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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
(McNeill, et al. 2006.) 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.
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Synonymy
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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
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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
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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.
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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 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
Biologial 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.
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Living Collections Management
Management of living collections formed the original core of BG-BASE, and although
the system now does much more than simply manage living collections information, this
remains the most widely used part of BG-BASE. 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.
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Inventory / Stock Taking
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Living collections inventory is handled by using information stored in the LOCATIONS
table, to which each plant (living or dead), each propagule (living or dead) and each
germplasm record (living or dead) is attached. Using a softkey in the LOCATIONS entry window, you can produce an
inventory for all plants currently in or ever in a particular location; the same
user-definable reports can be generated from the INVENTORY program. By linking individual
location records into one or more LOCATION_GROUPS records, you can generate inventories
and stock-taking lists for multiple locations in a single command.
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
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As noted under Inventory / Stock-taking above, BG-BASE can be linked to one of a number
of mapping systems that have been designed for use with BG-BASE, such as BG-Map and the
system designed for the Arnold Arboretum.
These maps can be generated for particular beds, for particular taxa, for particular
collectors, etc. Maps can be displayed on screen or printed to paper, and living vs. dead
plants can be placed on different layers.
Horticultural Labels
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BG-BASE produces a wide variety of horticultural labels (laser, continuous form dot
matrix pot labels, engraved, embossed, barcode, etc.). These are controlled through the
LABEL_REQUESTS table, as shown in this example. See the Outputs document for further
information.
Plant Suppliers
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A module designed for the Royal Horticultural Society (RHS) allows them to track which plants are in the horticultural trade. Each year, RHS
staff update approximately 330,000 NURSERY_ITEMS records that are linked to their
110,000-record NAMES table and to their 2,000-record NURSERIES table. Information in
these tables is exported from BG-BASE in RTF format to produce the annual RHS Plant
Finder, which a print run of over 30,000 copies.
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Preserved Collections Management
Management of information concerning preserved collections is similar to - but
differs in significant ways from - management of information concerning living
collections. These similarities and differences have been incorporated into
BG-BASE.
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.
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Herbarium Labels
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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
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Multiple determination or verifications can be attached to a preserved specimen. When
more than one determination is attached to a specimen and those determinations link to
different names, the system prompts you for the name under which the specimen is to be
filed; in other words, you do not have to accept the latest determination as the correct
one. Specimens are indexed under the name used in each determination, so it is possible
to "find" a specimen no matter which name you use. A softkey in the SPECIMENS file shows
you a summary of all determinations attached to a particular specimen.
Loans, Gifts, and Exchanges
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BG-BASE tracks loans, gifts, and exchanges in the LOANS table; each record in this table
can represent an incoming loan, an incoming gift, an incoming exchange, an outgoing loan,
an outgoing gift, or and outgoing exchange. The HERBARIA table, to which loans are
linked, keeps track of transaction statistics to and from the institutions and can
display the current "balance" of gifts or exchanges between the institutions. BG-BASE can
produce packing lists of what is in the loan, mailing labels and its information can be
used to mail-merge overdue reminders.
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Conservation
BG-BASE handles a wide variety of species-, distribution-, protected area-, botanic
garden- and legislation-related conservation topics useful for monitoring biodiversity.
These include:
- 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.
This information can be either literature- or specimen-based. Conservation
information is tightly integrated with the nomenclatural and taxonomic information, the
geographic information, the preserved collection information and the bibliographic
information mentioned above.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.
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Bibliography
Handling bibliographic information is an essential, but often overlooked, aspect of
collection management. The main tables used to manage bibliographic information are DS
(data sources), JOURNALS, CITATION_FORMATS, IMAGES, DS_LOCATIONS and DS_SUB_LOCATIONS.
Together, these tables handle full bibliographic citation of virtually any type of data
source - books, journal articles, chapters in books, newspapers, letters, unpublished
works, field notebooks, specimens, annotation labels, conversations, and so on. Extensive
linkages are made from the DS table to the COUNTRIES, BRUS, FAMILIES and GENERA tables so
that camera-ready bibliographies can be produced for any of these (or other)
topics.
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.
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Bibliographic Tools
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BG-BASE allows you to quickly find any reference based on a variety of search
criteria (author, title, subtitle, journal, keyword, family, genus, country, BRU, etc.).
These records can be found using the normal indexing logic inherent to all entry windows.
These records can be used to create camera-ready bibliographies, as has been done by the
World Conservation Monitoring Centre (WCMC) to produce its 1997 IUCN Red List of
Threatened Plants.
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People and Institutions
Personal and institutional data are managed primarily through the CONTACTS,
HERBARIA, INSTITUTIONS, PSOURCES, STAFF and STAFF_GROUPS tables. Although some of these
tables seem to overlap, each has a distinct function. Many institutions tend to keep
"people" and "collection" data on separate database systems, but there are many inherent
links between these data types, and all can be managed seamlessly through BG-BASE.
- 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.
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The CONTACTS, STAFF, and STAFF_GROUPS tables also link to the EVENTS table, allowing
you to maintain personal and institution-wide calendars.
Last edited 12 January 2009
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