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talk · Thursday 24 September · 09:25–⁠09:38 · SAL C

Integrating Specify in broader Science infrastructure

Niels Klazenga · Meeting Biodiversity Data Standards Using Specify Software

Recording time 1:45:26–1:58:00Open on Vimeo ↗

Summaries and key moments are machine-produced. Check the recording for the speaker’s exact words.

The short versionSpecify works best at RBG Victoria as one component of a wider hub-based science infrastructure, with custom tools filling its gaps.

Overview

What this was about

Niels Klazenga described how RBG Victoria, a Specify user for over 16 years, embeds Specify as a 'collections hub' among other hubs: a Canto digital asset management system, VicFlora, a documentation hub, a traits hub of Lucid keys, KeyBase, and the Australasian Virtual Herbarium within the Atlas of Living Australia, which is its only dissemination channel. A separate 'bystander' application and a GraphQL API provide what Specify lacks or does differently, such as ZPL label printing, duplicate labels, partial loan returns, an event system and taxonomy syncing. He noted that moving from ABCD to Darwin Core felt like a step back and that a more structured model will help. He also called for Specify to support linking identifications to taxon concepts.

Why it matters. Real-world integration patterns, such as a taxon tree as backbone for other systems, a GraphQL API feeding a IIIF image portal, and IPT-to-ALA-to-GBIF delivery, show how a CMS fits into institutional infrastructure and where CMS vendors could improve.

Key ideas

In the room

  • RBG Victoria started with Specify 6.0.1 and chose Specify mainly to deliver high-quality data to AVH.
  • Hubs: Specify (collections), Canto (media/DAMS), VicFlora (flora of Victoria and horticultural flora of south-eastern Australia), a documentation hub, a traits hub (Lucid keys) and KeyBase (pathway keys).
  • Specify is not used for dissemination; all data go through AVH/ALA via the IPT, and ALA passes them on to GBIF as Australia's GBIF node.
  • A bystander app handles things Specify cannot, e.g. starting label printing mid-sheet on sheets of 30, ZPL labels for new printers (PDF quality too low), duplicate labels, partial loan returns and an event system.
  • The Specify taxon tree is the taxonomic backbone for other applications such as the image portal and living collections database, synced via a GraphQL API that predates Specify's own API.
  • A IIIF-compliant image portal is under development; Specify data populates the IIIF Presentation API.
  • Seed bank germination tests and orchid conservation data do not fit Specify and will get separate databases.
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Notable moments

In their words

Transcript

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Programme abstract

Integrating Specify in broader Science infrastructure

Niels Klazenga

At the Royal Botanic Gardens Victoria, Specify is used to deliver high-quality data to the Australasian Virtual Herbarium (AVH), as well as managing the herbarium's holdings and transactions like loan and exchange. Specify is embedded in our broader science infrastructure and we have built various extensions and integrations.

We make use of the flexibility of Specify to handle complex workflows. We use a separate discipline, rather than the Borrows table, to manage loans from other institutions. This way we can link up images and DNA sequences we have taken to specimens data, while keeping the data separate from the National Herbarium of Victoria (MEL) collection. We also use "staging" collections for exchange data, so we can make sure we have the specimens and validate the data before it is incorporated into the main collection. There is also a dedicated collection for the Victorian Conservation Seed Bank, which shares most of its data with the main collection.

We have a "bystander" application that provides functionality that Specify does not have or where the Specify functionality does not quite fit our workflows, e.g., handling ZPL-based label-printing, storage assignment and loan returns.

The Specify taxon tree functions as the taxonomic point of truth for our Digital Asset Management System (DAMS). At the same time, we have applications to sync the Specify taxon tree with national and global taxonomies, including VicFlora, APC, AusMoss, AusFungi, Plants of the World Online (PoWo), Bryonames and Tropicos.

The AVH is our collection's portal in to the world. We use the Global Biodiversity Information Facility (GBIF) Integrated Publishing Toolkit (IPT) to publish collections data to AVH.

Submitted to the conference programme before the talk, so the talk itself may differ.