You are here: Digital Project Analyst

eFlora

 

Background
The following extract was taken from Sowing Seeds in the Digital Garden, a paper prepared for the 2006 conference: Sustainable Data from Digital Fieldwork: From creation to archive and back. The paper was authored by Murray Henwood, Su Hanfling, Rowan Brownlee, Belinda Pellow and Tristan Gutsche and may be read in its entirety at http://ses.library.usyd.edu.au/handle/2123/1298

 

One of the main outputs of plant taxonomic research is the production of keys to the identity of the plants of a particular geographic region. The keys are often accompanied by descriptions and illustrations of the species under consideration, and they sometimes provide an indication of the relationships between and within the various levels of the taxonomic hierarchy.

Traditionally, keys have employed a dichotomous structure comprising a series of parallel and mutually exclusive choices or couplets. When identifying a plant, a user chooses the most appropriate description of a characteristic at each couplet and proceeds through the key until they reach the name of their unknown plant. Dichotomous keys are often grouped together with illustrations, maps of distribution and descriptions of each species in what is known as a regional Flora. The Flora of a particular geographic area, then, consists of a repository of taxonomic knowledge in the form of descriptions and a tool by which users can identify the plants from the area.

Floras differ from other means of plant identification such as guides or manuals - by providing a comprehensive coverage of all species for a particular geographic region. In addition, Floras can contain information on flowering time, chromosome number, common name(s), uses, conservation status and ecology. In this way, floras provide core data for field scientists but are also powerful learning tools as students move through an experiential pathway to gain new knowledge.

The hierarchical nature of plant classifications provides a structured framework that can be readily displayed in a web environment. Since individual dichotomous keys are usually arranged according to these classifications, these keys can also be effectively presented via the internet. Online interactivity enables users to traverse hyperlinked pathways through the keys in a way that is much easier than moving from one section to another within a printed book. The learning potential of the web-based keys can be further enhanced by incorporating associated learning objects such as high quality illustrations of plants and their defining characteristics, and by providing immediate access to the technical language of botany by way of electronic glossaries.

A project that combines these attributes has been developed by the University of Sydney and the University of Wollongong, supported by funding from the New South Wales Environmental Trust. The printed Flora of the Sydney Region (Carolin & Tindale, 1994) is being revised, updated and digitised to form the centre-piece of a multifunctional, web-based resource - the eFlora - for the presentation of information on botanical diversity. An integral part of the Flora of the Sydney Region is an illustrated glossary of technical botanical terms.

The eFlora comprises keys to all 3000 vascular plant species found in the geographic region from the Shoalhaven River to the Hunter River, and west to the Great Divide. The text of the Flora of the Sydney Region will be marked-up in XML. This approach has a number of benefits including the long-term storage and management of the text, the ability to generate a word index to enable fast keyword searching and the capability to support online interactivity and generate outputs for a variety of uses including print and web publishing. One of the most significant advantages of this approach is the ease with which the content of the eFlora can be updated to reflect the latest concepts in plant taxonomy.

Production of the eFlora has required the investigation and enhancement of standards for the presentation of Floras in a web environment. The Australian Biological Resources Study (ABRS), for example, has developed a schema (Australian Biological Resources Study, 2004) for use with its multi-volume publication, Flora of Australia (Australian Biological Resources Study, 2006). ABRS are currently reviewing their schema with reference to work being undertaken by TDWG (International Union of Biological Sciences Taxonomic Databases Working Group, 2006b). The project team for eFlora are planning discussions with TDWG to ensure that the current projects are compliant with emerging standards being developed across the international botanical community.

One of the associated aims of eFlora is that it should reflect the content of the printed version of the Flora of the Sydney Region, but with enhanced operability. To this end, the glossary component of the Flora of the Sydney Region will be marked-up in XML and integrated with the text of eFlora by way of automatically hyperlinked keywords from the glossary. This format will ensure that the glossary can be used independently of eFlora (for stand-alone teaching purposes) or can be integrated with other botanical information services.

 

References included in extract

Australian Biological Resources Study. (2004). XML Schema for the Flora of Australia Online. Retrieved October, 2006, from http://www.deh.gov.au/%20biodiversity/abrs/online-resources/flora/pubs/fl-australia-schema.html

Australian Biological Resources Study. (2006). Flora of Australia Online. Retrieved October, 2006, from http://www.deh.gov.au/biodiversity/abrs/onlineresources/

Carolin, R. C., & Tindale, M. D. (1994). Flora of the Sydney Region: Reed Books, Chatswood, N.S.W.

International Union of Biological Sciences Taxonomic Databases Working Group. (2006b). Standards. Retrieved October, 2006, from http://www.nhm.ac.uk/hosted_sites/tdwg/standrds.html

 

Application development

 

Prototype
To assist discussions within the project team, I created a prototype which demonstrates some of the features planned for an interactive Flora of the Sydney Region. I marked up a selection of keys as XML files using the ABRS schema, and rendered a navigable html interface using a combination of XSLT, Saxon 9B and Python. I also developed a simple Javascript application enabling a user to record and review steps taken through a key.

Technical assessment
Gary Browne, the Library's development programmer undertook a technical assessment of the project and provided the team with a set of recommendations and estimated costs.

Technical development
Conal Tuohy was appointed as project development programmer, and created the eFlora application using Cocoon and Lucene. Site styling was created by Alex Motyka from the University of Sydney Digital and Print Media.