IW Meeting 2013-01-24

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Meeting Information



  • James (will be available by 3:45)

Meeting Preparation

Around the room

 * Add a section for yourself 2 hours before meeting.  * Mark any discussion point that you would like to raise during meeting (with DURING MEETING).   * Otherwise, assume that others will read the rest before meeting.   * Also, please be considerate and read others' discussion points before the meeting starts.



  • Further work on the PML 3 mapping
  • Finished submission for Prizms grant
    • Datapubs: nanopublications for datasets, dataset provenance is embedded


  • Finishing up Prizms for melanoma DILS application paper
  • Implement a Datapub extension for CKAN
  • Journal article (Journal of Biomedical Semantics?) on SIO/PROV mapping, showing how biospecimen provenance issues from my OWLed paper are resolved using specOf and altOf + SIO domain classes.
  • More PML 3 mapping



  • Explore using olap for Fuse phase 2, two approaches:
    • Existing software, olap client <-> olap4ld <-> olap4j <-> triple store 
    • Expanding Fuse ontology with RDF Datacube vocabulary, incorporate olap concepts and build on top of existing Fuse ontology/data.

      • from deborah - can cynthia share with  jim and have him look at the extensions to fuse for datacube   (and wow - i could type from a browser within aol but not from any other browser outside aol)





DONE: Tim to create an example for the replacement of antecedentList.

  • 101 hasIndex
    • hasIndex will be most directly replaced with prov:atLocation [a pml:Position, prov:Location; prov:value 3 ]
    • hasIndex will also be replaced with pml:atIndex -- a datatype analogue to prov:atLocation that avoids creating an intermediary object to carry the prov:value. see example
    • both of these alternatives are shown in (example)
  • 45 AgentList replaced with, e.g. pml:Authorship (example)
    • For cases that the Agents are not authoring things, prov:Association can be annotated with the prov:atIndex attribute (see above).
  • 105 hasAntecedentList will be replaced with the same pattern as the previous two, using pml:atIndex. See example

DONE: make meeting on wednesday.

DONE: Tim to grep for:

  • pmlj:hasMetaBinding was NOT found among ~50 GB of files from escience.rpi.edu inference-web.org logd.tw.rpi.edu rio.cs.utep.edu trust.utep.edu www.rpi.edu
  • pmlj:hasVariableMapping was found in 1,865 4.0k files using this term. They were all loaded into the endpoint.
    • The following query executed shows the attributes of the objects of pmlj:hasVariableMapping.
PREFIX pmlj: <http://inference-web.org/2.0/pml-justification.owl#>

select distinct ?g ?p ?o

where {
  graph ?g {
    ?inf pmlj:hasVariableMapping ?mapping .
    ?mapping ?p ?o
order by ?g ?p ?o
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