a virtual herbarium

A Virtual Herbarium Repatriated data for Papua New Guinea

A model for the southwest Pacific?

J.R. Croft, R.W. Purdie, B.J. Lepschi, J. Sabi, R. Kiapranis,

B. Wellington, M. Turnbull

Acknowledgements

Acknowledgements

• Australian Dept of Sustainability, Environment, Water, Population and Communities

• Heritage Division, Dept SEWPAC

• Papua New Guinea Dept of Environment and Conservation

• Papua New Guinea Forestry Research Institute

• CSIRO Biological Collections

• Atlas of Living Australia

• Council of Heads of Australasian Herbaria

• Council of Heads of Australian Fauna Collections

• Council of Heads of Australian Entomology Collections

• Council of Heads of Australian Biological Collections

Disclaimer

Disclaimer

• A ‘work in progress’

• Long-term project, long-term vision

• Professional view, not official policy

• Includes work and ideas of colleagues

• Mistakes are our own

• Some things may work, some may not

• Botanical focus, applicable to museums

• High level, descriptive, generalized

Some personal background

Some personal background

• Deputy Director Science and Information, Australian National Botanic Gardens

• Team Leader Information Management, Australian National Herbarium – to 1960 – Australia, Papua New Guinea, Fiji, New

Caledonia

– 1971 – Lae, PNG, Division of Botany (15 years)

– 1986 – Canberra, Australian National Botanic Gardens

Context

Context

• Biodiversity data, data management

• Biodiversity inventories, surveys of PNG

• Biodiversity analyses

– Environmental research

– Environmental planning

– Environmental decision-making

– National development

– Community development

– Conservation

Context

• Biodiversity survey of PNG, by PNG, for PNG

• Assistance from overseas biologists

– Interest in taxa

– Interest in region(s)

– Interest in biota origins and relationships

• Australia Government assistance

• International assistance

Outline

Outline

• Historical context

• Modern context

• Australia’s biodiversity collections

• PNG’s biodiversity collections

• Potential for PNG

• Potential for Australia

• ‘Issues’

Outline

• The data

– How much is there?

– How compatible is it?

– How good is it?

– How can we get it?

– Where can we keep it?

– How can we manage it?

– What can we do with it?

– How much will it cost?

Outline

• A way forward…

Historical context

Historical context

• Early Colonial

– Specimens to Europe

• British and Australian Administration pre war

– Specimens to Europe, Australia, N America

• Australian Administration post war

– Specimens to Australia, PNG, Europe, N America

• Self Government and Independence

– Specimens to PNG, Australia, Europe, N America

Modern context

Modern context

• Modern biodiversity surveys:

– Multidisciplinary

– Multi-institutional

– International

– Collaborative

– Data exchange

– Linked data

– Shared maintenance

– Ongoing maintenance

Modern context


– Atlas of Living Australia

• Australia’s Virtual Herbarium

• Online Zoological Catalogue of Australian Museums

• Identify Life – Identification tools

• Biodiversity Data Recording System – Survey tools

• Images – Habitats, organisms, specimens, literature

• Multimedia – sound, video, animation, etc.

Modern context


– Global Biodiversity Information Facility

– Encyclopedia of Life

– Biodiversity Heritage Library

– Taxonomic Databases Working Group

– Global Plants Initiative

• ‘The Plant List’

• Images of Type specimens, on-line

Current status of GBIF Participation in Oceania

Updated: 10 September 2012

Current status of GBIF Participation in Oceania

Updated: 10 September 2012

(Hawaii)

Trends in data publishing

Oceania is the smallest region (based on number of participants) and 3rd largest data publisher.

Australia’s biodiversity collections

Australia’s biodiversity collections

• National collections

– National and international focus

– Significant PNG collections

• State and territory collections

– Generally regional focus

– Some with significant PNG collections

• University collections

– Generally teaching and regional focus

Victorian Agricultural Insect Collection

INSTITUTIONS – Tasmania

Hobart

Australian National Fish Collection (CSIRO)

Tasmanian Museum and Art Gallery, Zoology

Tasmanian Herbarium

Tasmanian Environmental Invertebrate

Collection Tasmanian Forest Insect Collection

Australian Collection of Antarctic Microorganisms

(University of Tasmania)

Culture Collection of Microalgae (CSIRO)

Devonport

DPIW Insect Reference Collection

Launceston Queen Victoria Museum and Art

Gallery, Zoology Section

Adelaide

Perth

INSTITUTIONS – Victoria

Melbourne Museum Victoria

National Herbarium of Victoria

University of Melbourne Herbarium

Melbourne

Hobart

Launceston

Townsville

Devonport

Armidale

Darwin

Brisbane

Lismore

Orange

Sydney

Canberra

INSTITUTIONS – South Australia

Adelaide

South Australian Museum

South Australia Herbarium

Waite Insect & Nematode Collection

Mycology Culture Collection (Women’s and

Children’s Hospital)

Clinical Microbiology Culture Collection (IMVS)

Australian Wine Research Institute

INSTITUTIONS – Western Australia

Perth

Western Australian Museum

Western Australian Herbarium

King Edward Memorial Hospital/PMH Culture

Collection

Western Australian Department of Agriculture

and Food, Invertebrate Reference Collection

and Plant Research Division Culture Collection

CALM Forest Insect Reference Collection

University of Western Australia Microbiology

Culture Collection

Murdoch University Algal Collection

INSTITUTIONS – Northern Territory

Darwin

Museum & Art Gallery of the Northern Territory

Northern Territory Herbarium

Northern Territory Economic Insect Collection

Phytoplasma DNA Collection (Charles Darwin

University)

Biocatalytic Microbe Collection (CSIRO) Microbiological Diagnostic Unit, Public Health

Laboratory, The University of Melbourne

Maroochydore

Gosford

INSTITUTIONS – Australian Capital Territory

Australian National Insect Collection (CSIRO)

Australian National Herbarium (CSIRO)

Australian National Wildlife Collection (CSIRO)

GAUBA Herbarium

Australian Biological Resources Study

Canberra

Lismore

Australian Plant DNA Bank

Armidale

N.C.W. Beadle Herbarium

Australian Museum

National Herbarium of NSW

Downing Herbarium (Macquarie University)

John Ray Herbarium (University of Sydney)

The John T. Waterhouse Herbarium (UNSW)

Forestry Commission of NSW Insect Collection

(FCNI)

Macleay Entomology Collection (MAMU)

Food Research Collection (CSIRO)

Microbiology Culture Collection (University of NSW)

Plant Pathology Herbarium (DPI)

NSW Agricultural Scientific Collections Unit

Australian Collection of Plant Pathogenic Bacteria

INSTITUTIONS – New South Wales

Sydney

Orange

Gosford

Australian Legume Innoculants Research Unit (DPI)

Queensland Museum

Queensland Herbarium

DPI&F Plant Pathology Herbarium

DPI&F Insect Collection

University of Queensland Insect Collection

BSES Insect Collection

Australian Collection of Microorganisms

(University of Queensland)

INSTITUTIONS – Queensland

Townsville

AIMS Marine Bioresources Library

Microbial Gene Research and Resources Facility

(Griffith University

Brisbane

Maroochydore University of the Sunshine Coast Microbial Library

Biological collections contribution to the ALA

PNG’s biodiversity collections


• PNG botanical collections

– Many (most?) specimens duplicated in Australia and other overseas herbaria

– Potential for ‘data repatriation’

– ‘PNG Plants’ database

• Compilation of PNG data from 4 major Aus. Herbaria

• Served on the Internet from Herbarium NSW


• PNG zoological collections

– ‘Duplication’ of specimens not possible

– Some series of collections represented overseas

– Potential for ‘data repatriation’

Potential for PNG

Potential for PNG

• More people studying PNG species

• More people identifying PNG specimens

• More recent research, taxonomy

• More accurate and up to date data

• More repatriated data

– Research

– Planning, management

– Seed data for PNG institutional databases

Potential for Australia

Potential for Australia

• Regional focus for biodiversity research

• National and international collaboration

• Attention to significant regional collections

– Curation

– Identification

– Geolocation

– Digitization

• Regional development, capacity building

– Training

AD Robyn Barker Acanthaceae

Ainsley Calladine Loranthaceae

CANB Jim Croft Pteridophytes

Lyn Craven Myrtaceae

BRI Gordon Guymer Myrtaceae, Myrtoidieae; Sapindaceae: Mischocarpus, Arytera,

Elattostachys; Sterculiaceae

Tony Bean Myrtaceae: Eucalyptus, Leptospermoideae; Rhamnaceae,

some genera of Asteraceae

Peter Bostock Pteridophytes

Laurie Jessup Annonaceae, Symplocaceae, Ebenaceae, Celastraceae

Paul Forster Euphorbiaceae, Apocynaceae

David Halford Tiliaceae

Bryan Simon,

John Thompson

Poaceae

CNS Darren Crayn Epacridaceae, Elaeocarpaceae

Ashley Field Pteridophytes

Frank Zich PNG plants is Australia

DNA Ian Cowie General knowledge of Timor flora

Greg Leach Aquatic Flora

NSW Barry Conn Tree species, Loganiaceae. Urticaceae

Issues

• Access to data

– Biodiversity data and ‘Open Access’

• Increasing globally

• No general acceptance in PNG?

• Local sensitivity <= very important

– Sensitive data

• Rare and endangered species

• Commercial in-confidence

• Traditional concerns

Issues

• Data licenses

– Existing data licenses / use agreements

• In PNG (?)

• Overseas (?)

– Creative Commons licenses

• Creative Common By Attribution (CC-BY)

• Other CC licenses?

The data

The data

• How much is there?

• How compatible is it?

• How good is it?

• How can we get it?

• Where can we keep it?

• How can we manage it?

• What can we do with it?

• How much will it cost?

The data

• What is it?

– Specimens

• Taxonomy can be checked

• Random, presence only data

• Few points, variable precision

• Relatively expensive

– Surveys

• Often without vouchers, taxonomy doubtful

• Structured survey design

• Many data points, consistency

• Relatively cheap

The data

• What is it?

– Other data

• Nomenclatural / taxonomic data – National species lists (e.g. APNI / APC, AFD)

• Species profiles; descriptive data

• Images, illustrations, multimedia

• Identification tools

• Literature

The data – how much is there?

• PNG specimens in Australian herbaria

– Survey sponsored by AVH Trust and CHAH

– How many PNG specimens?

– Where are they?

– How well are they identified?

– How many are geolocated? How well?

– How many are databased? How many not?

– Costs to curate and database the remainder?

BRI NSW ANH MEL HO AD PERTH DNA CNS Total

Angiosp. 74,178 11147 39,081 2080 21 18 180 4924 131,611

Gymnosp. 899 61 1,134 27 50 2171

Pterioph. 6,083 1067 10,712 49 1 50 17,961

Bryophytes 638 674 18,341 488 24 5 20165

Lichens 114 89 5,907 126 106 2 6342

Fungi 79 656 230 965

Lycophytes 15 15

Algae 379 527 117 2 23 1025

Total specs 82,370 13,565 75,948 3,017 151 49 118 180 5,024 180,422

Databased PNG herbarium specimens in Australia

BRI NSW ANH MEL HO AD PERTH DNA CNS Total

Not db’d 37,000 56 000 136,000 21,300 150 4000 0 <200 0 254,650

No family id 0.4% 0.08% 0% 0% 0% <1%

No genus id 3.5% 10.8% 0% 0% 0% 0-11%

No spec. id 28% 100% 51.5% 5% 1% 20% Very

variable

No geocode 45% 100% 53.2% 100% 100

%

0% 45-100%

Not mounted 14% ?

Undatabased PNG herbarium specimens in Australia

Total PNG herbarium specimens in Australia

180,422 + 254,650 = 434,892

The data – how compatible is it?

• TDWG standards • Taxonomic Databases Working Group

• International acceptance

• Uses existing standards where possible

– Most biodiversity databases TDWG compliant

• Fields defined

• Collections, other biodiversity data

• Content recommendations

• Protocols for data exchange

The data – how compatible is it?

• TDWG standards

– Common export formats

• ABCD – Accommodates complex structured data

• Darwin Core – Accommodates occurrence data

– Commonly used

• ‘CSV’ – Spreadsheet data

– Worst case, but effective

The data – how good is it?

• Conceptually very simple

– Who. What. Where. When. How. Why.

• ‘Dots on maps’ - Occurrence

– What – identification

• Wrong name = useless data

– Where – geolocation

• Wrong place = useless data


• Identification

– State of knowledge of the group

– Available revisions, keys

– Scope of revisions

– Age of revisions

– Quality of the revisions

– Familiarity, skill of identifiers

– Complexity of the group


• Geolocation

– Age of the specimens

– Available technology

– Accuracy of locations

– Precision of location

– Familiarity, knowledge of geocoders

• Renamed or moved localities

– Available maps, gazetteers, satellite/aerial imagery


• Some good news

– Many specimens often collected at same locality

• Database stores previously calculated geocodes

• Usable if acceptable accuracy, precision

• Improves data capture rates

– Some batches of specimens not incorporated yet

• Batches of insects still filed under ‘expedition’


• Some good news

– All data is good for something

• An unidentified specimen might be identified

• A misidentified specimen might be corrected

– ‘Fitness for purpose’

• GBIF and ALA data statements

• All data is useful a some scale – Hierarchy of localities

– Generalized localities sufficient for regional checklists

The data – how can we get it?

• Background activity

– ‘Ratchet principle’

– All new collections

– Specimen loans and exchange

– Routine identifications

– Strategic research projects

• New Projects

– Australian funded (Heritage, AusAid, ...)

– Aid funded (GEF, NGOs, Foundations, …)

The data – how can we get it?

• Other issues – access to specimens

– Herbaria and museums generally arranged in taxonomic order

– Survey generally based on a region

– Difficult to extract, process individual specimens

– Smallest effective ‘management unit’

• Species, genus, family, … shelf, draw, cupboard, …

• ‘Ratchet principle’

• Select ‘management units’ well represented in region

The data – where can we keep it?

• In the custodial institutions

– Needed for management

• In PNG

– Institutional capacity issues

• In Australia or other overseas

– Costs, access, bandwidth, reliability, trust

• In ‘the cloud’

– Costs, trust, access, bandwidth, reliability


• Sustainability

– Who will look after it?

– Where will they look after it?

– Who will pay for it?

• Access

– How will PNG use it?

– How much will be available to others?

– How will others use it?


• Updates

– How will data be updated?

– How will updates be propagated?

– Synchronization?

• ‘Escape Route’

– If project closes down

– Standards

– Compatibility


• A model for consideration:

– Primary data with custodial institutions

– Data integrated in a ‘PNG portal’ of the ALA

– (Mirrored PNG instances of PNG portal)

• Hosted by? Managed by?

• Data seeding PNG biodiversity collections

– Data shared with GBIF etc.

• Additional backup

• International access

The data – how can we manage it?

• Data is not a once-off activity – Documentation, maintenance

– Costs

• Shared data requires shared maintenance – Propagated updates, corrections, new data

– Hardware, servers, networks

– Database engine

– Data base design, structure

– User interface, reports, …

The data – how can we manage it?

• A ‘PNG Portal’ model for consideration: – Custodial institutions manage their data

– ALA provides management of integrated data

– PNG data managed with other data

– ALA provides propagation mechanisms

– ALA maintains hardware, networks, database, …

– PNG selects the data it needs

– (Mirrored in PNG, elsewhere)

– Currently being developed for New Zealand • New Zealand Virtual Herbarium (NZVH)

The data – what can we do with it?

• Repatriate to PNG collections

• Access to PNG NRM / conservation agencies

• Available on-line for research, education

• Census of PNG biodiversity

– Regional inventories

• Spatial analyses, visualizations

• Species profiles, identification tools

The data – how much will it cost?

The data – how much will it cost?

This page

intentionally

left blank

The data – a way forward

• Complete current herbarium specimen study

– Scoping

– Pilot data capture

• Extended scoping study

– Refine costings

– Herbaria and museums

– Negotiate priorities

• Taxonomic

• Regional


• Pilot project(s)

– Herbarium

– Wildlife colln., fish colln., insect colln.

– Training, capacity building

• Seek funding

– PNG agencies

– Australian and overseas agencies

– Aid agencies

– NGOs, foundations, benefactors


• ‘PNG Biodiversity Portal’

– Negotiate with Atlas of Living Australia, etc.

• Hosting

• Governance

• Development

• Maintenance

– Engage partners

• PNG collections

• Australian collections

• Overseas collections

‘The message’

‘The message’

• Rich biodiversity but poorly understood

– Exciting opportunity to record and document

– Needs to be driven by PNG, ‘in country’

– Australian institutions eager to collaborate

– Existing technology for effective collaboration

– Policy, governance and operational mechanisms

– International data standards

– Proven models of data capture, management

– Huge task; need to prioritize; needs funding

a virtual herbarium

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