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Biological Informmation System

UNIVERSAL BIOLOGICAL IFORMATION SYSTEM BIOBASE

 

 On the base Agarkov’s multipurpose information system RADBASE (Agarkov, 1996, 1998, 1999, 2000, 2004; Afanacieva at al., 2005) was propose universal biological information system of all biological objects of the world BIOBASE.

Start form of micrpaleontological block of informational system
Fig. 2. Start form of micrpaleontological block of informational system


This database is a complex geoinformation system, which contains constantly updating data on the fossil and recent organisms studied by this author, and extensive published data. The database is composed of several interconnected blocks, including same biological (with micropaleontological) and bibliographic databases, a database of the codes of geological space, and cartography. Each of these blocks is a separate information system, which can be used also for creating other databases (Fig. 2). provided by the radiolarian informational system used.

A model of data
A model of data

 

The biological and micropaleontological block is universal and allows the storage of information on any groups of fauna and flora irrespective of their morphology, geochronological range, and variations of ecological settings. Presently, to access the morphological analysis of biological data it includes data on extant and fossil radiolarians, diatoms, silicoflagellates, ebriideans, actinomycids, coccolithophorides, foraminifers, dinoflagellates, synuracids, fungies, mollusks, insects, animals and plants.
 

In total, the biological block includes series of relational worksheets for each of the above groups of microorganisms connected by the systems of key fields. Because of the uniformity of the worksheets of storages of information and flexibility of data processing, the system allows the analysis for both each class, or section, and all taxa of higher rank together. The following worksheets are most important in the block described:

  1. Check-list of species
  2. Systematics of species
  3. Description of species
  4. Images of species
  5. Distribution of species
  6. Morphological feature of species
  7. Glossary of morphological characters of species
  8. Skeletal parameters of species
  9. Ecology of species
  10. Geochronological distribution of species
  11. Check-list of genera
  12. Descriptions of genera
  13. (Systematics of generic taxa
  14. Check-list of suprageneric taxa
  15. Systematics of suprageneric taxa
  16. Descriptions of suprageneric taxa
  17. Worksheet of synthesis for the analysis of distribution.

The main check-list of species and subspecies taxa contains about 17000 synonyms of radiolarians of about 11000 valid species and subspecies, diatoms (8000 species, subspecies; varietets, form and subform): silicoflagellates (900 names), ebriideans (100 names), coccolithophorides (6 000 names), foraminifers (8 000 names), fungies (1000 names, mollusks (2 000 names), insects (5 000 names), animals (2 000 names) and plants (11 000 names).
The check-list of genera includes data on 10 000 valid taxa and their synonyms. For each of  them, all available description in the original language and data on the geochronological range based on the ranges of the species of this genus are provided.
Apart from the existing synonymy encoding, the program allows alternative encoding of taxonomic synonyms and choice of variants of suprageneric systematics.
The above worksheets in accordance with the structure shown in Fig. 1 include over 40 various glossaries and check-lists determining the type of a record in the information system (species, basinonym, synonym, doubtful species, etc.), methods of quantities calculations, author who determined the taxon in a probe, type of presentation of the material in a publication (data on a sample, a group of samples, group of outcrops, or borings, general summary for a region), the level of certainty in identification of a specimen, precision and method of obtaining coordinates for the sample collection, weather, lithotypes of rocks and their description, and many other parameters, which are presented in a uniform style (Fig. 3).
The main form contains series of bookmarks reflecting a certain type of information of this name (record). Figure 3 shows a fragment from the list of names (Edit species information). When the cursor is pointing a certain name (species) from this list, the list includes the main attributes (name, author, code of the source of information, old name of the genus), while a complete name of the taxon appears at the top of the general part of the form, and the right part contains complete synonymy. A series of buttons above the list are highlighted menu items that allow quick entry of a new record, identification of synonyms, or to enter information on the taxonomy of the species and the possibility of generalized information on all synonyms of this name.

Page “Editing of the list of species” in the main sheet of the radiolarian informational system
Fig. 3. Page “Editing of the list of species” in the main sheet of the radiolarian informational system


The page “Photo and Description”, the field “Name” gives the opportunity to screen all images and descriptions related to this name (scanned and reduced in a same format) that are related to this name (Fig. 4). The same field provides the information on the geochronological range of the species. The series of deeper fields “Name table” contains all lists of images with explanations and all descriptions with notification of the type of data (descriptions of the holotype, redescriptions, notes, etc.). When necessary these data, but for the entire species with a possibility of choice of the alternative synonymy, may be found in the field “Species”.

Representation of comprehensive information of the species description, illustrations, synonymy, and taxonomy of a species.
Fig. 4. Representation of comprehensive information of the species description, illustrations, synonymy, and taxonomy of a species.

Fig. 4. Representation of comprehensive information of the species description, illustrations, synonymy, and taxonomy of a species.

To view several images of a synonym or species, there is a page “Multiphoto” (Fig. 5). Using it, it is possible to view eight images simultaneously or retune it to any amount of simultaneously viewed images depending on the hardware. This page, like the previous one, contains all images in a uniform format. Special fields of the worksheet of images contain the same images, which are shown in two standard scales depending on the quality of the original source, which allows small and large radiolarians to be viewed. This system of presentation of graphic information allows evaluation of morphological features of specimens and to visually estimate changes in their size, which is especially valuable in analyzing the geographical distribution and introducing the images onto the maps.

Multiform representation of the illustrations of a species.
Fig. 5. Multiform representation of the illustrations of a species.

 

The block of spatial–age distribution allows storage of information on the taxa in any convenient system of identification of locations (administrative, tectonic, etc.), including geographical coordinates connecting the information system with electronic maps. The information is organized on principle taxon–sample, with all available information on the sample, including the certainty of species identification, age, and geographical location of the site provided. The age is given in various variants (stages, formations, zones) and does not restrict the user’s opportunity to input an alternative dating based on other fossil groups, multiple alternative encoding, etc.). The stratigraphic dictionary includes over 2300 stratigraphic terms, while the block itself includes over 200000 records. The bibliographic block in the micropaleontological analysis is generally used for data about the source of information, although it can work as an independent bibliographic information system, including over 11 000 papers and representing the most complete Russian-language bibliography of micropaleontology. Apart from the standard description of the source of information in the original language, this block contains a summary of the publication and, sometimes, the complete source with all available illustrations.
The search system of this block allows publications and manuscripts to be found based on virtually any key (three-levelled indicator of the topic of the publication, author and year of publication, language, classes of organisms described, geological age, fourlevelled indicator of the geographical scope of the paper, petrographic characterization of objects, etc.).
The use of the information system allows the construction of the maps of the geographical ranges of species, establishment of zones of divergence, determination of the geological age of samples based on the summary of their morphological features, analysis of the ecological conditions of the environment, estimation of the species diversity of the supraspecific taxa with a precision from erathem to subage, taking into account any additional conditions (morphological elements and parameters of skeletons, ecology, etc.).

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