Hackathon 2013/UseCases

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These stub notes were taken during the hackathon. The canonical versions of these will ultimately be recorded at Use Cases and Milestones.



  • 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 by facilitating making basic comparisons with related species. This involves retrieving and organizing literature, images, sound files and related taxonomic information and making this available for reintegration into a publishing workflow system that is streamlined with major outlets such as Zootaxa, Zookeys, Phytokeys and more.
  • 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

Doing revisionary taxonomy & systematics

  • Background: Integrating diverse and complex data to facilitate taxonomic revisions, cladistic analyses and developing classifications as critical component of researcher workflows.
  • Approach:
  • Challenges:
    • Advanced nomenclatural handling
    • Multiple hierarchies
    • Use trees as a method of batch import/export of OTUs and hypotheses
    • Can we make a fully marked-up tree in NeXML that has nodes annotated with, for example, clade names, informational tags, bootstrap values, 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?
  • Additional 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?
  • Preconditions
  • Steps

Modeling the biogeography of a family

  • Background: Modeling the distribution of taxa in terms of ecological interactions and changes over time and space are critical components of taxonomic work. TW provides tools for taking specimen level data and generating maps integrated with a diverse set of standards at different levels of granularity and geopolitcal systems,
  • Approach:
  • Challenges:
    • Specimens on Google maps using KeyHole API
    • Shape files
    • Map of Life API
    • Tile servers from GBIF

Researching coevolutionary relationships

  • Background: Research into host-parasite, predator-prey and other coevolutionary relationships poses special problems for data management and information workflows.
  • Approach: Enable user to easily go between the interacting organisms, for example with links to the host OTU page on the parasite OTU page.

Facilitate data exchange with data aggregators

  • Background:Increasingly taxonomists will need import/export data from a variety of specimen (GBIF, Tropicos), nomenclatural (ITIS, Catologue of life), and sequence (databases). Additionally publishing to these databases will increasingly be an important part of the taxonomic workflow.
  • 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
    • Import and export Genbank sequence data

Maintain a useful and user friendly web interface

  • Background: One of the most frequent complaints about existing taxonomic workbenches, and biological software in general, is that they're not very user friendly. It's imperative that this software have a solid web interface.
  • Challenges:
    • Display data in user friendly form
    • Facilitate querying of Collections data using Illinois Natural History Survey as model institution

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