Presentation on theme: "AUSTRALIA’S VIRTUAL HERBARIUM"— Presentation transcript:
1 AUSTRALIA’S VIRTUAL HERBARIUM A national collaborative model for integrated access to distributed biological informationJim Croft, Greg WhitbreadAustralian National HerbariumKey Innovations in Biodiversity Informatics: Integrating Biodiversity DataAustralia's Virtual Herbarium: a national collaborative model for integrated access to distributed biological informationJim Croft &.Greg Whitbread (15-20 minutes)Australian National Herbarium, Centre for Plant Biodiversity Research, CanberraThe Australia's Virtual Herbarium (AVH) is a collaborative project of the Australian botanical community providing integrated access to on-line botanical information from the scientific collections and resources of Australian herbaria in a national partnership with a formal agreement between participants. With new funding of $Aus 10 million over 5 years, the initial phase of the AVH project is to database and make available taxonomic, distribution and occurrence information associated with all 6.5 million herbarium specimens held across the country through a simple on-line GIS application; the ultimate aim is to provide a complete integrated flora information system as a tool for scientific research, environmental decision-making and public information.The AVH is based on a distributed heterogeneous database information system, so that the data resides with and is managed and controlled by the custodians and each herbarium has a portal to receive requests and to deliver data from its institutional databases. A shared common AVH query interface in each herbarium polls all participating herbaria and delivers a single integrated result. The design philosophy of the AVH is based on information standards developed by and for the botanical community, open architecture, public domain software and free availability of the application and information management structures for use in other biodiversity documentation projects. It is the intention of the AVH to adapt its architecture and information standards to those being adopted or endorsed internationally in biodiversity informatics frameworks such as TDWG and GBIF.The AVH marks an unprecedented level of cooperation between institutions at a national level and has been driven by a collective desire on the part of the herbarium community to be more responsive to community needs in providing access to larger amounts of data more rapidly and the need for herbaria to work more efficiently within a declining resource framework. The acceptance and thus success of the project lies in the relevance of the product for a wide range of users, including applications for research, industry and education, for conservation agencies, land managers and environmental decision makers.
2 Outline of presentation Background to the AVHWhat is the AVH ?Aspects of the AVHPlant names, specimensPlant images, plant identification toolsUses and users of the AVHBotanical researchCommunity projectsSummary
3 What is a Virtual Herbarium? The physical resources and biological information of a herbarium represented digitallyOn-line access to herbaria and to botanical information managed by herbariaIntegrated access to botanical information from various sources in a herbarium and other on-line botanical information
4 What is the AVH?A collaborative project of the Australian Herbarium communityDigitalCollaborativeOn-lineIntegratedPartnership and shared accessReal-time accessShared access to common authority filesShared data-hosting, archiving and backupCo-ownership
5 Where is the AVH? Spread across Australian herbaria Data distributed; resides with custodiansEach herbarium has a portal to receive requests and to deliver dataA common single query AVH interface in each herbarium polls all herbariaMajor Australian Herbaria
6 AVH Partners State Herbarium of South Australia Queensland Herbarium Australian National HerbariumNorthern Territory HerbariumTasmanian HerbariumIndustry Partner:KE SoftwareNational Herbarium of VictoriaNational Herbarium of New South WalesWestern Australian HerbariumAustralian Biological Resources Study
7 Why is there an AVH? Pressure on Herbaria to work more efficiently Demand for access to larger amounts of dataDemand to access data more quicklyDemand to view data in different waysPressure on herbaria to appear and to be more responsive to community needs
8 Potential users of the AVH The participating herbaria have access to all the data at the highest precisionPublic access filter restricts access to work in progress, sensitive locality data, etc.Research and educationPublic general interestAccess to conservation agencies, land managers, environmental decision makers
9 There is some urgency … Historical ignorance Australia’s biodiversity has been damagedAt risk from inappropriate land management practicesWe know a lot about what not to doRedressing the damage, and managing better for the future, requires sound informationSustainable natural resource management needs scientific knowledgewhat was there and where it occurredwhat is there now
10 There is some urgency …19072002In concluding our presentation this afternoon I want to bring you back to think about the importance of collaborative efforts and of disseminating the results of our researchWhen this picture, from a 1907 land sale catalogue, was being used as a positive image, well meaning govt subsidies had resulted in what you see here – ringbarked trees and cleared land, although one selling point was that it was yellowbox country – with the implication that it was good country.Now – with govt money in the NHT and the NAP we are now replanting these same landscapes [Murray’s slide of planting sites]We need to do this intelligently using the best information and knowledge we canSo that the decisions are not made in isolation of that knowledge, we as researchers need to make it accessible for our partners and to synthesise it for others to use and apply.In this way we see that the collections and national botanical databases will contribute significantly to the Healthy Country Flagship program with biodiversity informatics playing a strong underpinning role in such areas as restoration biology.And hopefully we can win back far more of the resources than the division commits to the BHAG.I hope we’ve given you a snapshot of how we are going about that via biodiversity informatics.
11 What is the problem? > 20,000 species of higher plants > 64,000 available namesExtensive synonymy (4 names per plant)Many alternative taxonomic concepts8 major government-funded herbariaSimilar number of university herbaria> 6,500,000 specimens in Aust. herbariadata elements per specimenSeveral Kb per specimen (excl. images)
14 The AVH Agreement - $ 4 million State/Territory - $ 2 million private $10M over 5 years to database all major Australian herbarium collections$10 million: - $ 4 million Commonwealth- $ 4 million State/Territory- $ 2 million privateInitial focus on capture of herbarium specimen dataUltimate aim a complete flora information system
15 Australia’s Virtual Herbarium On-line access to herbarium specimen information and botanical knowledge
16 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?
17 Data refinement Envir. decision making Policy & strategy conservationrestoration biologyresource mgmtutilisationPolicy & strategygovernmentcorporateindividualactionknowledgeinformationIncreasing refinement & utility of datadataThe real world - The natural and modified landscapeObservations of the real world - Measurements, occurrences, photographsCollections from the real world - Herbarium specimens, living specimensCollated into datasets which are analysed in various ways to develop information and results which are interpreted and through that knowledge we can take decisions, we can implement and take actionsAnalysis of observationsVisualization of analysesInterpretation of resultsobservationsthe real world
20 Specimen data Core information is from herbarium specimens Collections data:Scientific nameCollection dateCollector name & numberLocationSoilsHabitat (incl. topography)Vegetation communityAssociated speciesPlant features, e.g. colourSo there are many data elements associated with each collectionWhat will become clear as we talk this afternoon is that in addition to the specimens being used for taxonomic research, the associated data is now being used for very different purposes from which it was originally collected – largely for taxonomic purposes.Among the many questions being asked –What species does a plant belong to?What is its name?What other species is it related to?What does it look like?How does it grow?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?
25 How does the AVH work? Need for common semantic schema recognized Standard syntaxRace to databaseHISPIDBotanical ontology?Need for semantic standard recognizedExchangeDistributed queryEvolution of the AVH
26 AVH General Architecture DatabasesGatewaysCommon Web portalsClients
27 Australia’s Virtual Herbarium Some views of the data
41 Plant distribution analysis Pultenaea species in eastern AustraliaIncurvedRecurved20 classes and excluding those cells with 2 or less species. Highly similar groups were grouped again..with the resultant zones with taxonomic affinities.Zones with shared species emerged, which were not apparent when groups were considered together.Incurved group:Similarity values were relatively low ( ) – but six different zones with taxonomic affinities were identified. 6 clear groups were apparent.Recurved group:Similarity values were much higher in this group. ( ). 3 clear groups were identifiedThe question is what do these classes relate to?Groups of species with shared ecologies—environmental requirements? OR or groups of species with shared evolutionary histories? OR a combination of both.Information on the later possibility can be gleaned by comparing the classes to phylogenetic info—showing the genetic r’ships between species.Can see from this cladogram, most species in the incurved group Zone4 in SA and most of Vic all cluster in the top part of the phylogenetic tree as a similar group. That is are all related species.Also that species in the yellow incurved yellow group form a clear phylogenetic cluster.It suggests that at least in the incurved group the major taxonomic patterns in the landscape might be reflecting evolutionary histories of these groups—some of the classes probably represent environmental preferences. The taxon zones of recurved species however do not correspond with closely related groups of species on the cladogram. This may indicate that distributions represent the environmental domains of the groups rather than any historical evolutionary patterns. More work is required to test these hypotheses.??IncurvedRecurved
47 Portraits of Plant species National Plant Photograph IndexSearch on-lineSome digital images available35,000 images of Australian plants and vegetationA number of potential candidates, more or less fitting, these criteria have been identified.And of them I’ve started looking at spatial distribution patterns of the bush Peas Pultenaea—and I’m going to present some of the initial findings of that work.
53 Why it is working Communication - CHAH, few herbaria Collaboration - long-standing, data sharing, overcoming Australia’s Federal/State systemChampions - management, publicLobbying and profile of herbariaRelevance of productAnd now…we need to maintain commitment to project
54 Summary Australia’s Virtual Herbarium: A collaborative national projectMaking botanical information availableUsing modern technologyUsing cheap readily available componentsA model for regional and global cooperation
55 Acknowledgements State Herbarium of South Australia Queensland HerbariumAustralian National HerbariumNorthern Territory HerbariumTasmanian HerbariumIndustry Partner:KE SoftwareNational Herbarium of VictoriaNational Herbarium of New South WalesWestern Australian HerbariumAustralian Biological Resources Study