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, update as needed (Aimee - DONE)

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
• make SOAP server more robust (1 week max)
• Integrate LSID server (Thau, Robert, Aimee)

New functionality for TOS

• API's to receive and output TCS and OWL
• Kepler actor?
• Algorithms (Aimee, Robert, experts)

• 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
• add MSW data, changes over time, in TCS format
• 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)