building the atlas of living australia
DESCRIPTION
Donald, Hobern, the Director of the Atlas of Living of Living Australia presented a talk entitled, "Building the Atlas of Living Australia"The Atlas of Living Australia (ALA) is a partnership between Australian natural history collections and biodiversity research groups. It is developing systems to provide integrated access to all classes of biodiversity data (including names and classification, geospatial data, images, sequences, literature, identification tools and species interactions). The central component will be an information repository which catalogues all data sources and makes them available to support research, policy and education.TRANSCRIPT
The Environment InstituteWhere ideas grow
Donald Hobern
Building the Atlas of Living Australia
Atlas of Living Australia - sharing biodiversity knowledge
Banksia serrata L.f.
Kingdom: Plantae
Division: Magnoliophyta
Family: Proteaceae
Subfamily: Grevilleoideae
Tribe: Banksieae
Subtribe: Banksiinae
Genus: Banksia L.f.
Old Man Banksia
= Isostylis serrata (L.f.) Britten
Identified as
Root rot
Phytophthora cinnamomi
Pathogen of
Banksia jewel beetle
Cyrioides imperialis
Larvae mine
stems
New Holland Honeyeater
(Phylidonyris novaehollandiae)
Feeds upon
nectar
Biology and
ecology
Molecular
biologyDistribution
Literature
Pollinates
= Sirmuellera serrata (L.f.) Kuntze
Saw Banksia
Biodiversity information
Atlas of Living Australia - sharing biodiversity knowledge
Biodiversity information
Locality: Reid, ACT
GPS: 35.280S 149.138E
Date: 1 January 2008
Uresiphita ornithopteralis (Guenée, 1854)
Kingdom: Animalia
Phylum: Arthropoda
Class: Insecta
Order: Lepidoptera
Family: Crambidae
Subfamily: Pyraustinae
Tribe: Pyraustini
Genus: Uresiphita Hübner, 1825
English: tree lucerne moth
= Mecyna ornithopteralis Guenée, 1854
Identified as
Braconidae - ? Chaoilta sp.
Parasitises
Huntsman spider
Holconia montana
Preys upon
Tagasaste (tree lucerne)
Chamaecytisus palmensis
Feeds upon
Biology and
ecology
Molecular
biology
Distribution
Fact sheets
Atlas of Living Australia - sharing biodiversity knowledge
The Atlas of Living Australia (ALA)
• Government-funded (NCRIS) project to June 2011
• Mission:
– To develop an authoritative, freely accessible, distributed and federated biodiversity data management system that links Australia’s biological knowledge with its scientific reference collections and other custodians of biological information
– To share biodiversity knowledge to shape our future
• Key data types:
– Specimens and Observations
– Names and Classifications
– Descriptions and diagnostic keys
– Images and other multimedia
– Molecular sequences
Atlas of Living Australia - sharing biodiversity knowledge
The Atlas of Living Australia (ALA)
• Funding– $8.2M for ALA from NCRIS in 2006-2011– $26.5M in-kind from ALA partners– $30M for ALA from EIF in 2009-2012
• Partnership– Government:
• CSIRO• Department of the Environment, Water, Heritage and the Arts• Department of Agriculture, Fisheries and Forestry
– State museums:• Australian Museum• Museum Victoria• Queensland Museum• Tasmanian Museum and Art Gallery
– Representative bodies: • Council of Heads of Australasian Herbaria• Council of Heads of Australian Faunal Collections• Council of Heads of Australian Entomological Collections• Council of Heads of Australian Collections of Microorganisms• Council of Australian Museum Directors
– Universities:• Southern Cross University• University of Adelaide
Atlas of Living Australia - sharing biodiversity knowledge
Implementation
Metadata (source, methods, ownership, access, etc.)
Data (collections, field observations, literature, molecular, images, expert knowledge, etc.)
Metadata
repository
Names and
ClassificationDistribution
Species
PagesRegional
Atlas
Annotation
Tools
Biosecurity
Portal
Uses (biosecurity, land-use, climate change, crop development, resource management, materials, forensics, taxonomy, etc.)
Links to
international
projects
Atlas of Living Australia - sharing biodiversity knowledge
Delivery
• Principles
– Open access to biodiversity information
– Link users to original data providers
– Support applied use of data
– Adopt and promote international data standards
– Develop open source software components
• Implementation
– User needs analysis – online report (December 2008)
– Geospatial data portal (GBIF code) (beta, June 2009)
– Taxonomic checklist services (beta, June 2009)
– Biodiversity information explorer (December 2009)
– Image, sequence, literature repositories (2010)
– Pest factsheets and regional atlas (2011)
– Citizen science portal (2011)
Atlas of Living Australia - sharing biodiversity knowledge
Project components
Conservation
Portal
Pest
Information
Portal
Biodiversity
Information
Explorer
Citizen
Science
Portal Regional
Atlas
GIS Tools
Geospatial
Data Cache
Directory of
Environmental
Layers
Field Capture
of Metadata
Accession
Processing
Digitisation
and Imaging
Support
Database
Integration
Wrappers
Integrated Data Sets
OZCAM AMRiN
AVH APPD
OBIS
ALA Project Office
Web Services
and User
Interfaces
Completed
National
Checklists
(AFD, APC,
etc.)
Community
Editing and
Workflow
Tools
Directory of
Taxonomic
Expertise
Legislative
and Thematic
Lists
Ontologies
and
Vocabularies
Quality
Control and
Sensitive
Data Tools
Metadata
Repository
Annotation
Services
User
Authentication
and Identity
Management
Species
Interactions
Sequences
(BOLD)
Digital
Literature
(BHL)
Descriptive
Data
(IdentifyLife)
Images
(MorphBank)
Data Dissemination Geo
sp
atia
l Data
Man
ag
em
en
t
Collection Data
Management
Au
stra
lian
Na
tion
al
Ch
eck
lists
Data Integration
Rich Data Stores
Atlas of Living Australia - sharing biodiversity knowledge
Australian national checklists
• Names and classification of all Australian organisms
– National checklists
– All groups of organisms
– Accepted names and synonyms
– Common names
– Informal and morphospecies names
– Legislative and thematic lists (red lists, invasive, etc.)
– Collaborative editing tools
– Tools to support use of lists
Atlas of Living Australia - sharing biodiversity knowledge
Geospatial data management
• Geospatial Information Systems
– Partnership• Terrestrial Ecosystem Research Network
• Intgrated Marine Observing System
– Interoperable tools• Data caches
• Environmental layers
• Mapping tools
• Analysis frameworks
– Data from all sources• Collections
• Ecological field work
• Amateur observations
– Report species by region• Local government area
• Water catchment
• Bioregion
Atlas of Living Australia - sharing biodiversity knowledge
Collection data management
• Accession and curation of specimens– Whole collection community
• Herbaria• Faunal/entomological collections• Microbial collections
– Investment areas• Field capture of metadata• Imaging systems• Databasing software• Web hosting for data
– Enhance and support existing networks
• Australia’s Virtual Herbarium• Online Zoological Collection of
Australian Museums• Australian Plant Pest Database• Australian Microbial Resource
Information Network
ScientificName: Imbophorus pallidus
Family: Pterophoridae
Locality: Stirling Range
State: WA
DateCollected: 1963-09-15
Latitude: -34.3
Longitude: 118.0
CoordinatePrecision: 10000
CoordinateMethod: Google Earth
TypeStatus: Paratypus
Atlas of Living Australia - sharing biodiversity knowledge
Rich data stores
• Shared data repositories
– Descriptive data and diagnostic keys
• IdentifyLife – including DELTA support
– Images
• Mirror MorphBank
– Sequences
• Mirror Barcode of Life Database
– Digital literature
• Mirror Biodiversity Heritage Library
– Species interactions
• Develop national repository
• Project-based data management
– Store data centrally; present locally
Atlas of Living Australia - sharing biodiversity knowledge
Data integration
• Integrate data and information from all sources
– Shared structures, vocabularies and ontologies
– User comments, corrections and tags
– Data quality and potential sensitivity
– Organise data:
• By species
• By geographic region
• By ecosystem or habitat
• By trait (descriptive character, ecological function, etc.)
GBIF data for “Australia” intersecting Australian continent
GBIF data for “Australia” not intersecting Australian continent
Atlas of Living Australia - sharing biodiversity knowledge
Additional metadata from data mining
Resource: ANICSpecies: Cryptotermes cynocephalus
Species: Cryptotermes gearyi
Species: Cryptotermes hilli
…
Region: State NSW
Region: State QLD
Region: State: NT
…
Google Earth layer: http://data.ala.org.au/ …
Region: IBRA Central KimberleySpecies: Eucalyptus apodophylla
Species: Eucalyptus argillacea
Species: Eucalyptus bigalerita
…
Resource: ANH
Resource: ANIC
Resource: NSW Herbarium
…
Google Earth layer: http://data.ala.org.au/...
Species: Macropus giganteusResource: OZCAM MV
Resource: OZCAM SAMA
…
Region: State NSW
Region: State VIC
Region: State SA
…
Google Earth layer: http://data.ala.org.au/...
Enriched
Metadata
Atlas of Living Australia - sharing biodiversity knowledge
Data dissemination
• Develop tools and portals to deliver biodiversity information to end users
– Biodiversity Information Explorer
• Overview of all information (species pages)
• Linked pages for habitats, traits, etc.
– Conservation Portal
• Integration and analysis of site-based and collection data
• Habitat quality indicators
– Pest Information Portal
• Support biosecurity projects (ABIN, DEWHA, DAFF, etc.)
• Species factsheets and distribution analysis
– Citizen Science Portal
• Data management for amateur naturalists
• Links to research and data sharing networks
The Environment InstituteWhere ideas grow
Tomorrow’s Science Seminar
Speaker: Prof. Kym Anderson
Regional implications of climate change for the
Australian wine industry.