Electronic Pteridophyte Flora of Australia
a collaboration to create and maintain a dynamic interactive resource of Australian ferns and fern allies
Project Plan
There are c. 456 species of Australian ferns and fern allies, arranged in c. 112 genera. These are well described and well illustrated in the Flora of Australia, the Ferns of Queensland and other state and regional floras. While much of this data was compiled electronically, little of it is available in a structured database format.
The Flora of Australia commitment to publication of ferns and fern allies is essentially complete with the publication of volume 48 in 1999. Previous accounts of ferns and fern allies can be found in Oceanic Islands volume 49 (1994) and volume 50 (1993). These three accounts were prepared at different times by different authors and there are differences in delimitation, circumscription and naming of taxa that need to be harmonized.
ABRS and other organisations have supported or are planning support for the production of interactive keys and electronic information systems for a number of large iconic and charismatic plant groups; a remaining large group in this category is the ferns and their allies. This project envisages an electronic resource of botanical information to be disseminated in a simple, intuitive format to general users as well as the practitioners of botanical taxonomy. The internet and the World Wide Web are seen as the primary vehicle for this project, planned to run over three years:
- Year 1: set-up and co-ordination of participants and collation of existing resources
- Year 2: preparation of taxon/character matrices, data compilation and development of interim application interfaces
- Year 3: finalisation of the interactive keys and links to associated data and remote databases
The project will start off gradually and the resources applied to it will increase each year until its completion. The project design is modular and allows for a deliverable at the completion of each year of the project:
- Year 1: On-line integrated flora treatments
- Year 2: interim interactive keys with coded character data and character help files
- Year 3: Working interactive keys with character and taxon illustrative material
There will however be overlap of the modules with anticipation and testing of the work to be done in years 2 and 3 being done in the previous years. Years 2 and especially 3 of the project will see the emphasis move from data compilation to data presentation and a need for additional specialist assistance is anticipated and planned for.
This is an ambitious project that depends on external technical support and multi-institutional collaboration for its success. The additional technical input is required to handle the volume of works and to assist the project managers deliver the outputs as planned.
Year 1
The focus of the first year will be getting the three existing Flora treatments into the Oracle database prepared for this purpose, integrating and checking the consistency of the taxonomy of each treatment and making the combined data available on-line. Outdated taxonomy will be corrected as part of this process. It is anticipated that some of the tasks from years two and three will be anticipated and start in the first year as the technology is evaluated and tested. Tasks to be undertaken in year 1, some of which will run concurrently will include:
- appoint part-time Technical Officer for text data mark-up and standardization
- workshop to plan details of collaboration, data structure, character sets, etc.
- negotiate with ABRS on access to published text and image data from Flora of Australia
- establish copyright and intellectual property components of project elements
- design database structure based on layout and headings of Flora of Australia
- export Flora of Australia MS-Word documents in XML-tagged format
- build Oracle database, XML hierachy and XML-schema
- migrate documents to Oracle database using XML import facilities
- integrate data from volume 48, 49, 50 treatments
- prepare Internet available XML query, output and display from database
- update pteridophyte name entries in APNI, including synonymy
- link published names in Flora of Australia to relevant entries in APNI
- link current names in APNI to Flora of Australia treatments
- make pteridophyte nomenclature and taxonomy available through What's Its Name
- scan line drawings and maps from Flora of Australia treatments
- link line drawings and maps to Flora of Australia treatments
- link data gateways to ABIF-Flora and to Australia's Virtual Herbarium
- external review of online Electronic Pteridophye Flora of Australia application
- release of on-line Electronic Pteridophyte Flora of Australia
During this phase, the Austalian Plant Name Index will be updated and checked for Australian Pteridophyte names and their synonyms. After linking these APNI entries to the appropriate Flora of Australia entries, the APNI entry will become the Flora of Australia nomenclature and taxonomy, and vice versa.
Year 2
The focus of the second year will be to prepare the data matrix of characters and character states for all taxa, and to build and test the draft interactive key. It is expected that some of these tasks will have been anticipated and started in year one, and will be accelerated in this phase. Similarly, tasks started and larely completed in year one will be revisited, tested and refined in this second year.
- refinement of the character set
- curate and check identification of Australian taxa in the Australian National Herbarium
- Appointment of full time technical officer primarily for character data matrix scoring
- populate character and state definitions and glossary
- score character sets for families, genera, species and infraspecific taxa
- design and build database table to hold taxon and character state matrices
- design and build XML query and export from taxon and character state tables
- database Australian taxa in the Australian National Herbarium for map generation
- liaison with state herbaria on databasing Australian fern collections
- evaluate and decide on on-line interactive key technology
- build and test interactive key applications
- source images for interactive key application
- integrate exemplar character images with database and interactive keys
- integrate exemplar taxon images with databae and interactive keys
- negotiate copyright and intellectual property arrangements for external sources
- link data gateways to ABIF-Flora and to Australia's Virtual Herbarium
- external review of draft interactive key
- release of interim interactive keys with exemplar images to Pteridophytes of Australia
During the second year collaborating Australian herbaria will attempt to curate and database their Australian Pteridophyte collections. Pteridophytes are in the second rank priority for the Austrlaia's Virtual Herbarium project and the timing of both efforts are quite compatible.
Year 3
The focus of year 3 will be the integration of images and illustrative material with the interactive keys and the finalization of the database and on-line products. It is expected that some of these tasks will have been anticipated and started in years one and two, and will be accelerated and finalized in this phase. Similarly, projects started and largely completed in years one and two will be revisited, tested, refined and finalized in year three.
- workshop to plan details of the integration of images, associated data and final layout for interactive keys
- continued appointment of full-time equivalent technical officer for interactive key building and testing
- engagement of graphic designer services for image and graphic preparation for interactive key
- testing and revising scoring of characters for interactive keys
- accumulation of external images (photographs, line drawings,etc.) for final product
- preparation of images for integration with interactive keys and database
- integration of images in database and interactive keys
- incorporation of image metadata
- enhancement of database gateways for images and associated information
- quality and consistency testing of interactive keys
- link additional data gateways, especially those for images, to ABIF-Flora and to Australia's Virtual Herbarium
- external review of interactive keys and images
- release of the Electronic Pteridophyte Flora of Australia
Year 4 and beyond
By the fourth year the compilation of the datasets will be complete and the project will be in on-going maintenance and update mode. The collaborators will need to establish protocols and the basis for sharing tasks for the on-going maintenance of this database resource.
- Nomination of a co-ordinator for the Electronic Pteridophyte Flora of Australia
- Nomination of taxon specialists for Pteridophtye groups
- Compilers of APNI and others alert the on-line Flora coordinator of new treatments
- Taxon specialists consulted and consult on relevance of new information
- Taxon specialists decide on relevance and prepare new material for the Flora
- New material incorporated with database
- New material immediately available to the public
- Data, database structure, application design migrated in line with advances in technology
- Application interfaces enhanced and developed
By the time the project is complete, and even before, negotiations will have started with State herbaria to prepare their Pteridophyte floras in a similar format, using similar standards, so that an integrated vitual flora giving access to all of the State floras will be available through Australia's Virtual Herbarium.
The workshops
The purpose of the workshops is to engage the pteridological community, ABRS and other partners on the project and establish areas of collaboration. They will provide opportunities to pool expertise and plan critical stages of the project.
Year 1 workshop
A workshop will be held early in the first year to bring the principal investigators and principal collaborators together to kick start the project. It will:
- confirm the scope of the project
- clarify details of the project
- map out and confirm realistic project time-lines and milestones
- identify potential technical problems
- identify potential taxonomic problems
- compare and integrate taxon character lists
- agree on character scoring methodologies
- identify suitable supplementary sources of data, information and images
Year 3 workshop
A second workshop of principal investigators and collaborators will be held early in the third year to review progress and map out the final stages of the project:
- review of the project to date
- identify and address any technical problems encountered
- identify and address any taxonomic problems encountered
- identify potential problems in final project stages
- confirm project time-line and milestones
- assess image requirements for final product
- identify sources of additional images
- decide appearance and layout details for the final product
- address any other outstanding issues of the project
Infrastructure and support
Although the database and server for the Electronic Pteridophyte Flora of Australia will be maintained at the Australian National Herbarium (CANB) in Canberra, the collaborative nature of this project aims to derive support from a wide national and international user base from the outset. In addition to technical support provided through ABRS, considerable infrastructural support will be provided by the participants:
- Database and computing applications, storage and network services provided by the Australian National Botanic Gardens and the Australian National Herbarium (CANB)
- Office accommodation and support provided by CANB and host institutions of collaborators
- Additional technical and botanical support provided by herbarium staff at these institutions
- Library support provided by staff at these institutions
- IT support and network connections provided by the IT sections at these institutions
- Taxonomic expertise and information will be provided from acknowledged experts in the pteridological community
Access to data and information
The data, information and other objects required for this Electronic Pteridophyte Flora of Australia project are held by a variety of institutions and jurisdictions. Access to and permission to use these items will be sought from the relevant sources:
- Negotiations will take place with ABRS and the publishers on access to electronic information on pteridophytes in volumes 48, 49 and 50 of the Flora of Australia for use in this project
- Negotiations will take place through ABRS, the publishers and copyright holders on access to illustrations and photographic images of pteridophytes in volumes 48, 49 and 50 of the Flora of Australia
- Negotiations will take place with publishers and copyright holders on access to supplementary text, illustrations and photographic images of pteridophytes in other published works that may be of use or relevance to this project
- Negotiations will take place through CHAH and HISCOM on access to herbarium specimen data and images of Australian pteridophytes.
- Pteridophyte images from the National Plant Photograph Index are available for this project and additional Pteridophyte photographs will be sought for this collection.
- Public contribution of images of Australian Pteridophytes will be invited, and appropriate copyright arrangements will be established for all images used in the project
Project management and quality control
The project will be managed by the principal collaborators at the Australian National Herbarium in consultation with external project collaborators. Quality and appropriateness of design and information content will be assured through the following:
- Information content will be subject to peer and editorial review following the guidelines for Flora of Australia
- Staff will work in close collaboration with ABRS Flora editorial staff to ensure harmony with current editorial convention and standards.
- Project control will be through regular meetings (quarterly) of Canberra-based investigators, support staff, with representatives from ABRS
- Products from each of the three stages of the project will be offered for external peer review
The Future
There are 94 species in common between Australia and New Zealand, representing c. half the fern flora of New Zealand and almost a quarter of fern flora of Australia. This suggests fruitful avenues for partnership and the sharing resources and effort between the two projects.
Collaborator Bob Chinnock has extensive knowledge of the Australian and New Zealand fern floras. New Zealand collaborator Patrick Brownsey has wide knowledge of a number of complex Australian genera (Asplenium and Hypolepis) and has a well advanced DELTA interactive key to the pteridophytes of New Zealand.
Collaboration and joint development in this area will be pursued at the outset of the project. Of particular interest is the prospect of shared maintenance and ongoing support of the datasets, and the development of a supplementary project proposal in this area will be explored.
Indicative duties of additional technical and other support
The following are indicative duties that would be performed by the external technical support at each stage of the project:
Part-time technical support - Year 1
- Checking Flora data exports provided by ABRS for completeness and consistency
- Editing data exports to ensure well-formed XML and compatibility with XML loading process
- Checking Oracle database for correct loading and consistency
- Checking and editing of data elements in database tables
- Liaising with APNI staff on Pteridophyte names missing or wrongly recorded in APNI
- Verifying links of Flora names to APNI names, correcting where necessary
- Verifying and correcting links to currently accepted names, based on advice from APNI
- Scoring exemplar taxa/character matrices as a test for year 2 phase
- General project support
Full-time technical support - Year 2
- Data checking, verifying and correcting tasks in line with Year 1
- Score characters for all taxa in line with agreed character sets
- Advise on workability of characters and adjustments that may be necessary
- Assist with building interactive key application
- Test and evaluate interim key for all taxa
- Correct data matrices as necessary
- Prepare exemplar taxon and character images as a test for year 3 phase
- Incorporate exemplar images into interim interactive key application
- General project support
Full-time technical support - Year 3
- Data checking, verifying and correcting tasks in line with Year 1 and Year 2
- Continue verifying and correcting data matrices
- Assist with selection of character and taxon images
- Liaise with graphic designer on images needed for interactive keys
- Incorporate character images into interactive key application
- Incorporate taxon images into interactive key application
- Check and correct placement of all images in interactive key application
- Test and evaluate final interactive key for all taxa
- General project support
Graphic design services - Year 3
- Digitize character images from line art and photographic slides
- Digitize taxon images from photographic slides
- Liaise with project staff on suitable image formats and standards
- Adjust images to appropriate formats and resolutions for interactive keys and web delivery
- Provide advice and input on visual aspects of interactive key application