Science Environment for Ecological Knowledge
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Development Tasks Nov 2004

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What are our software development priorities?

Organize!

  • Draw dependency diagram of tasks with names (wiki) - get input from responsible parties (Aimee, Thau)
  • Add API calls to WIKI page next to WSDL link (Aimee)

Finish/improve current work on TOS

  • update object model
    • Pre: Decide on version of TCS to work from for now (Trevor, Aimee)
  • finish the parser
  • use Hibernate for database abstraction
  • add MSW data, changes over time, in TCS format
  • make SOAP server more robust (1 week max)
New functionality for TOS
  • API's to receive and output TCS and OWL
  • Kepler actor?
  • Integrate LSID server (Thau, Robert, Aimee)
  • Algorithms (Aimee, Robert, experts)
TCS work
  • Jessie will meet with Paul Kirk to discuss variation in valid name types and generate an appropriate schema with list of examples (2 weeks)(Name Work)
  • Map between TCS, DarwinCore, EML (Trevor)
      • Pre: Name Work above

Tools: Visualization, Browsing, and Editing Tools

  • Bob, Nico and Xianhua will summarize issues on wiki (2 weeks)
    • 3 timeframes (January, semi-short, long)
    • look at Napier work/proposal and see if/how they can work together
    • Who are the users of each tool?
    • Use cases for Tools
  • Should we have seperate browsing/editing tools? There should be coordination between the 2 - not different displays for user to view
  • Tool for marking up EML datasets with concepts
    • Pre: modification of EML taxonomic section
    • manual/auto markup of dataset metadata
  • Tool for adding relationships between existing concepts
    • How does current work fit in?
      • Napier's (Martin) visualization tool for tree comparison - doesn't edit
      • Xianhua's TaCBE tool, browsing and editing - where does this fit in?
  • Tool for creating new concepts
    • What kind of editing tools are needed?
      • single concept
      • batch addition, editing
    • User Guide: Walk the experts through the concept creation steps()
  • Tool to define mappings from other dbs to TCS (Trevor)
    • will look at MapForce

SEEK Integration Tasks

  • Find experts, Mark S. will talk to Jim Richman and ?? about bat data
    • Nico - Identify 1-5 taxa to target (with Mark and Deana identifying ecological datasets and markup in EML with Taxonomic Concepts)
      • Pre: Dave Thau will narrow the field by looking at MaNIS for families with lots of georeferencing data (Nov 12 or so) to help identify taxa
      • Pre: Town will help narrow the field with experts
    • Jessie and Trevor will look for taxonomic databases to help identify taxa
    • Populate concepts for those taxa
    • Experts to help map relationships b/w historical concepts (who?)
      • Pre: Broad guidelines first, then experts will help modify. Example driven guidelines for experts - beginning of User Guide (Nico, Trevor, Bob, Jessie)
    • Create TCS doc for import of concept data into SEEK Taxon cache (Nico, Jessie)
    • Dave V. will help from Ecogrid perspective

  • Dataset annotation (learning step)
    • Test concept dataset generation (name, source) (Jessie, Trevor, Thau)
    • Generate LSIDs for the concepts within (Thau)
    • Annotation of EML with test concepts (Matt, Thau)
    • Maybe use controlled vocabulary (Smithsonian?)

  • Integrate functionality of TOS with Kepler (Robert, Aimee, Thau)
    • Learn Kepler
    • Determine what actors to build

LONG Term

  • integrate TOS with Ecogrid
    • Incorporate TOS into current data queries
      • smart searching - currently divided into 2 searches, need to integrate SMS and Taxon searching
    • Aggregation node vs individual providers, regularly scheduled updates

  • Modify taxonomic part of EML (Matt, Jessie)
    • Can use additionalMetadata with no changes to EML tools for experimentation
    • Could use simple name/rank/publication composite key with/without LSID
      • Pre: Name Work above
    • Using only LSID might be best long-term solution

  • Integrate dataset annotation with TOS
    • Pre: SMS annotation for smart data discovery
    • Pre: EML modification
    • 2 types: Ecological datasets vs specimen datasets
    • How do we annotate datasets - metadata generation
    • Modify Morpho tool which is pulling taxonomic names/info from datasets to use TOS for concept matching
    • How do we interface with ecological dataset creators that don't use Morpho?

  • How do we use the rich TOS result to query on DiGIR resources with sparsely populated taxonomic information?
  • Annotate Darwin Core records with proxy - LSIDs for specimen records and Concept LSID

Publications

  • concept language - Nico, Bob, Jessie (1 month)
  • for Ecologists - Trevor, Bob, Nico ()
  • General SEEK Taxon paper, where the field is going (Beach) (not begun)
  • QRB (submitted)
  • Concepts and GUIDs (Systematics Biology - Nico, Thau, Jessie) (3 months for internal review)
  • Technical aspects of concepts and GUIDs (Thau and ??) (not begun)



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This particular version was published on 05-Nov-2004 12:04:07 PST by KU.stewart.