Meeting Notes 20081013 PI Meeting (10/13/2008)
From Nemo
10/13/2008
PI Meeting (Dejing, Gwen, Allen and Don)
- 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
- 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…
- 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…
- 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…
