Presentation on theme: "Jim Croft Centre for Plant Biodiversity Research, Australian National Herbarium & Australian National Botanic Gardens Helen Thompson ; Scott Payne Australian."— Presentation transcript:
Jim Croft Centre for Plant Biodiversity Research, Australian National Herbarium & Australian National Botanic Gardens Helen Thompson ; Scott Payne Australian Biological Resources Study, Environment Australia Greg Whitbread Centre for Plant Biodiversity Research, Australian National Herbarium & Australian National Botanic Gardens Jim Croft – initial schema design, proof of concept Helen Thompson – project management, schema design, MS Word macros for XML markup, image scanning Scott Payne – database and application design, Java Greg Whitbread – initial database and application design, data import, Java
Outline Background to the project Structure of a Flora Structure of a Flora in XML Structure of a Flora in a database Using structured Flora data Flora of Australia examples A general structure for Floras? Concept for Flora production Issues for Flora production Suggestions / Recommendations
Flora of Australia pteridophytes Three separate volumes in the Flora of Australia The Electronic Pteridophyte Flora of Australia will integrate all these treatments a single on-line resource. Volume 48 includes all ferns and fern allies from mainland Australia Volume 49 covers the oceanic islands of Norfolk Is and Lord Howe Is. Volume 50 covers the oceanic islands of Christmas Is and Macquarie Is.
Electronic Flora of Australia Design schema for published Flora Using XML Schema; accommodate all data elements Markup published Flora MS Word macros to replace style with XML tags Design relational database Structured tables in Oracle; accommodate all data elements Import Flora XML files Oracle; accommodate all data elements
Electronic Flora of Australia Test, adjust schema, correct markup, re-import Refinement of structure, data and process
Electronic Flora of Australia Design query interface Using HTML forms Design output formats HTML for maximum compatibility Test output results For structure and completeness Adjust, correct code, correct markup, rerun etc., etc., etc…
What is XML? XML, or Extensible Markup Language A text markup language using simple and intuitive embedded plain text coding tags Similar in appearance to the Hypertext Markup Language, HTML, used on the World Wide Web. HTML controls the appearance of text delivered to Internet browsers XML describes and controls the structure and content of a document. XML and other style-sheets control the appearance on text based on its structure and content Hierarchical sets of rules known as XML Schema can transform a word-processed text document into a structured, internally consistent, flexible database XML can be imported into other databases or modern XML enabled browsers and computer applications to present selected views of the data in different ways.
What does XML look like? Example in HTML Platyzoma microphyllum R.Br., Prodr. 160 (1810) Gleichenia platyzoma F.Muell., Veg. Chatham.-Isl. 63 (1864). T: Facing Island, Qld, R.Brown Iter Austral. 102 ; lecto: BM. Illus.: S.B.Andrews… Rhizome short-creeping… Sporangia in zones in distal half of frond. Fig. 55 Widespread across northern Australia… Grows in sandy or swampy soils.... Map 135. W.A.: 14.4 km NW of Mt… Example in XML Platyzoma microphyllum R.Br, Prodr Gleichenia platyzoma F.Muell. Veg. Chatham.-Isl T: Facing Island, Qld, … Illus.: S.B.Andrews… Rhizome short-creeping… Sporangia in zones in distal half of frond. Fig. 55 Widespread across northern Australia… Grows in sandy or swampy soils... Map 135. W.A.: 14.4 km NW of Mt…
Fl. Australia XML Schema fragment
XML Schema is itself a structured XML document
Fl. Australia database structure
Interactive Plant Identification
Telopea speciosissima (Proteaceae) the ‘Waratah’ State flower of New South Wales
Potential for a virtual multi Flora Using the ‘Virtual Herbarium’ model / DIGIR A shared generalized Flora schema Structured Flora in on-line databases Common gateways to access Flora data XML packaging of data Integrating portal to pull in data from several sources View taxa according to various search criteria View taxa in different sort orders View restricted subset of taxon information Compare different Flora treatments of the same taxon with a single query Add contemporary information from other data sources Taxonomy; species lists; illustrations; maps
ClientsCommon Web portals GatewaysDatabases Potential for a virtual multi Flora
W-P file EditorsW-P file Botanist Publisher C-R Copy Book, etc. An old process of publication
W-P file EditorsW-P file Botanist Publisher C-R Copy Book, etc. An new process of publication XML file DatabaseXML fileOutputs
Editors Botanist Publisher C-R Copy Book, etc. An future process of publication XML file DatabaseOutputs Database Outputs
Issues & implications for Flora publication Application of XML, relational database and Internet technology for Flora publication: Compilation Production Query and Delivery process It offers considerable benefit in terms of: Data management, integrity Flexibility Productivity.
Issues & implications for Flora publication Compilation of Floras in a database context: greater control over consistency and completeness high standards for the printed product in mind. XML transformation capabilities: greater flexibility in how information is displayed maintains editorial style and standards production of the traditional printed product.
Issues & implications for Flora publication Internet access to Flora information: will facilitate access to a wider audience Management within an on-line database framework: will facilitate on-going maintenance reduce the progressive aging of Flora treatments. Access to information on demand: will enable local production of tailored and more focused treatments based on local regional, taxonomic and other requirements.
Availability The on-line Flora of Australia will be freely available. ABIF-Flora Australia’s Virtual Herbarium XML is already freely available. XML development tools are available, but not free e.g. XMLSpy, XML Authority Browsers that use XML are freely available IE6, NS6 Other products are becoming XML enabled MS Word MS Excel, etc. The ABIF-Flora DTD/Schema will be freely available.
Recommendations Floras can apply database and XML technology to compile and manage past, present and future Flora treatments Floras could use existing treatments to evaluate and test this technology and obtain permission to make the data, images and maps from these treatments available on the Internet. Floras can start doing it now… Concept being considered by Flora of Paraguay, Flora of Taiwan. ?Flora Malesiana? ?FNA?