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Definitions

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Definitions – PowerPoint PPT presentation

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Title: Definitions


1
AVH - Australias Virtual Herbarium Logo
Jim Croft Centre for Plant Biodiversity
Research Australian National Herbarium
2
Australias Virtual Herbariumstoring and
interchanging botanical data on-line
  • Jim Croft
  • Centre for Plant Biodiversity Research
  • Australian National Herbarium
  • jrc_at_anbg.gov.au
  • http//www.anbg.gov.au/jrc/

3
Storage Industry speak
  • Role of Industry / Cost of storage infrastructure
    relative to project / Business competetiveness /
    Strategic business advantage / Justify investment
    / Return on Information (ROI) / Ever-changing
    environment / Interoperability / Linking
    geographically dispersed sites/ Availability all
    the time, everywhere, forever / Storage strategy
    / Effective storage management / Right storage
    architecture / Faster storage environment /
    Advanced database technologies / Optimising
    availability, performance, placement, recovery /
    Flexible future-proof IT infrastructure / Data
    storage to assist RD / Replication for disaster
    recovery / Benefits of central disaster recovery
    / Necessity to plan ahead / Staged implementation
    approach / Lead organizational change

4
Herbarium botany speak
  • Herbarium / Plants / Regional floristics /
    Preserved botanical specimens / Taxonomic
    hierarchy and taxon ranks / Nomenclature,
    synonymy / Alternative phylogenies and
    classifications / International Code of Botanical
    Nomencalture / Identification keys / Original,
    derived and modifided data / Localities, geocodes
    / Data accuracy and precision / Habitat,
    altitude, depth, substrate / Biological images /
    Geospatial modeling and visualization /
    Environmental modeling and prediction / Species
    distributions and occurrence / Biological
    descriptive frameworks / Interactive
    identification / Flora Information systems /
    Landcover species / Curatorial standards /
    Cryptogams / Gymnosperms / Platyzomataceae /
    Eucalyptus camaldulensis

5
AVH - The Big Questions
  • The 6 Ws
  • Who?
  • What
  • Where?
  • When?
  • Why?
  • hoW?

6
AVH - The Big Questions
  • What is the AVH?
  • Why should the AVH happen?
  • Where does the AVH happen?
  • Who does the AVH happen for?
  • When does the AVH happen?
  • hoW does the AVH happen?
  • Whence the AVH?

7
What is a Herbarium?
  • A physically and administratively secure building
  • A managed archival scientific collection of
    preserved plant specimens
  • A research environment and resource for botanical
    systematic and taxonomic resource
  • A taxonomic, spatial and temporal information
    base for botanical research, environmental
    decision-making and public information

8
Platyzoma micropyllum
9
Platyzoma micropyllum
10
Platyzoma micropyllum
11
Platyzoma micropyllum
12
Herbarium Specimens
13
Compactus storage units
14
Compactus storage units
15
Botanical Library
16
Botanical literature
17
Specimen Data Capture
18
Public Reference Herbarium
19
What is a Virtual Herbarium?
  • The physical resources and biological information
    of a herbarium represented digitally
  • On-line access to herbaria and to botanical
    information managed by herbaria
  • Integrated access to botanical information from
    various sources in a herbarium and other on-line
    botanical information

20
What is the AVH?
  • A collaborative project of the Australian
    Herbarium community, providing
  • Partnership and shared access to each others data
  • Real-time access to current working data
  • Shared access to common authority files
  • A shared development environment
  • Opportunity to shared data-hosting, archiving and
    off-site backup.
  • Co-ownership of the final product

21
The pilot distribution of Acacia aneura, mulga
22
Acacia aneura Distribution of specimens from
each herbarium
23
Overlays
24
Geocode accuracy Survey data
25
A Herbarium Database Structure
26
(No Transcript)
27
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 be and appear more
    responsive to community needs

28
What is the Problem?
  • 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 Aust. herbaria
  • 50-100 data elements per specimen
  • Several Kb per specimen

29
Where is the data?
  • In each herbarium (largest 1.3 million specimens)
  • Pooling data centrally not acceptable for
    operational, political and emotional reasons.
  • Therefore we need a distributed data management
    and access solution, maintaining and ensuring
    custodial responsibility

30
Where is the data?
  • Images compound the problem
  • Several Kb and up for plant images (possibly
    100,000 available)
  • Specimen images need high resolution, up to 20 Mb
    or more
  • Need to be sub-sampled for web display
  • At least 100,000 type specimens
  • Ideally all 6.5 million should be done

31
Where is the AVH?
  • Spread across Australian herbaria
  • Data distributed resides with custodians
  • Each herbarium has a portal to receive requests
    to and deliver data from its database
  • Each herbarium hosts a common AVH query interface
    that polls all herbaria and integrates and
    returns data as a single query

32
Major Australian Herbaria
33
Who are the participants?
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
34
Holdings of Aust. Herbaria
35
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36
Who runs the AVH?
  • The Council of Heads of Australian Herbaria
    (CHAH).
  • The Herbarium Information Systems Committee
    (HISCOM)
  • IT staff at each herbarium (technology)
  • Botanical staff at each herbarium (content)
  • Scientific staff at each herbarium (validation)

37
Aust. NZ Environment Conservation Council
  • Government committee of Commonwealth and
    State/Territory Environment Ministers
  • Accepted that the community wanted the product
  • Funding options and regional support
  • Working group
  • Project design input - new name

38
The Agreement
  • 10 million project over five years
  • Capture new data and validate old
  • State/Territory to contribute amount relative to
    specimens to be databased/validated
  • 4 million Commonwealth 4 million
    State/Territory 2 million private
  • Sharing data critical to cost (cf. 16 million)

39
Who uses the AVH?
  • The participating herbaria get access to all the
    data at the highest precision.
  • Public access filter restricts access to work in
    progress, sensitive locality data, etc.
  • Access to conservation agencies, environmental
    decision makers
  • Research and education
  • Public general interest

40
GREENING THE GRAINBELT
Uses
41
Uses
42
When did the AVH happen?
  • Basically this year
  • But we have been working towards it for over 12
    years
  • And there have been the occasional dead ends and
    setbacks, waiting for technology, capacity,
    support, etc.

43
Brief History of the AVH
  • 1995 - HISCOM recommends the AVH concept (a
    distributed database) to CHAH
  • 1997 - Canvassed at Systematics meeting
  • 1999 - Proof of concept with Acacia
  • 2000 - Government Minister shows interest
  • 2000 - Interest from industry/foundations
  • 2000 - Negotiating cost lobbying

44
Recent Activity
  • Major item at October CHAH meeting- Agreement on
    what information we provide to community -
    Priority groups and Who does what?
  • Trust to oversee financial arrangements
  • Liaison and Advisory Committee

45
Evolution of the AVH
Need for common semantic schema recognized
Standard syntax
Race to database
HISPID
Botanical ontology?
Need for semantic standard recognized
Exchange
Distributed query
46
hoW does the AVH work?
  • On a number of different levels
  • Politically
  • Administratively
  • Technically
  • Scientifically

47
AVH General Architecture
48
(No Transcript)
49
Standards
URL
XSL
T
XPATH
RDF
XML
SVG
BNF
UML
ITF
UDDI
Z39.50
URI
XHTML
SOAP
Dublin Core
Z39.19
HTTP
DOM
RDFS
PNG
HISPID
ASN.1
SAX
CSS
WAIS
XML schema
cgi
RMI
50
Whence the AVH?
  • A new era of integrated access to botanical
    information
  • New ways of visualizing data form different
    sources
  • New ways on managing and validating data across
    remote databases
  • More automation, more speed, higher throughput

51
Added extras - the real AVH
  • Stage 1 databasing (dots on maps)
  • Plus map overlays, precision flags, spatial
    queries, pretty interfaces, etc.
  • Conflicting taxonomies - towards a National
    Census
  • Stage 2 images, descriptions, identification
    tools
  • Multiple resources and options (cf. library)

52
Botanical illustrations
53
Plus
54
But...
55
Integrated strategies for tackling fungal
biodiversity
But...
  • Problem 250,000 spp., 5 known, few herbarium
    collections
  • Solution Fungimap
  • Community mapping of 100 common species by 600
    volunteers
  • Distribution and habitat data leads to better
    conservation and systematics

56
Australian eFloras and other digital products
57
Australian eFloras and other digital products
58
Australian eFloras and other digital products
59
Why it will work
  • Communication - CHAH, few herbaria
  • Collaboration - long-standing, data sharing,
    overcoming Australias Federal/State system
  • Champions - management, public
  • Lobbying and profile of herbaria
  • Relevance of product
  • And nowwe need to maintain commitment to project
    (e.g. impact on research outputs and other
    organisational initiatives)

60
Future technology
  • Currently very simple architecture and technology
  • Increase in Complexity and bulk is inevitable
  • Can not avoid engaging computer scientists and
    the computer industry
  • Optimize data storage
  • Optimize data access and delivery
  • Optimize analysis and visualization
  • Optimize knowledge discovery

61
Participants
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
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