Meeting Notes 20081013 PI Meeting (10/13/2008)

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10/13/2008

PI Meeting (Dejing, Gwen, Allen and Don)

  1. Updates on Ontology Development
    • NEMO_ERP new version of owl ontology
    • Strategy is to begin with core concepts that can be linked to OBO relational (OBO-R) and basic foundational (BFO) ontologies. Advantages of this approach: top-down approach improves ability to merge with other ontologies (e.g., BIRNlex); and forces us to think through implications of defining concepts in a certain way, check for internal consistencies as we go
    • CMAP can be used as link between development phases I-II (informal conceptualization & formal coding of concepts in Protege). Concept maps use graphical components to represent classes, subclassof (isa) and properties/relations. We can incorporate formal ontology constraints into CMAP in order to facilitate the translation to Protege
  2. Project Documentation
    • Junelet (?) vs. Liferay Trac and Wiki: natural language explanations of concepts and relations. How to relate it to NEMO Portal? Jason? (Allen will talk him) Add a Trac ticket
    • Need to begin assembling “encyclopedia” of terms that are being entered into our ontology - include term ID, term name, definition, etc. following standards for documentation in other ontologies Add a Trac ticket
  3. Meta-analysis of data from multiple labs:
    • Gwen is continuing this. 8 labs' data - preliminary findings presented at SPR08. Goals are: (1) reliably label patterns and map them across different data sets (similarities) & (2) look for reliable differences in patterns that could plausibly be linked to variables that differ across experiments (differences). Add a Trac ticket
    • Data Mining (we should continue strategy we discussed) -- Mapping Discovery (new milestones in Trac with tags) -- Deadline: special issue of next January. Add a Trac ticket
  4. Involvement of Consortium members
    • Both ontology development and meta-analysis
    • We can show the 3rd version of NEMO ontologies to the consortium members once the documentation is ready Add a Trac ticket
    • Don suggested to send something to Cohen by December, since she has expressed an interest in seeing that consortium is actively involved Add a Trac ticket
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