Future Data Exchange Standard/Teleconferences

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Teleconference, Feb 3, 2009

Mark, Peter, Jeet (Kansas); Rutger; Hilmar, Jim (NESCent); Enrico; Arlin (recording)

  1. NeXML C++ parser status
    • Mark tried auto parser generated from Code Synthesis, experienced difficulties incorporating this into NCL, dedcided to give this up, though someone else could pick it up; did not recall in detail what were the reasons-- possibly some problems with compiling and with validating id links
    • (Hilmar) GPL a barrier to commercial implementations such as PAUP*, prefer L-GPL
    • (Mark) ok to relicense NCL with L-GPL
  2. NeXML Java parser status (and Mesquite integration)
  3. Ontology-mediated dictionary attachments
    • (Jim) Phenex-- part of Phenoscape project; effort to translate data sets associated with Zebrafish project
      • each OTU annotated with dict references to OBO id, OBO specimens, OBO collections
      • each state annotated with phenotype terms
    • (Rutger) Sawsdl (http://www.w3.org/2002/ws/sawsdl/), in schema have model ref attribute of URI to ontology term; provides uniform syntax for referring to ontology terms
      • (Jim) example problem: on the fly extension of ontology, e.g., bony process on hyoid bone
      • (Enrico) can't do that with sawsdl
      • (Rutger) important for hackathon to come up with way to add ontology-mediated meta-data, not just using term directly, but extending
      • (Enrico) on-the-fly annotations are instances
      • (Jim) don't want to create new terms; (Peter) want to avoid too many terms in ontology
  4. Character partitions; Referencing character columns in a matrix: separating ordering of characters from the referencing strategy
    • (Jeet) referencing character columns by position rather than element index; should we allow both?
      • (Hilmar) strongly in favor of element ids
    • (Jeet) character partition concepts; currently have no facility to refer to char partitions or blocks
      • (Rutger) already have facility in schema for defining sets of characters
  5. Identification of the "niche" / use-case scenarios for NeXML 1.0 (given its more lightweight scope, i.e. sans models etc.)
    • (Jeet) where do we see 1.0 being used?
    • (Hilmar) declare 1.0 before or after hackathon? Let this be driven by the hackathon.
  6. Target state of development for "NeXML 1.0" feature set (and maybe a freeze/release date)?
    • expect that this is going to come together with hackathon

We adjourned at 2:45 Eastern time.