on visualization from speci-alists;
  • E:
  • agreed; not all visualizations make sense for everyone;
  • probably will require iterative process to find good visualizations;
  • how about tighter TMO-triplestore integration?
  • M:
  • URL to instantiated classes in triple store exists:
  • which TMO classes are in triple store? after mapping them one would be able to do queries based on TMO;
  • not currently working on that;
  • M&J:
  • discussion on content at
  • [experiencing technical problems with TC ...]
  • E:
  • thanks for first overview;
  • will need a few days to go over information, recently communicated links and docs;
  • will try to set up follow-up meeting for beginning of next week;