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Biodiversity%20Informatics

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Title: Biodiversity%20Informatics


1
Biodiversity Informatics
  • Biodiversity informatics and the manipulation of
    biological information
  • Jim Croft
  • jrc_at_anbg.gov.au

2
Outline
  • Biodiversity Informatics
  • Australias Virtual Herbarium as a model of use
    and management of biodiversity knowledge
  • New ways of managing biological knowledge
  • Information management issues
  • Current trends and future directions in
    biodiversity knowledge management

3
Biodiversity Informatics
  • Management of our knowledge of biodiversity using
    modern techniques of data and information
    management

4
Taxonomy of Database Interoperability
Multi-database systems
Autonomous
Non-federated
Federated
Loosely coupled
Tightly coupled
Multiple schemas
Unified schema
Sheth Larson (1990)
5
Tightly Coupled
  • Central administration
  • Semantic consistency
  • Schemas
  • Authority files
  • Common technology
  • Difficult to implement
  • Proprietary solutions tolerated
  • Expensive

6
Loosely Coupled
  • Closer to Reality
  • Independent management
  • Suited to scientific systems
  • Common publication syntax
  • Export schema
  • Less functionality Doable
  • Need open standards

7
Intermediate Coupling
  • Scientific Independence
  • Common syntax semantics for the exchange of
    information.
  • Import/export
  • HISPID, Darwin Core, TDWG/CODATA abcd
  • Leverage Existing Open Standards
  • Participation in wider, more loosely coupled
    federations
  • Simplicity
  • Distribution of effort

8
Data Refinement
action
knowledge
information
Increasing refinement utility of data
data
observations
the real world
9
Herbarium Specimens
10
Specimen Data Capture
11
Specimen Data
  • The core information is from herbarium specimens
  • Beyond taxonomy names
  • Collections data
  • Scientific name
  • Collection date
  • Collector name number
  • Location
  • Soils
  • Habitat (incl. topography)
  • Vegetation community
  • Associated species

12
A Herbarium Database Structure
13
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14
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15
What do we want to know?
  • What species does a plant belong to?
  • What is its name?
  • What other species is it related to?
  • What does it look like?
  • Where does it grow?
  • Where might it grow?
  • What other species grow with it?
  • What species grow in a defined area?
  • How did they get there?

16
What is a Virtual Herbarium?
  • An on-line digital representation of a scientific
    collection of preserved plant specimens and
    botanical information

17
What is the AVH?
  • Spread across Australian herbaria
  • Data distributed resides with custodians
  • Each herbarium has a portal to receive requests
    and to deliver data
  • A common single query AVH interface in each
    herbarium polls all herbaria

Major Australian Herbaria
18
AVH Partners
State Herbarium of South Australia Queensland
Herbarium Australian National Herbarium Northern
Territory Herbarium Tasmanian
Herbarium Industry Partner KE Software
National Herbarium of Victoria National
Herbarium of New South Wales Western Australian
Herbarium Australian Biological Resources Study
19
Why is there an AVH?
  • Pressure on Herbaria to work more efficiently
  • Demand for access to larger amounts of data
  • Demand to access data more quickly
  • Demand to view data in different ways
  • Pressure on herbaria to appear and to be more
    responsive to community needs

20
What is the AVH task?
  • gt 18,000 species of higher plants
  • gt 64,000 available names
  • Extensive synonymy (4 names per plant)
  • 8 major government-funded herbaria
  • Similar number of university herbaria
  • gt 6,500,000 specimens in Aust. herbaria
  • 50 -100 data elements per specimen
  • Several Kb per specimen (excl. images)

21
Herbarium database status
22
The AVH Agreement
  • 10M over 5 years to database all major
    Australian herbarium collections
  • 10 million - 4 million Commonwealth
  • - 4 million State/Territory
  • - 2 million private
  • Initial focus on capture of herbarium specimen
    data
  • Ultimate aim a complete flora information system

23
Australias Virtual Herbarium
  • On-line access to herbarium specimen information
    and botanical knowledge

24
Australian Plant Name Index (APNI)
25
www.anbg.gov.au/apni
26
www.anbg.gov.au/win
27
http//www.chah.gov.au/avh.html
28
Acacia
salicina
29
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30
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31
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32
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33
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34
Research PotentialPlant distribution analysis
Pultenaea distribution classes in eastern
Australia
?
?
Incurved
Recurved
35
Flora Information Systems
  • On-line systems
  • Often regionally based
  • Integrating
  • Plant names and synonyms
  • Descriptive Flora treatments
  • Illustrations
  • Distributions
  • etc.

36
Flora Information Systems
37
Botanical illustrations
38
National Plant Photograph Index
  • Search all records on-line
  • Digital images available (best of class)
  • 35,000 images of Australian plants and vegetation

www.anbg.gov.au/anbg/photo-collection/
39
Type Images on demand
High resolution image oftype specimen of
Austrobaileyadownloaded over the Internetfrom
the Herbarium of theNew York Botanical Garden
40
Flora Revision Databases
  • New ways of managing and delivering botanical
    information

41
A Flora in XML
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
42
A Flora XML Schema fragment
43
A Flora database structure
44
A Flora database report
45
An old process of publication
W-P file
Botanist
Editors
W-P file
Publisher
C-R Copy
Book, etc.
46
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
47
A future process of publication
Botanist
Database
Editors
Publisher
C-R Copy
XML file
Outputs
Book, etc.
Database
Outputs
48
Interactive Identification
  • Using computers to identify and name plant
    species and display information about them

49
Interactive Plant Identification
50
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51
Current trends, future directions
  • ?

52
Trends in Biodiverssity Information Management
  • Nomenclatural
  • Regional
  • Text-based
  • Taxon-based
  • Individual effort
  • Single user
  • Standalone
  • Centralized
  • Proprietary System
  • Idiosyncratic Design
  • Nonstandard data content
  • Conventional
  • Developmental
  • Access charges
  • ? Taxonomic
  • Global
  • Image-based
  • Spatially-based
  • Partnerships
  • ? Multiuser
  • ? Networked
  • ? Distributed
  • ? Open System
  • ? Standard Architecture
  • ? Standard data content
  • ? Innovative
  • ? Stable
  • ? Freely available

53
Global Organization
  • Several parallel and complementary initiatives
  • Global Biodiversity Information Facility (GIF)
  • Taxonomic Databases Working Group (TDWG)
  • Global Taxonomic Initiative (GTI)
  • International Organization for Plant Information
    (IOPI)
  • Species 2000
  • All Species Foundation (ALL)

54
www.gbif.org
55
Data Flow within GBIF Network
User Browser
HTML Data
HTML Data
GBIF Portal
Participant Node
Participant Node
Aggregated Data
Aggregated Data
Service Metadata
Service Metadata
Detailed Specimen Data
Service Metadata
Detailed Specimen Data
Specimen Index Data
Service Metadata
Collection Node
Collection Nodes
56
www.all-species.org
57
www.all-species.org
58
www.all-species.org
59
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60
Requirements for Interoperability
  • Standards

61
Standards for Interoperability of Biodiversity
Databases
cgi
URL
XSL
T
XPATH
RDF
SVG
abcd
BNF
UML
ITF
UDDI
Z39.50
URI
XHTML
SOAP
Dublin Core
Z39.19
HTTP
DOM
RDFS
PNG
HISPID
ASN.1
WSDL
SAX
CSS
WAIS
XML schema
DARWIN CORE
RMI
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