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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.

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On line flora of australia

  • 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

On-lineFlora of Australia

Jim CroftCentre for Plant Biodiversity Research, Australian National Herbarium & Australian National Botanic Gardens

Helen Thompson ; Scott PayneAustralian Biological Resources Study, Environment Australia

Greg WhitbreadCentre for Plant Biodiversity Research, Australian National Herbarium & Australian National Botanic Gardens

Structured data management in modern on-line Flora treatments


Outline
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
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
Electronic Flora of Australia

  • Design schema for published FloraUsing XML Schema; accommodate all data elements

  • Markup published FloraMS Word macros to replace style with XML tags

  • Design relational databaseStructured tables in Oracle; accommodate all data elements

  • Import Flora XML filesOracle; accommodate all data elements


Electronic flora of australia1
Electronic Flora of Australia

  • Test, adjust schema, correct markup, re-importRefinement of structure, data and process

  • Test, adjust schema, correct markup, re-importRefinement of structure, data and process

  • Test, adjust schema, correct markup, re-importRefinement of structure, data and process

  • Test, adjust schema, correct markup, re-importRefinement of structure, data and process


Electronic flora of australia2
Electronic Flora of Australia

  • Design query interfaceUsingHTML forms

  • Design output formatsHTML for maximum compatibility

  • Test output resultsFor structure and completeness

  • Adjust, correct code, correct markup, rerunetc., etc., etc…




What is xml
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
What does XML look like?

Example in HTML

<p><b>Platyzomamicrophyllum</b>R.Br., <i>Prodr.</i> 160 (1810)</p>

<p ><i>Gleichenia platyzoma</i> F.Muell., <i>Veg. Chatham.-Isl.</i> 63 (1864).T: Facing Island, Qld, <i>R.Brown Iter Austral. 102</i> ; lecto: BM.</p>

<p>Illus.: S.B.Andrews…</p>

<p>Rhizome short-creeping… Sporangia in zones in distal half of frond.Fig. 55</p>

<p>Widespread across northern Australia… Grows in sandy or swampy soils....Map 135.</p>

<p>W.A.: 14.4 km NW of Mt…</p>

Example in XML

<taxon><name>Platyzomamicrophyllum</name><author>R.Br</author>, <publication><title>Prodr.</title><page>160</page><date>1810</date></publication>

<synonym> <name>Gleichenia platyzoma</name><author> F.Muell. </author><publication>Veg. Chatham.-Isl.</publication><page>63<page><date>1864</date><type>T: Facing Island, Qld, …</type></synonym>

<illustration>Illus.: S.B.Andrews…</illustration>

<description>Rhizome short-creeping… Sporangia in zones in distal half of frond. </description><figure>Fig. 55 </figure>

<locality>Widespread across northern Australia… </locality><habitat>Grows in sandy or swampy soils...</habitat> <map>Map 135.</map>

<specimens>W.A.: 14.4 km NW ofMt…</specimens></taxon>


Fl australia xml schema fragment
Fl. Australia XML Schema fragment




Fl australia database structure
Fl. Australia database structure





Telopea speciosissima proteaceae
Telopea speciosissima (Proteaceae)

State flower ofNew South Wales

the ‘Waratah’






Potential for a virtual multi flora
Potential for a virtual multiFlora

  • 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


On line flora of australia

Potential for a virtual multiFlora

Databases

Gateways

Common Web portals

Clients



On line flora of australia

An old process of publication

Botanist

W-P file

Editors

W-P file

Publisher

C-R Copy

Book, etc.


On line flora of australia

An new process of publication

Botanist

W-P file

Editors

W-P file

Publisher

Outputs

XML file

C-R Copy

Outputs

Database

XML file

Book, etc.


On line flora of australia

An future process of publication

Botanist

Database

Editors

Publisher

Outputs

XML file

C-R Copy

Outputs

Database

Book, etc.



Issues implications for flora publication
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 publication1
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 publication2
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
Availability

  • The on-line Flora of Australia will be freely available.

    • ABIF-Flora

    • Australia’s Virtual Herbarium

  • XML is already freely available.

    • http://w3c.org/

  • 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.



Recommendations1
Recommendations

  • Florascanapply database and XML technology to compile and manage past, present and future Flora treatments

  • Florascould 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.

  • Florascanstartdoing it now…

  • Concept being considered by Flora of Paraguay, Flora of Taiwan. ?Flora Malesiana? ?FNA?


On line flora of australia

Doodia aspera

(Blechnaceae)


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