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Taxon Integration Notes Nov 4

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Taxon Application Integration session

Discussion session intended to address the integraiton of taxonomic tools with other components of the SEEK architecture.

Need to change EML to handle taxon concepts

  • GCE is only institution with taxonomic coverage info in EML docs
  • Morpho needs to handle taxonomic markup

nice use case for Kepler - interactive decision making, expand concepts, relationships

Matt: good to have loop version that will resolve a list of taxa

Bertram: need to talk to Ilkay about the wsdl harvester and how it can work with TOS

data integration

  • map b/w 2 ecological datasets - must make value judgements on match b/w taxa within
  • data integration in Kepler - provide the mapping so scientists can match datasets
    • how does that relate to addRelationship
    • must keep those 2 separate - use taxon output vs add content to SEEK cache
    • do we want to store some of these decisions made during data integration?
    • may want to share synthesis decisions by a working group of scientists so that others can use or discard those opinions

BEAM: what are the taxa that have changed a lot and would be useful for use case

    • interesting ecological problem
    • abundance/ whatever data with spatial, temporal range
    • mammals is nice small group, name mapping issue is clear
    • 2 issues
      • name expansion
      • misspelling problems

Use case

  • NA mammal niche modeling (can get data with DiGIR query)
    • pick top 5 taxa to model
    • run mammal modeling with and without taxon service/ concept matching
    • need a mammals expert to evaluate results
  • western grasses concept data?
    • big societal impact
    • Vegbank should be getting data soon?

Engage taxonomists/data creators

  • encourage addition of concepts/relationships
  • catfish project?
  • increase use case understanding
  • Kepler functions here?
  • collaborate with well organized group or NSF funded project that is working on it now?

Tasks

General
  • Get real concept data relevant to larger SEEK context
    • BEAM group has identified NA mammals, let's get subset of that - 5 taxa
  • Need links between APIs and Ecogrid
    • Reindex existing datasets - ecological and specimen records, modify EML records
    • Query with name for concepts then datasets fro concepts

Specific Assignments

  • Mark Schildhauer: contact Reichman, Willig, and Stevens about mammal concept information
  • Deana Pennington: better describe the requirements and intention of the mammal niche modeling case study, with assistance of Nico and Dave
      • and identify ecological datasets, markup in EML with Taxonomic Concepts
    • Populate concepts for those taxa
    • Nico will help from Taxonomic perspective
    • Dave V. will help from Ecogrid perspective
  • Identify mechanism/plan for any given scientific study
    • Formulate plan
    • Walk the experts through the concept creation steps
  • Create TCS doc for import into SEEK Taxon cache (Nico, Jessie)
  • historical concepts/relationships
  • integrate functionality of TOS with Ecogrid
    • Incorporate TOS into current data queries
    • term expansion in client for now
    • smart searching - currently divided into 2 searches, need to integrate SMS and Taxonn searching, Shawn thinks - bring it in locally
    • Aggregation node vs individual providers, regularly scheduled updates
    • How do we annotate datasets - metadata generation

  • Modify taxonomic part of EML
    • Can use additionalMetadata with no changes to EML tools for experimentation
    • Could use simple name/rank/publication composite key with/without LSID
    • Using only LSID might be best long-term solution

    • Maybe use controlled vocabulary (Smithsonian?)

  • Modify Morpho tool which is pulling taxonomic names/info from datasets to use TOS for concept matching
    • Ecological datasets vs specimen datasets
    • 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

  • Map between TCS, DarwinCore, EML (Jessie)



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This particular version was published on 08-Nov-2004 09:13:55 PST by KU.stewart.