Taxon Task List

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 - DONE, v0.88)
• 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 - DONE)
• 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) - bats it is! (Dec. 04)
• Identify and access mammal taxonomic databases (Jessie, Trevor)
• Recruit experts to map relationships between concepts (Nico, Town) - Dr. Kate Jones! (Feb. 05)
• 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)