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On-line%20Flora%20of%20Australia

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Jim Croft initial schema design, proof of concept ... T: Facing Island, Qld, i R.Brown Iter Austral. 102 /i ; lecto: BM. /p p Illus. ... – PowerPoint PPT presentation

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Title: On-line%20Flora%20of%20Australia


1
On-lineFlora 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

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

2
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

3
Background
4
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.
5
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 database Structured tables in
    Oracle accommodate all data elements
  • Import Flora XML files Oracle accommodate all
    data elements

6
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

7
Electronic Flora of Australia
  • Design query interfaceUsing HTML forms
  • Design output formatsHTML for maximum
    compatibility
  • Test output results For structure and
    completeness
  • Adjust, correct code, correct markup,
    rerunetc., etc., etc

8
Structure of a Flora
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11
A Flora structure in XML
12
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.

13
What does XML look like?
Example in HTML ltpgtltbgtPlatyzoma microphyllumlt/bgt
R.Br., ltigtProdr.lt/igt 160 (1810)lt/pgt ltp
gtltigtGleichenia platyzomalt/igt F.Muell., ltigtVeg.
Chatham.-Isl.lt/igt 63 (1864). T Facing Island,
Qld, ltigtR.Brown Iter Austral. 102lt/igt lecto
BM.lt/pgt ltpgtIllus. S.B.Andrewslt/pgt ltpgtRhizome
short-creeping Sporangia in zones in distal half
of frond. Fig. 55lt/pgt ltpgtWidespread across
northern Australia Grows in sandy or swampy
soils.... Map 135.lt/pgt ltpgtW.A. 14.4 km NW of
Mtlt/pgt
Example in XML lttaxongtltnamegtPlatyzoma
microphyllumlt/namegt ltauthorgtR.Brlt/authorgt,
ltpublicationgtlttitlegtProdr.lt/titlegt
ltpagegt160lt/pagegtltdategt1810lt/dategt
lt/publicationgt ltsynonymgt ltnamegtGleichenia
platyzomalt/namegt ltauthorgt F.Muell.
lt/authorgtltpublicationgtVeg. Chatham.-Isl.lt/publicat
iongt ltpagegt63ltpagegt ltdategt1864lt/dategt lttypegtT
Facing Island, Qld, lt/typegtlt/synonymgt ltillustrati
ongtIllus. S.B.Andrewslt/illustrationgt ltdescriptio
ngtRhizome short-creeping Sporangia in zones in
distal half of frond. lt/descriptiongt ltfiguregt
Fig. 55 lt/figuregt ltlocalitygtWidespread across
northern Australia lt/localitygtlthabitatgtGrows in
sandy or swampy soils...lt/habitatgt ltmapgtMap
135.lt/mapgt ltspecimensgtW.A. 14.4 km NW of
Mtlt/specimensgtlt/taxongt
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Fl. Australia XML Schema fragment
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XML Schema is itself a structured XML document
21
A Flora structure in a database
22
Fl. Australia database structure
23
Using structured Flora data
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Interactive Plant Identification
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Flora of Australia Examples
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Telopea speciosissima (Proteaceae)
State flower ofNew South Wales
the Waratah
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48
A general structure for Floras?
49
Floras
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Monographs
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Serial Floras
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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

58
Potential for a virtual multi Flora
Clients
Common Web portals
Gateways
Databases
59
Concept for Flora production
60
An old process of publication
W-P file
Botanist
Editors
W-P file
Publisher
C-R Copy
Book, etc.
61
An new process of publication
W-P file
Botanist
Editors
W-P file
Publisher
C-R Copy
XML file
Outputs
Book, etc.
Database
XML file
Outputs
62
An future process of publication
Botanist
Database
Editors
Publisher
C-R Copy
XML file
Outputs
Book, etc.
Database
Outputs
63
Issues for Flora production
64
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.

65
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.

66
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.

67
Availability
  • The on-line Flora of Australia will be freely
    available.
  • ABIF-Flora
  • Australias 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.

68
Recommendations
69
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?

70
Doodia aspera (Blechnaceae)
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