Using Specify 6, 7 and Web Portal Instruments for the North Siberian Biodiversity Data Platform
Authors: Filippova Nina , Karpov Dmitry 
Published: November 2024

The digitization and mobilization of biodiversity data are actively ongoing in the northern part of Western Siberia (Tyumen Oblast, Russia), where the history of biodiversity research is relatively short. For small collections and young universities, it is essential to have a ready-made software product, like Specify*1, for managing the collection and publishing data openly. Our use of Specify tools began with a local installation on a single computer in 2015. Now we have a deployed system consisting of two disciplines and ten collections used by five organizations (Table 1), and we utilize Specify 6, Specify 7, the Attachment Server, and Web Portal tools.

The checklist of the Western Siberian Specify installation activities includes:

Personal collection of fungi since 2015

Using Specify 6 + Specify 7 + Web Portal since 2017 for university collections management

Development of a Northwest Siberia bioportal*2 since 2018

Development of a Mycological Portal of West Siberia*3 since 2024

Organization of educational events

Helping with localization in Russian language

Developing instructions and help videos in Russian language*4

Developing DNA-derived data schema in Specify 6 since 2023

Personal collection of fungi since 2015

Using Specify 6 + Specify 7 + Web Portal since 2017 for university collections management

Development of a Northwest Siberia bioportal*2 since 2018

Development of a Mycological Portal of West Siberia*3 since 2024

Organization of educational events

Helping with localization in Russian language

Developing instructions and help videos in Russian language*4

Developing DNA-derived data schema in Specify 6 since 2023

The main uses of the installation include storing specimen label information, the physical storage location of specimens, and associated digital information (e.g., scans, live images of objects, or microphotographs). We also utilize Specify's reports for generating customized labels and reports on loans or gifts. Taxonomical, geographical, and storage hierarchical trees are used to organize data. Recently, tables associated with molecular data have been more actively utilized to store DNA sequences, their metadata, and trace files.

The Specify database is linked via Structured Query Language (SQL) to the Global Biodiversity Information Facility's (GBIF) Integrated Publishing Toolkit (IPT) for publishing collections data through GBIF. The automatic updates are regularly done once a week. Using separate queries, our collection data is regularly exported and published on the local portals, where data on labels, molecular data, distribution maps (Fig. 1) and photographs are presented (Fig. 2).

Currently the Specify installation hosts 10 collections from two disciplines and has about 20 users. It contains about 22,000 specimens with 33,000 images attached, and about 1,500 DNA sequences (Table 1).

Two platforms for external access to collections were created using the Specify Web Portal tool, and serve as a hub for region- and discipline-oriented collections:

Northwestern Siberia Bioportal*2 for all regional collections (currently hosts 10 collections from 5 organizations);

Siberian Mycological Portal*3 specifically for mycology collections in Siberia (5 collections from 3 organizations).

Northwestern Siberia Bioportal*2 for all regional collections (currently hosts 10 collections from 5 organizations);

Siberian Mycological Portal*3 specifically for mycology collections in Siberia (5 collections from 3 organizations).

In recent years, we have been actively barcoding the specimens of the Fungarium of Yugra State University (YSU) collection. As a result, two related tables are exported to IPT: one for the collection specimens and another for DNA-derived data (the resulting dataset Filippova et al. 2024). Several ready-made queries were built to export DNA-derived data to other molecular data portals (GenBank, International Barcode of Life (iBOL), and PlutoF). A special protocol on DNA-derived data storage and export using Specify was published on Protocols.io to standardize the procedures and pass on the skills (Filippova and Zvyagina 2024).