Semantic resources project/Meeting notes/2010-02-25

I. OBI / Update on models of antibodies

(timD has been spending time learning and increasing understanding of OBI for last 2 week)


 * talk about the OBI paper, lessons learned
 * has a lot of terms already that we'll need. like antibodies, epitopes, certain assays
 * distinction between processes and deterrence, continuance, timelines etc, whole logical framework
 * new things: need to map disposition, role etc. other technical pieces and classes that are distinct to OBI to learn.


 * on one hand, working to build intellectual framework for how things should be asserted

'''II. PRO status and next steps'''


 * AR: EW reviewed upper level of PRO supplied cleaved and full length products - AR reviewed notes and confirmed, started a conversation with Chris Mungal and Darren Natale to work on this. Think now in a better position to say what full-length means, not that all proteins that are cleaved are derived from full-length form. So current def of full length contains all amino acis specified by mRNA generated, describe post-translational and co-translational cleavage


 * expect new upper level part from Darren


 * AR and EW to review lower part now of APP PRO file. EW and Gwen to take first stab this afternoon (Feb 25)


 * has_part relation restrictions, number of proposed solutions being discussed right now

'''III. Demo of Annotation Tool'''


 * started out by creating ontology to represent properties. loaded in to appellate enabled model underneath, now doing double checking to make sure not uploading poor RDF


 * resource displayed on one side, annotations associated highlighted within that, click on that get a set of annotations (interpretations of a span of text within some property of a resource)


 * there is a function to clear / mark incorrect annotations.
 * Alan requests not to remove the annotations, but instead mark as a "rejection" and "accepted" (with person / date)
 * Alan suggests that on the left side of the display, to have a check mark displayed so that someone could mouse over and see a tool tip and see what was accepted.
 * add title to the panes
 * needs to be new term requested at this time on this field
 * add search box to main antibody field
 * add title to the top level list
 * formulate a lookup interface to hook in alan's ABCL finders
 * repackages for distribution and general use
 * timestampes added to annotations
 * ability to note term requests (as annotations)


 * separate tabular display that tries to show for each antibody some of the basic info - catalog # and PRO identifiers for right now


 * use cases for the tool?
 * AlzForum
 * mouse models?
 * tool has 2 parts 1) generic annotations, and 2) antibody specific
 * input: initial input started at a very basic level with a RDF knowledgebase, and what resources to list. then goes and grabs any string value property for that resource from there.


 * TD to write up list of features and a proposed priority list. AR and PC to review.


 * Another 2 weeks of rounds of steady edits and review

'''IV. Action Items'''


 * PC: outline of paper for antibody modeling
 * PC: list of validation rules
 * PC: use Annotation tool for annotating AlzForum content
 * PC: PC wants to learn OBI through TimD
 * Alan going to follow up with Jackson labs about getting data
 * Alan has to check on Gwen and EW review of PRO
 * Still have to check on the cell lines
 * TD to work on display in Antibody Annotation Tool (AR recommended HTML view) HTML display not table
 * TD to give AR write access for annotation tool
 * AR to add ABCL finders
 * TD to write up list of features and a proposed priority list. AR and PC to review.
 * AR and EW to review lower part now of APP PRO file. EW and Gwen to take first stab this afternoon (Feb 25)