Biodiversity Data Journal :
Data Paper (Biosciences)
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Corresponding author: Aleksey V. Vaganov (vaganov_vav@mail.ru)
Academic editor: Alexey P. Seregin
Received: 20 Apr 2021 | Accepted: 06 Jul 2021 | Published: 13 Jul 2021
© 2021 Aleksey V. Vaganov, Alexander I. Shmakov, Sergey V. Smirnov, Nadezda A. Usik, Alena A. Shibanova, Aleksey A. Kechaykin, Petr A. Kosachev, Tatyana M. Kopytina, Elizaveta A. Zholnerova, Kristina E. Medvedeva, Vladimir F. Zaikov, Tatyana A. Sinitsyna, Alexander P. Shalimov, Evgenij V. Antonyuk, Polina D. Gudkova, Denis A. Dmitriev, Alexander A. Batkin, Dmitry E. Kasatkin, Denis L. Belkin
This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Citation:
Vaganov AV, Shmakov AI, Smirnov SV, Usik NA, Shibanova AA, Kechaykin AA, Kosachev PA, Kopytina TM, Zholnerova EA, Medvedeva KE, Zaikov VF, Sinitsyna TA, Shalimov AP, Antonyuk EV, Gudkova PD, Dmitriev DA, Batkin AA, Kasatkin DE, Belkin DL (2021) Virtual Herbarium ALTB: collection of vascular plants of the Altai Mountain Country. Biodiversity Data Journal 9: e67616. https://doi.org/10.3897/BDJ.9.e67616
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The herbarium of the South-Siberian Botanical Garden of Altai State University (ALTB) houses the largest collection of plants from the Altai Mountain Country (AMC), an area that extends across Russia, Kazakhstan, Mongolia and China. The collection of ALTB includes more than 450,00 specimens, making it the seventh largest in Russia and the fourth largest amongst Russian university herbaria. Altai State University (ASU), the home of ALTB, is one of the most important centres of academic education and research in Siberia and the Russian Far East. It is a sociocultural centre that provides a distinguished learning environment for undergraduate and graduate students in many scholarly and professional fields, meeting the needs of today's knowledge-based post-industrial society and contributing to regional development. It actively promotes international cooperation and strategic collaboration amongst countries of the AMC in the fields of science, education and culture. In particular, the activities of the South-Siberian Botanical Garden include: development of measures to protect rare and endangered plant species, research on the flora and vegetation of the AMC, preparation and publication of a multi-volume work "Flora Altaica", monographic study of individual plant groups, conducting laboratory classes, summer practicals and special courses. The main purpose of this article is to attract the attention of the scientific community to the botanical research of transboundary territory of the Altai Mountain Country (Russia, Kazakhstan, China and Mongolia) and to the future development of digital plant collections in partnership with Global Biodiversity Information Facility (GBIF).
The Virtual Herbarium ALTB (Russian interface - altb.asu.ru) is the largest digital collection of plants from the transboundary territory of the Altai Mountain Country and the main source of primary material for the "Flora Altaica" project (http://altaiflora.asu.ru/en/). Since 2017, when Altai State University became a GBIF data publisher, data from the Virtual Herbarium ALTB has been exported to the dataset "Virtual Herbarium ALTB (South-Siberian Botanical Garden)" in GBIF. Currently, it includes images and data from 22,466 vascular plants, of which 67% have geographic coordinates (accessed on 30.03.2021). Most of the specimens have been collected since 1977, with the most intensive collecting years being 1995–2008. In 2019, the label-data table of the Virtual Herbarium ALTB was modified to bring it into conformity with the Darwin Core specification (http://altb.asu.ru/). This effectively solved the major impediment to sharing plant diversity data from the AMC and adjacent regions in a multilingual environment.
Altai Mountain Country, ALTB, collections, dataset, digital herbarium, Flora Altaica, plants occurrence, specimen
The Altai Mountain Country (AMC) is the highest modern uplift amongst the continental mountain countries in Siberia, as well as in Northern and Central Asia in general (
Due to the exceptional diversity of environmental conditions, the vegetation cover of the Altai Mountain Country is also highly diverse in its different parts and, in some of them, it is exceptionally diverse (Flora Altaica,
The herbarium of the South-Siberian Botanical Garden (SSBG) of Altai State University (ASU) was added to the Index Herbariorum database in 1996 under the code ALTB. ALTB has the largest collection of plants from transboundary territory of the Altai Mountain Country.The foundation of the primary collection of Herbarium ALTB was connected with the establishment of Altai State University in 1973 and of the South-Siberian Botanical Garden in 1979. In 1983, the University directive aimed to create a herbarium that included 5,000 sheets of plants from mountainous and plain parts of Altai Krai, collected by I.V. Vereschagina, A.I. Shmakov, T.A. Terekhina, E.P. Prokofjev, V.P. Kutafjev and G.G. Sokolova. N.V. Revjakina was responsible for primary systematisation, arrangement and addition to the collection (
The herbarium's growth was stimulated in its early days by the extensive expeditions led by the SSBG and by the establishment of three scientific journals that focused on the regions flora: "Flora and vegetation of Altai" (editor A.I. Shmakov), "Turczaninowia" (editor R.V. Kamelin, from 2016 – A.I. Shmakov), "Problems of botany of South Siberia and Mongolia" (editor A.I. Shmakov) and "Botanical researches of Siberia and Kazakhstan" (editor A.N. Kuprijanov). In 2005, by the time the first volume of "Flora Altaica" was published, the Herbarium ALTB had more than 300,000 sheets. Since then, the collection has grown and now it contains more than 450,000 sheets. It ranks fourth in Russia amongst university collections and collections of institutes of the Academy of Sciences. Even today, numerous new specimens are collected yearly.
In 2009, the Virtual Herbarium ALTB was designed, based on the collections from ALTB and the experience of European herbaria. The registration of the corresponding database with digital images was made on 11 January 2010 (Federal Institute of Industrial Property, №2010620024). The creation of the virtual herbarium at that time was motivated by the need to protect the collections of the botanical garden, which is particularly important for type materials (so the sheets and the information on them can be accessed without damage) (
The "Flora Altaica" project (altaiflora.asu.ru) was initiated in 2018. It is designed to foster collaboration amongst botanists working on the flora of the AMC. The draft sections include, amongst other things, original layouts of the printed version of multi-volume "Flora Altaica", the keys of taxa and the AMC map. The map has 19 botanical-geographical areas (polygons) in the GeoJSON specification. The use of GeoJSON polygons, as well as the Shapefile obtained on their basis, makes it easy to generate distribution maps using GIS-programmes, thereby clarifying the current range of the taxa involved and facilitating the task of citing representative specimens. The AMC polygons are available for downloading to all interested users in the section "AMC Map" of the project.
The biodiversity of the AMC territory has been explored for over 200 years. The first report on the flora of Altai was written by C.F. von Ledebour and his disciples C.A. von Meyer and A.G. von Bunge and published in 1829 in four volumes (
Only the herbarium samples can reliably confirm the presence of the plant organism in a specific point of space at a certain time. Herbarium collections and the data they hold are valuable, not only for the traditional studies of taxonomy and systematics, but also for ecology, bioengineering, conservation, food security and the human social and cultural elements of scientific collection (
The main purpose of this article is to attract the attention of the scientific community to the botanical research of transboundary territory of the Altai Mountain Country (Russia, Kazakhstan, China and Mongolia) and to the future development of digital plants collections in partnership with Global Biodiversity Information Facility (GBIF).
Scientific depository of phytodiversity of Altai Krai and the adjacent territory of the Altai Mountain Country (Russian Foundation for Basic Research project №19-44-220004).
The exact boundaries of the AMC were presented in 2005 by 19 botanical and geographical areas in the first volume "Flora Altaica". This zoning became the background for polygons edited in the GeoJSON specification for working in GBIF and converted to shapefiles for GIS programmes (data are available to all researchers at http://altaiflora.asu.ru/ru/карта-агс/).
The result of the first period grant implementation to Global Biodiversity Information Facility (GBIF) from the ALTB Foundation (Altai State University) includes more than 22,466 records, backed up by a digital image of the Herbarium. During the inventory work, original tables for the following plant groups were obtained: rare and endemic, invasive, economically valuable and other promising plant species. The team identified 1,176 medicinal plants and 296 food plants in the studied area. In the group "other promising plant species", we made significant inroads on digitising the material of large genera of such families as Caryophyllaceae, Rosaceae, Fabaceae, Scrophulariaceae and others. To add value to the data on the labels, the records were georeferenced. This increased the proportion of specimens with coordinates from 53% to 67% (
Development of Virtual Herbarium ALTB is an integral part of the larger "Flora Altaica" project. Its goals are to aid that project by:
The stages of herbarium digitisation are clearly described in many works (
1. Pre-digitisation curation and staging
The Curator of Herbarium ALTB selects for digitisation only mounted specimens with label, checked by plant taxonomists. Prior to digitisation, a barcode with the name of the herbarium "Herbarium ALTB" and a ten-digit number (for example, 1100000005) is glued to the herbarium sheet. The first three digits indicate to which major group the specimen belongs, "101" means ferns, horsetails and club mosses, "110" means seed plants. Other sequences have been set aside for other groups present in the collection, for example, 102 – lichens, 103 – mosses 104 – algae, 105 – fungi.
2. Specimen image capture
From 2007 to 2012, type material and representatives of the family Caryophyllaceae were completely digitised (3,717 sheets) using the modified scanner (useful model patent "Herbarium sheet feeder", № 146036). Each sheet was placed on a soft foam mat, which also helped to reduce pressure on the sheet in the Mustek PageExpress A3 USB 600 scanner. Digital copies of the herbarium sheet were provided with the 12 basic palette colours standard (HSB model). The images were saved in JPEG format with a resolution of 2793 x 3969 pixels (primary DPI 150 – using camera, DPI 72 – on server). After scanning, each image was renamed according to its barcode, which serves as a unique identifier. After completion of the first phase, digitisation was more fragmentary, precedence being given to those relating to active research projects, including thesis projects.
In December 2017, Altai State University became a GBIF data publisher (www.gbif.org/publisher/943a5811-d56e-4c37-853d-bd64957d3833) and started a new phase of herbarium digitisation. In particular, images were recorded using a Canon-EOS 400D camera placed on a tripod. By the end of 2020, 22,466 images had been added to the ALTB database. In the near future, the imaging equipment will be changed again, to a Microtek 1600 Object Scanner. They will be recorded as TIFF files with a 600 dpi resolution and include a 24-sample colour standard.
3. Specimen image processing
The image is processed by cropping the margins that protrude beyond the borders of the herbarium sheet, manually renaming according to the voucher number and then saving it in *jpg format. Then prepared images are copied via SFTP to the server of Altai State University (www.asu.ru).
4. Electronic data capture
Information from the label was manually entered into the digital form which contained 17 fields: unique barcode number (occurrenceID); status of herbarium material (typeStatus); country of herbarium collection (country); taxonomic category of material (phylum); family name (family); genus name (genus); species name with author citation (acceptedNameUsage); internal number of the label (catalogNumber); collectors (recordedBy); exact place of collection (verbatimLocality); ecology (locationRemarks); coordinates (decimalLatitude, decimalLongitude); altitude above sea level (verbatimElevation); date of collection (eventDate); who identified the herbarium material (IdentifiedBy); notes (occurrenceRemarks); image (available / not available). The exact species name with its author citation was rechecked according the International Plant Names Index (IPNI). To manage the tables of the Virtual Herbarium ALTB database, we developed the same-named site (http://old.ssbg.asu.ru/altb_herbarium.php) in the PHP programming language using the web-interface MySQL phpMyAdmin 5.
In 2019, the table of accumulated label data of Virtual Herbarium ALTB was adapted to the Darwin Core specification (altb.asu.ru). Following this data standard resolved many technical problems encountered when attempting to share data about the phytodiversity of Altai Krai across countries and languages. The updated Virtual Herbarium ALTB website has been prepared using PHP programming language and Smarty template engine. The site interacts with the database and performs a structured visualisation of the information using the standardised HTML document markup language. In contrast to the previous version, the project used Yandex.Maps API to visualise the geographical location of the records, which allows the use of cartographic data and Yandex technologies in the project. The logic of the designed application allows an individual label to be formed of each herbarium sheet included in the Virtual Herbarium ALTB database with the ability to geo-position and zoom the image when hovering the cursor without the need to download the image (e.g. http://altb.asu.ru/page.php?page=1100035931).
In the current website version, label information is entered from the herbarium sheet directly into a designed data entry form in the personal office of the database operator. A printed label in PDF format is generated automatically when entering a label data and saving forms (Fig.
5. Georeferencing specimen data
The Herbarium ALTB is relatively young, so the proportion of herbarium labels with coordinates was about 50%. Additional manual georeferencing keeps this share around 70%. Georeferencing accuracy of 500 m is carried out using standard electronic mapping libraries (Yandex.Maps, Google Maps).
The beginning of Herbarium ALTB digitising and global positioning of the available samples in GBIF showed the expected focus of the collections in the Altai Mountain Country (Fig.
37N and 60N Latitude; 65E and 114E Longitude.
A taxonomic analysis of 22,466 occurrences from ALTB in GBIF showed the following taxonomic distribution of the records: ferns (Polypodiopsida) – 288 records, monocotyledons (Liliopsida) – 3,848 and dicotyledons (Magnoliopsida) – 18,330 (Fig.
This work is licensed under a Creative Commons Attribution (CC-BY) 4.0 Licence (http://creativecommons.org/licenses/by/4.0/). The licence covers images of the herbarium specimens deposited in http://altb.asu.ru and available in GBIF, as well as their metadata.
Column label | Column description |
---|---|
occurrenceID | An identifier for the Occurrence (as opposed to a particular digital record of the occurrence). In the absence of a persistent global unique identifier, construct one from a combination of identifiers in the record that will most closely make the occurrenceID globally unique. http://rs.tdwg.org/dwc/terms/occurrenceID |
references | A related resource that is referenced, cited or otherwise pointed to by the described resource. http://purl.org/dc/terms/references |
basisOfRecord | The specific nature of the data record. Included value: HumanObservation. http://rs.tdwg.org/dwc/terms/basisOfRecord |
country | The name of the country or major administrative unit in which the Location occurs. http://rs.tdwg.org/dwc/terms/country |
countryCode | The standard code for the country in which the Location occurs. http://rs.tdwg.org/dwc/terms/countryCode |
family | The full scientific name of the family in which the taxon is classified. http://rs.tdwg.org/dwc/terms/family |
genus | The full scientific name of the genus in which the taxon is classified. http://rs.tdwg.org/dwc/terms/genus |
specificEpithet | The name of the first or species epithet of the scientificName. http://dwc/terms/specificEpithet |
scientificName | The full scientific name. http://rs.tdwg.org/dwc/terms/scientificName |
catalogNumber | An identifier (preferably unique) for the record within the data set or collection. http://rs.tdwg.org/dwc/terms/catalogNumber |
recordedBy | A list (concatenated and separated) of names of people, groups or organisations responsible for recording the original Occurrence. http://rs.tdwg.org/dwc/terms/recordedBy |
verbatimLocality | The original textual description of the place. http://rs.tdwg.org/dwc/terms/verbatimLocality |
decimalLatitude | The geographic latitude (in decimal degrees, using the spatial reference system given in geodeticDatum) of the geographic centre of a Location. http://rs.tdwg.org/dwc/terms/decimalLatitude |
decimalLongitude | The geographic longitude (in decimal degrees, using the spatial reference system given in geodeticDatum) of the geographic centre of a Location. http://rs.tdwg.org/ dwc/terms/decimalLongitude |
minimumElevationInMetres | The original description of the elevation (altitude, usually above sea level) of the Location. http://rs.tdwg.org/dwc/terms/verbatimElevation |
eventDate | The date-time or interval during which an Event occurred. For occurrences, this is the date-time when the event was recorded. Not suitable for a time in a geological context. http://rs.tdwg.org/dwc/terms/eventDate |
IdentifiedBy | A list (concatenated and separated) of names of people, groups or organisations who assigned the Taxon to the subject. http://rs.tdwg.org/dwc/terms/identifiedBy |
typeStatus | A list (concatenated and separated) of nomenclatural types (type status, typified scientific name, publication) applied to the subject. http://rs.tdwg.org/dwc/terms/typeStatus |
locationRemarks | Comments or notes about the Location. http://rs.tdwg.org/dwc/terms/locationRemarks |
associatedMedia | A list (concatenated and separated) of identifiers (publication, global unique identifier, URI) of media associated with the Occurrence. http://rs.tdwg.org/dwc/terms/associatedMedia |
CoordinateUncertaintyInMetres | The horizontal distance (in metres) from the given decimalLatitude and decimalLongitude describing the smallest circle containing the whole of the Location. Leave the value empty if the uncertainty is unknown, cannot be estimated or is not applicable (because there are no coordinates). Zero is not a valid value for this term. http://rs.tdwg.org/dwc/terms/coordinateUncertaintyInMeters |
language | A language of the resource. http://purl.org/dc/elements/1.1/language |
The authors wish to thank Shashkov Maxim and Ivanova Natalia for guidance and technical assistance.
A. Vaganov – designed the project, plants sample collection, checked and managed the data and prepared the manuscript.
A. Shmakov, S. Smirnov, N. Usik – species identification, plants sample collection, data preparation, manuscript editing.
A. Shibanova, P. Kosachev, T. Kopytina, P. Gudkova, A. Kechaykin, T. Sinitsyna, E. Antonyuk – species identification, data preparation.
K. Medvedeva – managed georeferencing.
E. Zholnerova, V. Zaikov, A. Shalimov, D. Dmitriev, A. Batkin, D. Kasatkin, D. Belkin – data preparation.