User Stories

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The intent is to provide some broad concepts/stories that will lead to further discussion. Extensions/comments etc. are welcome.


Manage specimens metadata from field to collection, simply

Handle a simple workflow that starts with some generic information about a field site, then moves to labeling collected specimens with this data, then moves this data to an IPT instance/GBIF. Do this with a minimum of steps.

Complete A Taxonomic Revision

Taxonomic revisions tie everything that is known about an organism together in a current snapshot. Specimens, descriptions, nomenclatural histories, images/figures, measurements and more must be integrated within a framework that guides or directs as user to the steps that need to be completed.

A database of taxon concepts and associated literature

I'm particularly interested in a tool that can manage taxon concepts (not just scientific names) linked to publications, in ways that lets me get at the publication data separately from taxon concepts. Unfortunately, I won't be able to share the data I'm currently working on, since it's not mind to share, but I could build a dataset to play with. -- Gaurav (talk) 15:24, 25 September 2013 (CDT)

Tracking any data with scientific names is complicated. The simplest deliverable here would be a database which can track taxon concepts, relationships between names (synonymy, homonymy), and data objects using particular names. The database would be able to add data objects to names, then use synonymy to display all the names associated with that publication.
Incidentally, names + literature references = taxon concepts, so if you're planning to head that way, this is a good way to start.
  • ITIS: All of ITIS is in the public domain. A full database dump can be downloaded from (itisMySQLTables.tar.gz is probably the easiest one to work with). Dima has written a Ruby tool which can pull out scientific names from this dataset. The current download contains 9,781 hopefully unique references associated with 1,173,786 hopefully unique names.
  • EOL: EOL makes associated publications available for taxon names (example). Since I'm currently working on North American birds, I was thinking of maybe looking up all 2,090 bird species currently recognized by the American Ornithologists' Union as occuring in North America, and running them through EOL to find all associated publications.

Flow DwC archives

In the absence of a GUI import multiple DwCAs, do some manipulations on them, and spit out a filtered set. Do this in the context of the underlying TW models wherever possible.

Build a nomenclatural catalog in accordance to international standards

Standardize names against the rules of nomenclature. Provide warnings or enforce the governing rules where possible.

Build an interface to semantically describe taxa

Use anatomy and related ontologies to describe taxa semantically. Tie data to specimens, not species.

Manage my taxonomic metadata in a simple GUI, but expose it also via jSON services

See requirements for "Complete a Taxonomic Revision". Add an API to this.

Manage molecular vouchers

Specifically target the specimen->extract->reporting stages involved in a molecular study.

Build a set of identification guides to the taxa of my region

Using simple bifurcating or multi-entry keys and some distribution data provide a clean/simple interface to identifying taxa.

Compare my nomenclatural hierarchy to a phylogenetic or alternative nomenclatural hierarchy

Data cleanup/clarification is all about reconciling graphs, make this generic, and facilitate transforming the computed results into new projects.

Build simple set of text-based taxon pages

Allow a user to create their own topics on a per taxon basis, edit these topics, and publish the results as HTML or jSON to be plugged into some other software.