Digital Herbarium: Basic Usage

Features

Accessing to the Digital Herbarium’s data is provided via the web-page on the official website of the Botanical Garden Institute or HTTP API service. The latter approach is used for making search queries automatically (from R, Python or other computational environment).

Main features of the search service:

  • search in a given time interval either by date of collection or date of identification fields;
  • accounting species synonyms when searching;
  • search in a given rectangular region;
  • search within additional species (only for multispecies herbarium records);
  • search by record codes (e.g. field number, inventory number etc.);
  • search by the country of origin;
  • search by taxonomic name, e.g. family, genus or species epithet;

Search menu

General search possibilities are available via the search menu from the Digital Herbarium’s web-page (Fig. 1)

Basic search buttons

Fig. 1. Basic search menu

When search conditions are given simultaneously, the service is trying to perform an AND-type query; it retrieves records satisfying all search conditions. Currently only AND-type search queries are available. To perform OR-type queries it is recommended to use the HTTP API service.

Values of Family, Genus and Country search fields can be selected via drop-down menu that rises when typing.

Start date of collection and end date of collection are filled out from pop-up calendar when the mouse is hovering these fields.

If only start date of collection is given, the service retrieves records having later dates in the corresponding field.

If only end date of collection is given, the service retrieves records having earlier dates in the corresponding field.

If start date of collection and end date of collection are given, the service retrieves records if its corresponding date interval intersects the given.

Regarding the following text fields — Species epithet, Code, Collectors, Identifiers, Place of collection the condition satisfaction assumes containing the given value as a sub-string in the corresponding field (case insensitive comparison is performed).

If one performs search in the Collectors or Identifiers fields and fills these fields with Cyrillic letters, the service will automatically transliterate the given value into English (Latin letters) and return records satisfying both Cyrillic and transliterated values. If one provide the value only in Latin letters, no transliteration will be performed. Therefore, If you try, for example, to find records including “bakalin” as a sub-string in the field Collectors, the search will return the records which field Collectors (internally Collectedby field) includes the string “bakalin” (reverse transliteration (to Cyrillic letters) in this case wouldn’t be performed); If you try to search “бакалин” (Cyrillic equivalent of ‘bakalin’) combined search results for both “bakalin” and “бакалин” queries will be returned.

Boolean fields Search within synonyms and Search within additional species indicate that, in the first case — the search engine will take into account known (to the system) table of species synonyms, and in the second — the search engine do searching within additional species if those are provided.

Warning

When do searching within species synonyms, the search engine uses the table of species synonyms that, in turn, is being dynamically rebuilt each time records in the Table of known species are updated. The Table of known species can include errors. This could lead to surprising search results. These types of drawbacks (caused by incorrectness of species synonym relationships) tend to disappear in future, as the Table of known species will become more error-less.

Note

Search within synonyms works in cases when the exact names of the pair (genus, species epithet) are given.

Search by Code field

Herbarium records stored in Digital Herbarium of the BGI use triple coding system. Each record is provided with 1) inventory number (optional), used in the Herbarium’s storage; 2) mandatory ID field (unique, digits only), assigned by the system automatically; 3) field number (code), assigned by the collector (it is optional and quite arbitrary);

Therefore, the table of search results includes the column Complex code, which accumulates codes of these three types.

Complex code has the following structure:

Note

Inventory number (if provided) or * symbol/ID code/Field code (if provided)

So, the Complex code values can look as follows:

  • */27031/M.I.38 — denotes that the inventory number isn’t provided, ID = 27031, and field code is M.I.38;
  • 42/27029 — denotes that the inventory number is 47, ID = 27029, field code isn’t provided;
  • the following form of the code can take place as well: 132123/32032/F-3829-3k, where inventory number is 132123, ID is 32032 and field code is F-3829-3k (fake example);

When do searching by Code one should provide either an inventory number, ID or field code. For example, if the search field’s value is “231” the search engine will return records including “231” as a sub-string in either the inventory number, ID or field code.

Filtering search results

Standard filtering interface allows to restrict results of searching by Herbarium’s acronym, Herbarium’s subdivision or select desired number of items showed per page Fig. 2.

Search filtering panel

Fig. 2. Search filtering menu

It has the following fields:

  • Amount — the number of records showed per page;
  • Herbarium acronym — filtering by Herbarium’s acronym;
  • Herbarium subdivision — filtering by Herbarium’s subdivision;
  • Order by — ordering rule (choose field you want to perform ordering the results);

Results of search request with applied filter (records only under VBGI-acronym are shown) are presented on the Fig. 3.

Search results

Fig. 3. Search results tab

In the tab Common Info a table with the records satisfying current search and filtering conditions is shown (if no searching/filtering conditions were provided all published records are shown, by default the number-per-page is equal to 20).

The Details tab activates when a specific Herbarium’s record is clicked. It shows minified version of the Personal web-page of the record.

The Map tab is a copy of Common Info tab excluding records with no coordinates (records with coordinates are rendered on the Google map as clickable markers).

One can click Previous or Next (switch page) to get another portion of search results.

The Automatization tools tab includes general information on performing queries using automatization possibilies provided by the web-application.

Working with the map, one can filter search results by user-defined rectangular area. To do that, just initialize a rectangular area by pressing SB, edit the appeared rectangular region, and press SB again to activate the search (See Fig. 4, Fig. 5).

Search Herbarium's records by a region

Fig. 4. Initialize filtering region

Search Herbarium's records by a region

Fig. 5. Getting results of geographical filtering/searching

To clear particular search condition click small-trash icon near the corresponding search field.

To clear all search conditions press the CB button.

Search within polygonal regions isn’t supported by current database backend, but such behavior could be emulated programmatically with the help of the HTTP API Service.