• Home
• What's new?
• Introduction
• Features
• FAQs
• Interface
• Outputs
• Modules
• Tables
• Users
• Standards
• Training
• Support
• Documentation
• Newsletters
• History
• System requirements
• How to order
• References
• Glossary
• Guest book
• Copyright & licensing
• Disclaimer

Features

BG-BASE is a large system that is capable of performing many different tasks. This document briefly explains how the system functions. See also the modules, outputs and tables documents for further information.

Nomenclature and taxonomy

One of the most important and central features of any database dealing with biological material is its ability to handle scientific names. Scientific nomenclature and taxonomy are inherently complex and require a sophisticated and robust data structure to cope with the many rules and recommendations set out in the various codes of nomenclature. In BG-BASE, they are handled by a series of fields and tables covering taxonomic ranks from kingdoms down to subforms, grexes, and cultivars. Both plant and animal names, as well as names of most microorganisms, can be handled. For most purposes, it is the FAMILIES, GENERA, and NAMES tables that are the most important. The various rules of nomenclature as laid out in the International Code of Botanical Nomenclature (Greuter, et al. 2000.) and the International Code of Nomenclature for Cultivated Plants (Brickell, et al. 2004.) have been incorporated in BG-BASE as appropriate.

Despite its adherence to nomenclatural rules as noted above, the system still allows users to vary how scientific names appear - whether the scientific author appears as part of the name, the abbreviation (ssp. vs. subsp.) used for subspecies, the format (cv. vs. '') used for cultivars, etc. The internal data in BG-BASE do not change; rather the user sets various flags (either specific to that user, to that session, or for the institution as a whole) and all scientific names and synonyms change appropriately.

	Kingdoms - BG-BASE ships with values for Animalia, Fungi, Monera, Plantae, and Protista.
	Major taxa - BG-BASE ships with values for Fungi, Lichens, Algae, Bryophytes, Fern allies, Ferns, Gnetophytes, Conifers, Ginkgo, Cycads, Dicots and Monocots. Animal values are being added.
	Subclasses - BG-BASE ships with the Cronquistian subclasses Alismatidae, Arecidae, Asteridae, Caryophyllidae, Commelinidae, Dilleniidae, Liliidae, Magnoliidae, Rosidae, and Zingiberidae.
	Orders - BG-BASE ships with the Cronquistian orders for angiosperms.
	Families - BG-BASE ships with over 1,100 families of plants and fungi; these include all names covered by Brummitt, along with family names for bryophytes and many others. Animal families are being added. For botanical families, equally correct alternate names (such as Compositae vs. Asteraceae) are catered for via a flag set by the user.
	Genera - BG-BASE ships with nearly 29,000 genera of plants; these include virtually all vascular plant genera covered by Brummitt, along with many others, especially bryophytes and fungi. Animal genera are being added. Each genus has been assigned to a family, but these family placements may be changed at the user's discretion.
	Subgenera - handled as a multivalue field within the GENERA records; also available as a pick-list from the NAMES table.
	Series - handled through links in the NAMES table.
	Subseries - handled through links in the NAMES table.
	Sections - handled through links in the NAMES table.
	Subsections - handled through links in the NAMES table.
	Species - along with genera and families, the species level is one of the primary taxonomic levels of interest to most users. Species (as well as taxa below the rank of species) are handled in the NAMES table. Each NAMES record is linked via its GENUS field to a GENERA record, which then links to all higher taxonomic levels.
	Subspecies - handled as part of the multivalue INFRA_RANK field in the NAMES table.
	Varieties - handled as part of the multivalue INFRA_RANK field in the NAMES table.
	Forms - handled as part of the multivalue INFRA_RANK field in the NAMES table.
	Subforms - handled as part of the multivalue INFRA_RANK field in the NAMES table.
	Grexes - handled as part of the multivalue INFRA_RANK field in the NAMES table (grexes are non-Latin collective names, used especially for hybrids of orchids and Rhododendron).
	Cultivar groups - handled by the CV_GROUP field in the NAMES table.
	Cultivars - handled by the CULTIVAR field in the NAMES table.
	Selling names / commercial synonyms - handled by the multivalue SOLD_AS and SOLD_AS_FLAG fields in the NAMES table.
	Plant Breeder's Rights names - handled by the multivalue SOLD_AS and SOLD_AS_FLAG fields in the NAMES table.
	Registered trademark names - handled by the multivalue SOLD_AS and SOLD_AS_FLAG fields in the NAMES table.
	Awards - along with the AWARD_ORGANIZATIONS and AWARD_SITES tables, the AWARDS table can track all horticultural awards (FCC, AGM, etc.) given to a taxon or to a specimen; these awards can be displayed/suppressed as part of the scientific name at the user's discretion.

Authors

If the user obtains permission from the Royal Botanic Gardens, Kew, BG-BASE can be shipped with ca 30,000 records for authors of scientific names of plant taxa, following Brummitt & Powell (1992) (or users can manually enter the authors that are relevant to their collections); these are stored in the AUTHORS table. Authors can be displayed/suppressed as part of the scientific name at the user's discretion.

Synonymy

Synonymy is handled in the multivalue ALT_NAME field within the NAMES table; this supports a many-to-many relationship between alternate names for the same taxon. Each record in the NAMES table is coded as one of several types - accepted name, invalid name, manuscript name, orthographic variant, pro-parte synonym, synonym, unchecked name - and any particular record in the NAMES table can be linked to as many alternate names as necessary.

All records are indexed under all alternate names, making it easy to find a taxon, no matter which name is used. The alternate names for a taxon are available by pressing a softkey.

Typification

Names can be typified using the SPECIMENS table. Each specimen can typify more than one name, and multiple specimens may typify a single name; this many-to-many relationship is handled through multivalue fields. The types for a name are available by pressing a softkey.

Citation of names

The citation of scientific names (in monographic or floristic works, for instance) can be tracked through the NAME_DS multivalue field in the NAMES, GENERA, and FAMILIES tables.

Geography

Distributions at various geographic and geopolitical levels (continent, region, country, subcountry political unit, Biological Recording Units (BRUs) can be tracked. These distribution patterns can be based on either literature or specimens, or a combination of both. In addition to the standard COUNTRIES, SUBCOUNTRIES, and BRUS tables, there are also REGIONS and PLACES tables, which serve as an electronic gazetteer tracking user-defined areas or localities. The ACCESSIONS, COLL_BOOKS, GERMPLASM, and SPECIMENS tables have fields for latitude and longitude as well as one for national grid. This geographic information can be linked to various CAD or GIS packages to produce distribution maps.

	Regions - user-defined regions (usually continents or other large areas) are stored in this table, enabling institutions to sort living and preserved collections into the geographic areas appropriate to their needs.
	Countries - there are records for each of the 238 countries recognized by the International Standards Organization (ISO), containing information on the country's name, 2- and 3-letter ISO (International Standards Organization 3166) code, size, capital, population, language(s) spoken, international telephone dialing code, time zone(s), placement of postal codes within a mailing label, etc.
	BRUs - there are records for each of the 1,006 Biological Recording Units, a 4-tier hierarchical classification scheme for recording biological distributions adopted by the TDWG. These records contain information on BRU code, level (1-4), English name, French name, German name, Spanish name, political name, region, "parent" BRU, BRUs making up this BRU, as well as spelling variants.
	Subcountries - this table contains the geopolitical units making up countries, stored in a 3-tier hierarchical system. For each subcountry record, its level (1-3) within the country, name, and "parent" subcountry is given. This table is used to standardize the citation of geopolitical units within countries when producing herbarium labels, accessioning living material, etc. Unlike the BRUS table, there are no standardized codes for these records, and the information is stored here as free-text; however, the BRU system does not provide a mechanism for storing sub-country information for both large and small countries, which this table does (for instance, there are approximately 2,500 political subdivisions in China, each of which can be coded in the SUBCOUNTRIES table, but the BRUS table only tracks 44 subdivisions of China).
	Places - this table acts as an electronic gazetteer, handling records that refer to user-defined sites, cities, geopolitical areas, protected areas, etc. For each record, information on the name of the place, the country, sub-country units, BRU, latitude and longitude, habitat, vegetation, altitude, geology, collectors associated with this site, and any alternate names/synonyms are kept.

Living collections management

The major tables used in living collections management include ACCESSIONS, GERMPLASM, HORT_TASKS, LOCATIONS, LOCATION_GROUPS, QUARANTINES, PLANTS, PROPAGATIONS, SHIPMENTS and VERIFICATIONS.

	Accessions - all wild-collection and donor information about a living accession is stored in this table, which tends to be somewhat static (the changing elements of the living collections are handled in the PLANTS table)
	Germplasm - information about seeds, spores, frozen tissue and extracted DNA is stored here; these records are linked to the NAMES table and (optionally) to the ACCESSIONS table. Information on the preparation of the material, storage condition, viability, germinability, etc., are kept here. It is this table, along with the PLANTS and PROPAGATIONS tables, that ultimately determines whether an accession is "alive" or "dead"
	Horticultural tasks - keeping track of horticultural tasks is an essential element of living collections management; the HORT_TASKS, HORT_TASK_CODES, and MATERIALS tables facilitate this by handling information on person requesting work to be done; date of request; description; location code(s), genera and accession number(s) affected; material used; unit cost of material; people completing the task; number of hours spent; hourly rate; and completion date. The system calculates total and per-plant costs for the whole job, for the materials, and for the labor involved.
	Locations - the individual areas into which the living collections are broken and in which plants are grown are stored in this table; the system allows for quick reports (via the INVENTORY program) of all plants currently in a location as well as those that have ever been in that area (the latter report is especially useful when seedlings or root suckers show up unexpectedly; it can also prove invaluable when trying to identify from a photograph a plant that is no longer in a particular location)
	Location groups - each location can optionally be allocated to one or more location groups, thus allowing for easy reporting (via the INVENTORY program) by groups of location codes
	Plants - the dynamic portion of the ACCESSIONS table, this table tracks all information that is likely to change about an accession, such as location, condition (alive, good condition, fair condition, poor condition, dead, etc.), reproductive status/phenology, sex, size, label needs, etc. This table also allows you to track individuals within an accession instead of simply the accession as a whole, a critical features for conservation collections and other research activities; it is this table, along with the GERMPLASM and PROPAGATIONS tables, that ultimately determines whether an accession is "alive" or "dead"
	Propagations - information about successful and unsuccessful propagation attempts can be stored here; this table includes fields for propagule type (seed, cutting, graft, etc.), date received, hormones used, lighting regime, environmental conditions, date germinated/rooted, success rate, cause(s) of death, date when the material was dispatched, and so on; it is this table, along with the GERMPLASM and PROPAGATIONS tables, that ultimately determines whether an accession is "alive" or "dead
	Quarantines - by entering information in the QUARANTINES and Q_BATCHES tables, institutions can track what is in quarantine, when it was received, the condition upon receipt, treatments of the material while in quarantine, and the release (or death) date
	Sequences-DNA sequence data are stored in this table; in addition to the sequence itself, there are fields for sequence date, gene sequenced, accession number and qualifier, germplasm number, specimen number, name number, published references to the sequence, where and when the sequence was submitted (for instance, GenBank), and staff who generated the sequence.
	Shipments - information on living (and extracted DNA) material leaving the institution is as important as the information about material entering the collection; information on material shipped, including recipient, date, amount of material, propagule type, accession number, taxon, phytosanitary permit, restrictions, purpose, shipping charges, etc., is stored here
	Verifications - plants making up the living collections may or may not be correctly named; this table allows institutions to track the verification process: who requested the verification, who verified the material, when the verification was done, the level of certainty of the verification, request for more material, references used in the verification, whether a voucher specimen was made, etc.; this allows users to find easily all accessions that have not been verified

Inventory / stock taking

BG-BASE keeps track of plants that are currently in a location as well as all plants that have ever been in that location; this is particularly useful when a once-"dead" plant re-appears from root suckers or seeds in the soil. This feature can also be useful when trying to identify specimens in old photographs, plants that might have died long ago. These indexes are maintained in real time by the system, and inventory lists can be produced for any area in a matter of seconds.

Mapping

Horticultural labels

Plant suppliers

Preserved collections management

The major tables involved in preserved collections management are COLLECTORS, HERBARIA, LABEL_FORMATS, LOAN_ITEMS, LOANS, SPECIMENS, VERIFICATIONS. In addition, the various tables handling nomenclature and taxonomy as well as those handling geography are used extensively.

	Collection books - the COLL_BOOKS table can be used as an electronic field notebook, allowing collectors to enter all relevant wild collection information directly into a subset of BG-BASE (using a laptop PC with a runtime version of OpenInsight and BG-BASE); when they return from the collecting trip, this information is transferred to the master copy. Each record is identified by a two-part key - collector code and collector number. Data from this table can be automatically transferred to the ACCESSIONS and SPECIMENS tables.
	Collectors - each collector, collector group, or collecting expedition is assigned a unique alphanumeric code, which is then associated with all appropriate ACCESSIONS, COLL_BOOKS, GERMPLASM, IMAGES, and SPECIMENS records.
	Herbaria - each institution holding preserved specimens is uniquely identified by a code. For the major herbaria of the world, these codes are those assigned in Index Herbariorum; however, you can add codes for other individuals or institutions not covered by IH.
	Label formats - this file controls the content and layout of herbarium and other preserved specimen labels. See the Outputs document for further information.
	Loan items - each preserved specimen may be part of 0 to many transactions (loans, gifts, exchanges) between institutions; this information is kept in this table, allowing you to instantly determine whether a specimen is currently on loan, or if it has ever been on loan; fields for the condition of the specimen before and after loan are also available.
	Loans - this table contains a record for each batch of specimens that is sent on loan, as a gift, or as an exchange. After the LOANS record is set up, one or more LOAN_ITEMS is created and linked to this loan as well as to the appropriate SPECIMENS record, using a barcode reader if one is available.
	Specimens - this table contains a record for each preserved specimen; in most cases, these specimens will be housed in the institution using BG-BASE, although the table can handle information on specimens from other institutions as well, enabling you to track exsiccatae used in monographic and floristic/faunistic work. Records in this table contain fields for herbarium where deposited, barcode, taxon name, collector, collector number, full wild- and garden-collecting details, associated materials, typification information, and citation information.
	Verifications - records in this table can be attached to either preserved or living material (SPECIMENS or ACCESSIONS, respectively). Each record stores the date of the determination/verification, the person making the determination, the level of accuracy of the determination, any data sources used in the determination, and so on.

Herbarium labels

In addition to managing information about specimens, BG-BASE allows users to produce herbarium and other specimen labels. They can be printed in a variety of layouts (1 to a page (for bryophyte packets, etc.), 4 to a page, 6 to a page, and 8 to a page); the format of each label is under user control, based on information in the LABEL_FORMATS table; each kind of specimen label has its own label format record, which must be created first.

Herbarium labels can also be produced by merging data from BG-BASE into Microsoft Word template. Word's mail merge wizard is used to produce the final labels containing the exported data. User's have full control over the design of the labels like adding institutional logo's, headers, footers, font sizes and more.

Determinations / verifications

Loans, gifts, and exchanges

Conservation

• IUCN Red Data Book categories of threat (both the "new" and the "old" IUCN categories are supported)
• The Nature Conservancy's Global Ranking system
• CITES listing (at family, genus, species and population levels)
• known or suspected threats
• population size/number of individuals left
• year last seen
• legal status
• presence in protected areas
• protected area survey information
• presence in botanic gardens, and
• habitat information.

Conservation information can be tracked at the global level down to BRU (Biological Recording Units) level 4. All relevant fields have an attached data source field, so that sources of information can be easily tracked. BG-BASE was used by the World Conservation Monitoring Centre (WCMC) to produce its 1997 IUCN Red List of Threatened Plants (Walter & Gillett, 1998), a 900-page book listing 34,000 threatened and extinct taxa; information from this book is also available as a searchable database on the Internet.

	Laws and conventions are handled through the LAWS table, as well as specific tables for the Bern Convention, CORINE, EEC annexes, Habitats Directive, and UNECE legislation.
	Protected areas and other areas of conservation concern are handled through three tables: CONS_AREAS tracks general information about the area (name, type of protection, year of designation, area, country, BRU, latitude/longitude, elevational range, realm, province, and biome); CONS_AREAS_INFO tracks plant and animal inventory information for the area (number of total taxa, species, genera, families, both endemic and non-endemic at a variety of taxonomic levels such as plants , angiosperms, dicots, monocots, trees, large mammals, small mammals, birds, amphibians, reptiles, etc.); CONS_AREAS_LINKS links individual taxa tracked in the NAMES table to protected areas - each record contains occurrence, introduced, and endemic flags (parts of the POSS standard), data source for the distribution information, abundance, vegetation, position within the protected area, elevational range, last seen, size class, and uses.
	Conservation projects are handled by the PROJECTS table, whether those projects are within or outside of the institution running BG-BASE. Each record contains information on the name and description of the project, status (on-going, completed, planned), institution(s) running, funding, and collaborating in the project, contact name, BRUS, countries, taxa, genera, and families involved, and data sources associated with the project.
	The PERMITS table tracks information on collecting and wildlife exploitation permits issued by an agency; each record has fields for the type of permit, purpose, contact name and phone, starting/ending dates, and renewal information.

Bibliography

Images form an important part of the bibliographic capabilities of BG-BASE. BG-BASE allows you to keep track of information about an image as well as to store digitized images online; such digitized images can be displayed in all appropriate parts of BG-BASE. These images might be photographs of individual plants or animals, habitat shots for collecting localities, expedition maps, maps of garden beds, line drawings from the original description, scanned images of herbarium labels, scanning electron micrographs, photographs of DNA gels, pictures of events, photographs of staff, and so on.

	Citation formats can be defined by the user; these formats control the order and appearance (bold, italics, etc.) of the various elements of a bibliographic citation
	Data sources - the DS table stores full bibliographic information (author(s), publication date, title, subtitle, journal, volume, number, pagination, publisher, place of publication, ISBN, ISSN), as well as keywords, abstract, relevance, call number, citation notes, language, countries mentioned, BRUs mentioned, families mentioned, genera mentioned, and scientific names mentioned. Multiple copies of references can be tracked, each with a separate barcode and location, and each reference can be loaned separately.
	Images are tracked separately from other, text-based bibliographic material. Each IMAGES record contains fields for format, process, quality, orientation, scale, subject, title, date, accession number(s), name number(s), country, locality, collector, artist, copyright, credit. In addition to information about images, this table also links to digitized images and can display stored images using a softkey. Like the DS table, records in this table have a COPYNUM field, with which are associated the barcode and location information; images can be loaned using the same process as for books and journals.
	Journals - the journal's full name, along with multiple abbreviations, publisher, first and last publication date, ISSN, call number and keyword are tracked. Records in the DS table can then be linked to the appropriate record in this table to simplify and standardize data entry.
	Loans of bibliographic material and images are tracked through the LIBLOANS table. There are fields for the name of the borrower, barcode of item being borrowed, date of loan, duration of loan/due date, return date, and condition when returned.
	Locations of bibliographic material and images are tracked through records in the DS_LOCATIONS and DS_SUB_LOCATIONS tables.
	Relevance codes - user-defined relevance codes can be set up in the DS_RELEVANCE table.

Bibliographic tools

People and institutions

	Contacts - all personal and institutional contacts are stored in this table, which has fields for name, institution, home and work address, phone, and fax, email, interests/expertise, and so on. Each CONTACTS record can optionally be linked to an INSTITUTIONS record, and each CONTACTS record can be linked to one or more user-defined mailing lists.
	Herbaria - institutions sending or receiving loans of preserved specimens are handled in this table, whose key is the code supplied in Index Herbariorum, (Holmgren, Holmgren & Barnett, 1990) supplemented by user-entered codes for non-IH institutions and individuals. Loans, gifts and exchanges of preserved collections are linked to records in this table.
	Institutions - institutional addresses, phones, faxes, and email addresses can be stored in this table and used to populate appropriate fields in the CONTACTS table.
	Psources - institutions or individuals acting as sources or recipients of living material are stored in this table. Since many institutions maintain both living and preserved collections, there are links between the PSOURCES and HERBARIA tables.
	Staff - all BG-BASE records are stamped with the user's initials who created or edited the record along with the date this was done. Codes for this information are stored in this table; records in this table are also used to set up individual calendars and to-do lists, tracking label requests, horticultural tasks, etc.
	Staff groups - staff may be grouped by means of this table, a feature that is used by BG-BASE to handle scheduling of meetings, etc.

The CONTACTS, STAFF, and STAFF_GROUPS tables also link to the EVENTS table, allowing you to maintain personal and institution-wide calendars.