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Tutorial on using Amazon Web Services

You can now access high resolution images of specimens from the National Herbarium of New South Wales (NSW) through our Public Data Set: HerbariumNSW on AWS. Images of the collections are all available in the herbariumnsw-pds bucket in the Amazon S3 AP-SouthEast-2 region.

The priceless and irreplaceable botanical collection of the National Herbarium of New South Wales (NSW) consists of preserved plant specimens. The collection holds specimens collected over 250 years, including more than 800 specimens from Banks and Solander collected during James Cook’s first voyage to the Pacific The scope of the collection focusses on the flora of New South Wales, but extends across Australia, the Pacific and has representation from around the world.

By releasing the National Herbarium of NSW specimens as a public dataset, the Royal Botanic Gardens and Domain Trust aims to create many more opportunities for collaboration and knowledge sharing with scientists across Australia and around the world. Digitisation also aids preservation by reducing the potential risk of damage due to repeated handling of the collections over time. 

Specimens housed in packet and attached to flat sheets held by the National Herbarium of NSW will be successively made available. The imaging and transcription of the collection will be completed by the end of 2021 with the full image and metadata collection being available shortly following completion of quality control processes. New additions to the National Herbarium of NSW collection will be made available quarterly, as additions are curated and imaged.

Amazon Web Services (AWS) has made the National Herbarium of NSW data freely available on Amazon S3 for biodiversity assessment, systematic botanical research, ecosystem conservation, policy development, for educational and other outreach tools. The entire botanical collection will be open to scientists, ecological consultants, community groups, students and members of the public.

You can learn more about how to access the data by searching for the Herbarium NSW here.

Accessing specimen images from the Herbarium of NSW

Each image is available as a high resolution JPG2000 lossless file and a lower resolution jpeg. The image metadata is hosted as a text file. Image data are organized by NSW specimen barcode number. For example, the files for a specimen of Dodonaea lobulata can be accessed via the URL. 

https://herbariumnsw-pds.s3-ap-southeast-2.amazonaws.com/images/NSW041500.jp2

or 

https://herbariumnsw-pds.s3-ap-southeast-2.amazonaws.com/images/NSW041500.jpg 

A zipped csv containing the biocollections metadata for the images is available as a DarwinCore Archive here.

Information about Darwin Core Archives and the metadata contained within can be found here.

What’s possible with HerbariumNSW on AWS

Herbarium data: Global biodiversity and societal botanical needs for novel research" published in Applications in Plant Sciences (2018) 6:e1024. https://bsapubs.onlinelibrary.wiley.com/doi/pdf/10.1002/aps3.1024

NSW Flora Online

The electronic Flora of New South Wales is developed and maintained by the National Herbarium of New South Wales and uses data and collections of the  herbarium. http://plantnet.rbgsyd.nsw.gov.au/

Restore & Renew

The Restore & Renew project, based out of the Royal Botanic Garden Sydney is a toolkit for ecological restoration practitioners, incorporating the latest science, helping them to restore diverse, resilient and adaptable ecosystems.

Using the data and collections from the National Herbarium of NSW models of the relationship between occurrence and environment have been produced for each Restore & Renew species. We have also mapped suitable environments for each species in 2070.

Atlas of Living Australia

The Atlas of Living Australia (ALA) is a collaborative, digital, open infrastructure that pulls together Australian biodiversity data from multiple sources, making it accessible and reusable.

The ALA helps to create a more detailed picture of Australia’s biodiversity for scientists, policy makers, environmental planners and land managers, industry and the general public, and enables them to work more efficiently

The Atlas of Living Australia already publishes the biocollections meta-data for those parts of the National Herbarium of NSW collection already databased (largely Australian-collected specimens).


These records include meta-data to link with the National Herbarium of NSW AWS public dataset, by the unique identifier assigned to each image.

https://collections.ala.org.au/public/show/co54


ALA provides search capability by taxon name, geolocation or keyword:

https://biocache.ala.org.au/search#tab_advanceSearch

The Australasian Virtual Herbarium

Australian and New Zealand herbaria house over eight million plant, algae and fungi specimens. Herbarium specimens are an important resource for research on the Australasian flora and provide a permanent record of the occurrence of a species at a particular place and time. The AVH provides access to the collecting data associated with these specimens.

The AVH publish the meta-data for all the National Herbarium of NSW collections currently databased:


AVH provide advanced search for the National Herbarium of NSW collection, including meta-data to link with the National Herbarium of NSW AWS public dataset: