Difference between revisions of "Hackathon 2013/UseCases"

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== Use cases ==
 
== Use cases ==
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* Taxonomists
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** Starting point for research
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===Describing a new species
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*** Existing hierarchy with nomenclatural data
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* '''Background''':
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*** References to relevant literature
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** With estimates of 10-20,000 new species being described every year, there is a need for tools to facilitate alpha taxonomy. Taxonomists will be able to use TW as a starting point for research.
−
*** Added information: specimen data, images, sound recordings
+
* '''Approach'''
 +
* '''Challenges''':
 +
** Existing hierarchy with nomenclatural data
 +
** References to relevant literature
 +
** Added information: specimen data, images, sound recordings
 
** Assistance during research
 
** Assistance during research
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*** Generate private copy with relevant scope
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** Generate private copy with relevant scope
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*** Add data in database
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** Add data in database
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*** Manage characters including molecular
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** Manage characters including molecular
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*** Handle OTUs in flux
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** Handle OTUs in flux
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*** Export text to drop in manuscript
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** Export text to drop in manuscript
 
** Upon publication
 
** Upon publication
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*** Merge private copy into public database
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** Merge private copy into public database
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* '''Preconditions'''
 +
* '''Steps'''
  
 
===Modeling the biogeography of a family===
 
===Modeling the biogeography of a family===

Revision as of 10:22, 3 October 2013

Contents

Members

  • Daisie Huang
  • David Eades
  • Marilyn Beckman

Topics to be covered

  • Use cases, identify types of users and what we must deliver.
  • Define implementation plan and milestones.
  • Map imports from Species Files, MX and 3i into TaxonWorks.

Use cases

===Describing a new species

  • Background:
    • With estimates of 10-20,000 new species being described every year, there is a need for tools to facilitate alpha taxonomy. Taxonomists will be able to use TW as a starting point for research.
  • Approach
  • Challenges:
    • Existing hierarchy with nomenclatural data
    • References to relevant literature
    • Added information: specimen data, images, sound recordings
    • Assistance during research
    • Generate private copy with relevant scope
    • Add data in database
    • Manage characters including molecular
    • Handle OTUs in flux
    • Export text to drop in manuscript
    • Upon publication
    • Merge private copy into public database
  • Preconditions
  • Steps

Modeling the biogeography of a family

  • Background:
  • Approach:
  • Challenges:
    • Specimens on maps

Researching coevolutionary relationships

  • Background:
  • Approach:
  • Challenges:

Facilitate data exchange with data aggregators

  • Background:
  • Challenges:
    • Import and Export DwC-A
    • to Catalogue of Life and ITIS
    • Develop data exchange with GBIF, ZooBank, others
    • Web service clients
    • Handles requests for hierarchy
    • Inquiries about status of names
    • Participate in attempts to resolve conflicts with Catalogue of Life Piping Tool

Maintain a useful and user friendly web interface

  • Background:
  • Challenges:
    • Display data in user friendly form
    • Facilitate querying of Collections data at Illinois Natural History Survey

Considerations for making a systematist-friendly taxonomic workbench

  • In TaxonWorks, the core concept of species is relaxed into two conceptual entities: the OTU and the taxonomic hypothesis.
    • OTUs represent either specimens or groups of specimens?
    • A taxonomic hypothesis is either itself an OTU or a collection of OTUs?
  • It would be very helpful if trees themselves could be used as a method of batch import/export of OTUs and hypotheses:
    • If one created a fully marked-up tree in NeXML that had nodes annotated with, for example, clade names, informational tags, bootstrap values, that should be importable into TaxonWorks.
    • These imported annotations should be propagated out as tags to everything (every OTU?) that inherits from a node, based on the hierarchy.
      • Question: is this going to litter the world with tags everywhere?
      • Will these tags be able to be used as characters associated with entities in their own right?

Implementation plan and milestones

  • Proof of concept, all data to be discarded
    • Create basic tables
    • Import taxonomic hierarchy from Plecoptera Species File
    • Develop user interface
    • Import taxonomic hierarchy from Embioptera Species File
    • Add log on with levels of access and saved user data
    • Enable editing
    • Handle citations including authors and publication data
    • Handle images
    • Add anything else required for LepIndex
    • Enforce compliance with Code of Zoological Nomenclature
    • Handle ecological relationships
    • Add anything else required for Universal Chalcidoidea Database
  • Import LepIndex
  • Import Universal Chalcidoidea Database
  • Complete functionality required for existing databases
    • Handle specimen data
    • Handle character data
    • Provide keys
    • Tools to assist taxonomic revisions
      • Private species files
      • Generate text to drop in manuscripts
      • Merge private data back into public database
    • Verify that all essential data from existing databases can be handled
  • Import all existing species file, MX and 3i databases
  • Develop data exchange with other applications
    • GBIF
    • ZooBank
    • Global Names Architecture
  • New functionality
    • Collection data for Illinois Natural History Survey
    • Nomenclature codes other than zoological

Links and Resources

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