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MOSCOW DIGITAL HERBARIUM: A CONSORTIUM SINCE 2019
TAXON ( IF 3.0 ) Pub Date : 2020-07-02 , DOI: 10.1002/tax.12228
Alexey P. Seregin 1
Affiliation  

The herbaria of the World, with 387.5M specimens (Thiers, 2019), are being rapidly digitized. At least 77M plant specimens (20%) are already databased throughout the globe in the standard form of GBIF‐mediated data. About 55M specimens are imaged, but only 21.6M of them are concentrated in the top‐ten largest digital herbaria – P, L, NY, US, PE, BR, MEXU, MW, K, and MPU. The contribution of smaller herbaria has been steadily growing in the last few years due to cost reduction, and usage of platforms and solutions developed by the leaders. The global trend is largely the same in Russia, where a dozen herbaria started to scan their holdings after imaging the specimens of the nation's second‐largest herbarium (Seregin, 2016).

A web‐resource, the Moscow Digital Herbarium (https://plant.depo.msu.ru/), was launched by Lomonosov Moscow State University in October, 2016 for publication of specimens imaged and databased in the Moscow University Herbarium (MW) (Seregin, 2018). From 2015 to 2018, a commercial partner scanned 93% of the regular herbarium collections at 300 dpi and 100% of the types at 600 dpi due to the financial support from the Russian Science Foundation. As of 31 December 2018, the web‐portal included 968,031 images of 971,732 specimens. About one‐third (i.e., 323,015 records) were georeferenced by that time. This dataset is available in GBIF (https://doi.org/10.15468/cpnhcc) since late 2017 and updated in a weekly synchronization mode.

Current regional activities of the Moscow team

In 2019, the Moscow University Herbarium failed to raise budget for further large‐scale digitization and research activities in line with the proposed “Atlas of the Russian flora”. Unexpectedly, some minor grant proposals were supported as regional activities. Therefore, we started to use the Moscow Digital Herbarium as a web‐repository for digitized herbarium specimens from some smaller Russian collections. That's how a single‐university system became a multi‐institutional consortium in April 2019.

The Herbarium of the Main Botanical Garden, Russian Academy of Sciences (MHA) is the fourth‐largest Russian herbarium, with 610K specimens of vascular plants. It holds vast collections from the Moscow metropolitan area (City of Moscow & Moscow Oblast), collected in the last 70 years, whereas MW holdings are fairly evenly distributed in time through 200 years. Altogether, MW and MHA have 130K+ specimens from the Moscow area, making it the most densely sampled region across Russia. The idea of the regional research proposal was to digitize and georeference this large dataset for proper understanding of changes in the flora around Moscow through time and space. From March to October 2019, the MHA team imaged 49.7K herbarium specimens of vascular plants at 600 dpi using a Microtek Object Scan 1600 scanner. In the following few months, 60% of them were georeferenced at Moscow University.

Further, MHA published 15K images of its eastern European collections, which are especially strong in plants from the xeric flora of the Lower Volga area. MHA collections are fully available in GBIF (https://doi.org/10.15468/827lk2), the Moscow Digital Herbarium and the newly established “Flora of Moscow” website (https://moscow.depo.msu.ru). At the moment, MHA provides the second‐largest set of imaged herbarium specimens of Russia (Table 1).

Table 1. Top‐ten largest digitized institutional herbaria of Russia (as of early 2020).
Institution Herbarium code Images Proportion of imaged specimens Web‐portal
1 Lomonosov Moscow State University (Moscow) MW 979K 94%

https://plant.depo.msu.ru/

https://www.gbif.org/

2 Main Botanical Garden, RAS (Moscow) MHA 64K 10%

https://plant.depo.msu.ru/

https://www.gbif.org/

3 Central Siberian Botanical Garden, RAS (Novosibirsk) NS+NSK 37K 5%

http://84.237.85.99:8081/

https://www.gbif.org/

4 Komarov Botanical Institute, RAS (Saint Petersburg) LE 33K <1% http://herbariumle.ru/
5 Botanical Garden‐Institute, RAS (Vladivostok) VBGI 30K 38% http://botsad.ru/herbarium/
6 Altai State University (Barnaul) ALTB 17K 6% http://old.ssbg.asu.ru/
7 Institute of Plant and Animal Ecology, RAS (Yekaterinburg) SVER 11K 9% https://herbarium.ipae.uran.ru/
8 Tula State Pedagogical University (Tula) TUL 9K 86%

https://plant.depo.msu.ru/

https://www.gbif.org/

9 Amur Branch of Botanical Garden‐Institute, RAS (Blagoveshchensk) ABGI 7K 30% http://botsad.ru/herbarium/
10 Kirov Forestry Academy (Saint Petersburg) KFTA 3K 2% https://plants.jstor.org/

The Herbarium of Tula State Pedagogical University (TUL) is the largest herbarium in Tula Oblast, a region south of Moscow. This area is strongly under‐represented in central Russian herbaria; thus, local digitization activities were highly awaited. A regional joint project aimed to digitize four small local herbaria starting with the largest, TUL, which contains 9K+ specimens from Tula Oblast as well as some occasional specimens from other areas. In late 2019, we moved the herbarium of Tula State Pedagogical University to Moscow for a couple of months. The same commercial partner engaged in our activities in 2015–2018 imaged these collections at 300 dpi. Currently, they are available both in GBIF (https://doi.org/10.15468/ca08cm) and Moscow Digital Herbarium.

In 2020–2021, we are planning to image and database the herbaria of Tula State University (3.7K specimens), Kulikovo Pole Museum‐and‐Reserve (2.5K) and Tula Regional Museum (2K). Finally, these data will be available on the “Flora of Tula Oblast” website.

Digitization activities across Russia

The list of the largest digitized herbaria of Russia (Table 1) is based on the number of imaged specimens. Three herbaria (MW, MHA, TUL) are currently forming the Moscow Digital Herbarium, a consortium with 1053K specimens and 1043K images (Fig. 1, top left). All members of this consortium are publishing their data in GBIF as independent institutional publishers, using a single integrated publishing toolkit (IPT) installed at Moscow University. KUZ and IRKU will join them with pilot datasets in 2020 (see below).

image
Figure 1
Open in figure viewerPowerPoint
Four leading web‐services used for publication of herbarium images in Russia. Top left , Moscow Digital Herbarium, https://plant.depo.msu.ru/; Top right , Vladivostok Digital Herbarium, http://botsad.ru/herbarium/; Bottom left , Web‐portal of Novosibirsk Herbarium, http://84.237.85.99:8081/; Bottom right , Web‐portal of Komarov Institute Herbarium, http://herbariumle.ru/.

The Vladivostok Digital Herbarium is another steadily growing Russian consortium, with two active publishers (VBGI, ABGI) and four smaller contributors. Now, one can browse 63K fully captured labels and 37K images from institutional members of the Far Eastern Branch of the Russian Academy of Sciences (Fig. 1, top right). The system was primarily written in Python and has several key original features described by Kislov & al. (2017).

The Novosibirsk Herbarium, the third‐largest digital herbarium of Russia, is also a consortium in fact. For decades, NS and NSK, housed in the same building, were managed as two separate units. They are still preserved separately, although being digitized in a single workflow. As of January 2020, NSK had imaged 20,050 specimens, whereas NS had scanned 16,772 specimens (Fig. 1, bottom left). The Novosibirsk collections are partly available in GBIF in a form of datasets devoted to some intensively studied taxonomic groups. Images and metadata are stored in the institutional online database generated by ScanWizardBotany and MiVappBotany software, Microtek, Taiwan (Kovtonyuk & al., 2018).

The herbarium of the Komarov Institute has its own portal (Fig. 1, bottom right). Currently, it consists of two separate e‐collections—12,216 regular images and 20,362 early‐scanned specimens recovered from an old server. This custom‐made web‐platform is also used by the Herbarium of Voronezh State University (VOR), where 2094 specimens were imaged in 2019 (available at http://herbarium.bio.vsu.ru/).

Future growth of the consortium

In late 2019, we raised a stable budget for launching further digitization activities across Asian Russia. Fortunately, local governmental authorities in Irkutsk and Kemerovo Oblasts supported two joint initiatives between local institutions and the Moscow University Herbarium. At least two newcomers will join the list of the largest digitized herbaria of Russia in the next two years and appear in the Moscow Digital Herbarium and GBIF.

The Herbarium of the Kuzbass Botanical Garden (KUZ) is the most active and probably the largest herbarium of Kemerovo. It contains 56K specimens from Asian Russia and Kazakhstan, including 19K specimens from Kemerovo Oblast. The KUZ team will image all their holdings in 2020–2022 at 600 dpi using a Microtek Object Scan 1600 scanner. Substantial parts of the grant will cover new intensive collecting missions in line with the project.

The Herbarium of Irkutsk State University (IRKU) is the largest herbarium of the well‐known Baikal area. It includes 100K specimens of vascular plants from Siberia and 30K specimens from other regions/groups. As of early 2020, it is the 19th‐largest herbarium of Russia. Staff of IRKU will scan the Siberian collections at 600 dpi using the same model of scanner in the next three years. The second herbarium of the Irkutsk region (Herbarium of the Siberian Institute of Plant Physiology and Biochemistry, IRK) will also contribute to the project, with 70K fully captured labels without imaging.

Recently, we launched a network of regional extensions of the Moscow Digital Herbarium to interact with local herbaria as equal partners in documentation and research of provincial floras. Our local partners, such as MHA, TUL, KUZ, and IRKU, help us to avoid mistakes in georeferencing and label capturing of MW holdings from definite regions, whereas Moscow University is providing them with the complete IT‐workflow for uploading, storing, retrieving and publishing specimen‐based e‐data on https://plant.depo.msu.ru/. The network of regional extensions of the Moscow Digital Herbarium will include five portals in the next two years—Moscow City (since 18 September 2019), Krasnodar Krai & Adygea (since 13 December 2019), Tula Oblast (to be launched in early 2021), Kemerovo Oblast (to be launched in mid‐2021), and Baikal Area (to be launched in late 2021).

Acknowledgments

The reported project was funded by the Russian Foundation for Basic Research (RFBR) and the Moscow city Government according to the research project #19‐34‐70018 (imaging and georeferencing of MHA Herbarium); RFBR and Tula Oblast Government according to the research project #19‐44‐710002 (imaging of TUL Herbarium); RFBR and Krasnodar Krai Government according to the research project #19‐44‐233012 (databasing and georeferencing of MW Herbarium).

    更新日期:2020-07-03
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