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Taxon Task List

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Building Blocks

Taxonomic Object Service (TOS)

Stabilize

  • Fix SOAP server
  • Update TOS Object Model (Aimee, Robert G)
  • Hibernate / DB relational model (Robert)
    • Parser (Aimee)
  • Integrate LSID server (Thau, Robert, Aimee)
  • Add MSW data with changes over time for immediate use

Improve

  • Create API's to receive and output TCS and OWL (Robert, Aimee)
  • Create calls to support Kepler
  • Modify to support visualization and editing tools
  • Add algorithms (Aimee, Robert, experts)

Taxonomic Concept Schema (TCS)

  • Fix version of TCS for current dev cycle (Trevor, Aimee)
  • Name schema for TCS: Meet with Paul Kirk to discuss variation in valid name types and generate an appropriate schema with list of examples (Jessie 2 weeks)
  • Map between TCS, DarwinCore, EML (Trevor)

Update/Maintain documentation

  • Add API calls to WIKI page next to WSDL link, update as needed (Aimee – DONE)
  • Create UML diagrams and put on SEEK Taxon wiki pages
  • Create javadocs and put on SEEK Taxon wiki pages

Overall Goals

Tools: Visualization - Browsing and Editing

Summarize

  • Put issues on wiki (Bob, Nico, Xianhua – 11/24 - will email)
    • Nico is preparing a summary document to be reviewed by Bob et al. on Nov. 23 - delivered on Nov. 24; see SeekTaxonTools
    • Who are the users of each?
    • Use cases for Tools
    • What kind of editing tools are needed?
      • Should we have separate browsing/editing tools?
      • There should be coordination between the 2 - not different displays for user to view
    • How does current work fit in (TCBE, Martin's viz tool)
    • look at Napier work/proposal and see if/how they can work together (UNC)

Needs as defined Nov 2004

  • Tool for creating concepts/relationships
    • Batch data dump
    • User Guide: Walk the experts through the concept creation steps()
  • Tool for viewing concepts/relationships
  • Tool for marking up EML datasets with concepts
    • Ecological dataset functionality
    • Specimen dataset functionality
    • Manual markup tool ("weird" taxa, loose relationships to known concepts)
    • Auto markup tool
    • Merge tool
  • Peer review interactions
  • Revisit Use Cases
  • Tool to define mappings from other dbs to TCS (mapForce?) (Trevor)

Integration: TOS with rest of SEEK

Mammal Use Case

  • Aquire taxonomic data
    • Identify 1-5 taxa to target
      • narrow the field by looking at MaNIS datasets (Thau – Nov 12 - DONE)
      • further narrow of target taxa to around 5 based on available expertise and taxonomic interest (Nico, Town, Mark, Deanna) - Nico, Nov. 24: we're close!
    • Identify and access mammal taxonomic databases (Jessie, Trevor)
    • Recruit experts to map relationships between concepts (Nico, Town) - Nico, Nov. 24: this is still in the works
      • create rough guidelines - example driven (Nico, Trevor, Bob, Jessie)
      • develop examples
    • Work with experts to create taxonomic concepts (Jessie, Robert K)
    • Encode taxonomic concepts in TCS (Jessie, Robert K)
    • Create TCS from mammal concept data (Nico, Jessie)
    • Import TCS into TOS (Aimee, Robert)
  • Annotate datasets
    • Identify likely sources of taxonomic information (Thau, Jessie)
    • Test concept dataset generation (name, source) (Jessie, Trevor, Thau)
    • Generate LSIDs for concepts within (Thau)
    • Annotate EML with test concepts (Matt, Thau)
  • Build Kepler actors (Robert, Aimee, Thau)
    • Learn Kepler
    • Determine actors to build (or extend existing Web Service actor)
      • identify candidates
      • consult for feasability and usefulness
    • Create example work flows

Longer Term

  • Integrate TOS with Ecogrid (Matt, Rod, Susan)
    • Incorporate TOS into current data queries
      • 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
      • Prerequisites: Name Schema Work above
    • Using only LSID might be best long-term solution
  • Integrate dataset annotation with TOS
    • Modify Morpho tool to use TOS for concept matching
    • How do we interface with ecological dataset creators that don't use Morpho?
    • Ecological and Specimen datasets
    • Prerequisites:
      • SMS annotation for smart data discovery
      • EML modification
  • Evaluate text extraction from primary literature to produce concepts (Joana)

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)
  • Quarterly Review of Biology (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 15-Dec-2004 09:18:51 PST by KU.stewart.