About the NIWA Taxonomic Information System

The NIWA Taxonomic Information System is made up of:

  • The Taxonomic Reference System (TRS)
  • The Taxonomic Attribute Database (TAD)
  • The Publishing & Reporting Service (PRS)
  • The NIWA Species Collections
  • The NIWA Species Atlas and Guides

Together these systems allow management of information associated with name and the generation of reports and publications based on that information.

TRS - Taxonomic Reference System

Paracrangonyx compactus
Paracrangonyx compactus

The TRS is a simple 'names' database that underpins the system. It contains all the names for all the species and other ranks that we expect to use within NIWA. Each name is stored as a NIWA ID, rank, parent, short e.g (philoxeroides) and long form e.g (Alternanthera philoxeroides) names and authorship. The database can efficiently compute the full hierarchy name for a taxon concept and we expect to expand the tables in the future to cross references ids with NZOR once these are available.

The database is fronted by a web service that provides a range of simple web calls that allow searching for a name and obtaining details of an id such as parents and children. This is minimal but sufficient to allow us to build 'species picker' user interface components and to validate species names in other contexts such as spreadsheets.

Information can be returned in either XML and JSON. Where possible we are using standard xml schemas such as Dublin Core and Darwin Core to carry the information.

See http://trs.niwa.co.nz for more details.

TAD - Taxonomic Attribute Database

Caulerpa taxifolia; green algae;
Caulerpa taxifolia; green algae; Nuisance Species

Information associated with a taxonomic concept falls into three categories, the names (including ranks, authorship etc), The core taxonomic details and everything else. The NZ Organism Register (NZOR) will be the master reference for the core information about a taxon,

Everything else consists of a wide range of facts and figures, photos, opinions and descriptive text that anyone might want to record about a particular taxon. These attributes (sometimes called traits) fall into types, are associated with individual taxon names and are owned by the author of the attribute.

The TAD is an entity attribute value database, set of web services and Web User Interface, that allows curators to define new attribute types such as Gill colour, invasive status, exemplar photo etc and then fill in these details for each name.

As there are a large number of potential attributes and many species the system allows each user to create and share collections of each. We might see therefore a list of pest plants along with descriptive attributes appropriate to a pest plants guide, alongside a list of edible organisms with attributes such as recipe and wine to serve.

When attributes are defined they can be text, numeric (with range limits), pick lists, URLS, and Images. Images can be from any Internet URL or from our Atlas Image Database. Attributes can be grouped together for example the Type Photo attribute might include Atlas ID and caption properties. Once attribute data has been entered for a range of species the information is then available as an XML document through the RESTful web service.

See http://tad.niwa.co.nz/api for more details.

This output is available for further processing by report generators, or inclusion in web pages or the intranet.

PRS - Publishing & Reporting Service

Having an easy way to collate attributes for species is useful but the ultimate goal is to be able to output this content in a useful form. The PRS project introduces into NIWA an overall report generation system and a specific reporting tool to go with TAD/TRS.

JasperReports is a Java based report generator tool that we can run both on desktops and servers. It comes with a local desktop based Report designer iReport. Reports are designed by connecting to a data source - either a SQL database or XML source, and then laying out the resulting information into pages. When run the report iterates over the given sources and outputs a report for each item. Reports can include local graphics and layout styles, data content, images, url links etc and can be output as Word Docs, PDF, and HTML formats.

As integrated with TAD you are able to pick a species list and preview or publish according to a chosen report. The output can be sent to a website or published document for printing.

The first application to use PRS/TAD will be a Freshwater Pests Guide expected March/April 2012. In the future we expect to link the reporting tools to generate a range of presentation and formatted output products associated with queries on the major aggregate databases - CLIDB & NEMO.

This project is carried out as part of NIWA's Environmental Information Centre, Information Management programme under Jochen Schmidt and Brent Wood.

The Taxa Reference Service (TRS) underlying database contains taxon names. The attributes data management system provides a maintainable source of data about those taxon names. E.g. whether indigenous, pictures, habitat details etc. This data is available to be browsed by staff and included in reports etc.

See http://prs.niwa.co.nz for more details.