Modules

BG-BASE is composed of a series of modules; each of these modules links with the others using shared fields / tables and a common user interface to create a seamless data management environment that does as much or as little as the user requires. No single installation of BG-BASE uses all of its modules or functionality; rather, each uses a different subset of the whole. However, all users remain compatible with one another because all share the same field definitions. In addition to the standard fields, there are 5-10 user-defined fields in most tables that can be used for institution-specific needs.

This flexibility is possible because BG-BASE is built using OpenInsight, whose variable-length and multivalue field technology permits everyone to share the same master data dictionary without wasting data storage space for fields and tables that they are not currently using. Since any field or record can vary in length, there is never a need to truncate data, and data storage requirements are significantly less than what fixed-length field systems (such as Access, dBASE, FoxPro, and Paradox) require to store the same data.

Currently there are modules for:

Although these modules are designed to do different things, there is a considerable overlap between several of them. The major functionality and main tables in each of the modules are explained briefly below.

Living Collections Module

The Living Collections Module allows the user to curate both large and small collections. As such, it handles a very broad range of topics, some of which are taxon-based and others are collection- or specimen-based.

The taxon-based information includes:

• Taxonomy / nomenclature: information for the taxonomic hierarchy - kingdom, class, subclass, order, family, genus, subgenus, section, subsection, series, subseries, species, subspecies, variety, form, grex, cultivar, and hybrids - is stored in separate fields and/or database tables. Much of this is stored in the central NAMES table, which has the rules of both the botanical and horticultural codes of nomenclature built into it. This table permits many-to-many links between scientific names and their synonyms as well as their common / vernacular names. Source of the name, range (both free-text and coded) habit, hardiness conservation status, flowering and fruiting times, flower and fruit colors, ultimate size and free-text descriptions can also be tracked.

The collection- and specimen-based tables include:

• Accessions: all information about the material as it enters the collection (the "passport" data) is stored in this table, including accession date, name received as, number received, type of propagule, condition upon receipt, source of material, accession number and/or Index Seminum number assigned by source, wild-origin details (country, three levels of subcountry geopolitical units, free-text locality, habitat notes, collection notes, elevation, latitude, longitude, collector, collector number, collection date, etc.), justification for being accessioned, lineage number (the accession number under which this genetic material first entered the collection), other accession numbers, and special characteristics (user-defined codes).
• Plants: individuals or masses within an accession are tracked as separate records in this table, which stores information on the location and condition of each plant or mass, planting date(s), grid location(s), check date(s), measurements, special characteristics, and cause(s) of death. Those fields whose values can change, such as location, condition, measurements, and so on, are multi-valued, allowing the user to keep track of this information over time.
• Shipments: records can be kept for both shipment invoices and individual shipments. The invoices table gathers information from the shipments table and can be used to produce either packing slips or invoices, including per-item charges and shipping charges. The shipments table stores information on the name of the taxon, accession number, propagule type, and number and date sent. Using these tables ensures that users know where particular genetic material or taxa have gone in the event of loss of that material from their own collection.
• Quarantines: information on quarantine batches (source of material, person(s) inspecting and handling the material, days in transit, arrival date) as well as individual quarantines (how received, name of taxon, accession number, condition of material upon receipt, collector information, location, required treatment, medium, when and where sent, cause of death) are tracked in these tables.
• Images: Information on the taxa, subject, artist, date, medium, format, camera, film, and geographic locality is tracked through the IMAGES table, which is linked to the ARTISTS, ACCESSIONS, COUNTRIES, DATA SOURCES, NAMES, and PLANTS tables. Individual images can be barcoded, allowing you to track these images as they are sent on loans. Images that are stored in electronic format can be displayed directly from the database. BG-BASE can produce stick-on labels for slides.
• Germplasm: records are kept for each lot of seeds, spores, pollen, or tissue culture material, including storage date, name of taxon, accession number, location, pretreatment, light and temperature regimes, environmental conditions, and viability.

Distribution information can be either taxon- or specimen-based

• Geography: distribution at various geographic and geopolitical levels (continent, region, country, subcountry political unit, Basic Recording Units [an internationally agreed standard for coding plant distributions] can be tracked. These distribution patterns can be based on either literature or specimens. In addition to the standard countries, subcountries, and brus tables, there are also regions and places table, which serve as an electronic gazetteer tracking user-defined areas or localities. This information can be linked to various CAD or GIS packages to produce distribution maps.

Other types of information tracked within this module include:

• Locations: records are kept on individual locations and location groups in the collection, through which the user can create inventories and stock-taking lists. Locations can be strictly rectangular grids or free-form bed-based areas. Lists of plants currently in each location as well as all plants ever in the location are kept by the system. Information in this and the plants table can be linked to various computerized mapping systems.
• Plant sources: tracks contact name(s), address, phone, fax, email information on all sources and recipients of plant material. Specialties at the level of family, genus, and special groups can be tracked. BG-BASE automatically keeps lists of all accessions received from as well as all shipments sent to each of these records. The table can be used to create mailing labels for sending seed lists, etc.
• Horticultural maintenance: records can be created to track specific horticultural activities (pruning, spraying, cabling, fertilizing) undertaken. These activities are user-defined and can be linked to individual plants within a collection, entire genera in a collection, or to all plants within a specific location. Also tracked is the date the task was requested, date completed, who requested the task, and who completed the task.
• Collectors: although use of this table is optional, assigning a collector code to each collector or expedition used in other related tables permit the user to instantly find all accessions, herbarium specimens, verifications, and propagations associated with a particular collector.
• Verifications: requests for verification of accessions as well as the actual determination are tracked in this table. This information includes the accession number, original name of taxon, person making the request, person doing the verification, date of verification, data source(s) used in the determination, level of confidence in the determination. Multiple verifications can be attached to a single accession.
• Data sources: full citation details, including type of the data source, author(s), publication date(s), title, subtitle, source, series/edition, volume/number, pagination, publisher, place of publication, ISBN, and ISSN, as well as keywords, call number, location of the material, purchase date and price, language, countries, families, genera, scientific names associated with the data source, relevance (user-defined codes), and a full abstract can be kept in the data sources table. This is a critical table that is linked to most other tables, allowing the user to track where various pieces of information have come from. The table can be used to create camera-ready bibliographies on a wide variety of topics, using standard or user-defined citation formats; it also allows for on-line querying in "library card" format.
• Awards: awards can be given either to individual plants or to taxa; the three major tables are award organizations (including the awarding committees within each organization and the types of awards given by that organization), award sites, and awards. These link to the names, accessions, and plants tables.

Data can be exported to various computerized engraving and embossing machines, as well as laser printers barcode printers and dot-matrix printers to produce a wide variety of labels.

Preserved Collections Module

This module shares many tables with the Living Collections Module, but it is designed specifically to manage information on herbarium and other preserved specimens. Its main tables are SPECIMENS, COLLECTION BOOKS, DETERMINATIONS, BARCODES, HERBARIA and TRANSACTIONS as well as NAMES, COLLECTORS, ACCESSIONS, and PLACES (see above).

• Specimens: information on herbarium and other preserved specimens (such as wood samples and liquid-preserved specimens) are stored in this table, which contains links to the ACCESSIONS, PLANTS, NAMES, COUNTRIES, PLACES, COLLECTORS, PLANT SOURCES, and DATA SOURCES tables. Using the associated LABEL FORMATS table or Microsoft Word mail merge functionality, the user can design the contents and layout of specimen labels produced by the SPECIMENS table; these labels can be either viewed on screen or printed. Full wild-collection details (see ACCESSIONS above) as well as garden-collection details are tracked here, as are associated material, status as nomenclatural types, and citations of specimens. In addition to allowing the user to store and print herbarium label information, the SPECIMENS table can be searched by any number of criteria - country, subcountry political unit(s), locality, taxon, collector and collector number, collection date, etc.
  
• Collections: wild-collection details can be stored in this table, whose key field is a combination of collector code and collector number; this table can then serve as an electronic field collection notebook and can be used to flood-fill SPECIMENS records, ACCESSIONS records and GERMPLASM records, as appropriate. It can also be used to print field notebooks.
• Places: this table serves as an electronic gazetteer for user-defined collection locality and other geo-referenced places. Details from this table can be linked to the SPECIMENS, COLLECTIONS, and ACCESSIONS tables. Records in this table are linked to a geographic hierarchy through the BRUS, SUBCOUNTRIES, and COUNTRIES tables.
• Determinations: multiple determination records can be attached to a specimen (this information is actually stored in the VERIFICATIONS table to make it compatible with the Living Collections Module).
• Loans: this table tracks incoming and outgoing loans, exchanges, and gifts and prints packing slips, reminders, and loan statistics.
• Loan items: Individual specimens are tracked via barcodes and linked to LOANS records; each LOAN_ITEMS record contains information on the date of loan, date of return, and return condition. DETERMINATIONS can be attached to LOAN_ITEMS as they are returned.
• Herbaria: records are kept for herbaria with which an institution exchanges specimens.

Data can be exported to various computerized engraving and embossing machines, as well as laser printers barcode printers and dot-matrix printers to produce a wide variety of labels.

Conservation Module

This module handles taxonomic, nomenclatural and distribution details (see Living Collections Module above) as well as conservation assessment at both the global and country or subcountry level.

Distributions: attached to each taxon (NAMES table) can be one or more DISTRIBUTIONS records. Within each of these records, geographic qualifier, endemism, conservation status, numbers of populations or individuals left, date last seen, threats, legal status, presence in protected areas, and habitat information is stored; extensive use is made of the data sources table, and both conflicting conservation assessments and time series can be tracked by means of multivalued fields.

Laws: there are fields and tables to handle information on international conventions such as CITES and the Bern Convention, as well as specific or general conservation LAWS. These track the legal status of taxa within countries.

Conservation areas / protected areas: there are tables for storing information on protected areas and inventory data for these areas. Links can be made between the NAMES records and these protected areas records.

This module can be used to produce maps showing country-level distribution and conservation status of any taxon.

Propagations Module

This module manages information on all propagation and micropropagation activities.

Propagations: these records link to the NAMES, ACCESSIONS and PLANTS tables, and allow the user to track successful and unsuccessful propagation attempts using seeds, cuttings, or grafts. Information on scarification, stratification, hormones, environmental conditions, rooting or germination dates, potting dates, number of plants needed, number and date sent, and cause of death are stored here.

Protocols: the mp protocols table stores micropropagation "recipes" that have been tried and/or proven for a taxon, including information on pre-treatment, post-treatment, etc.

Transfers: the MEDIUM_TRANSFERS table follows each transfer from one medium to another for micropropagation activities.

This module makes extensive use of a series user-defined "code" tables that allow an institution to customize and standardize all propagation activities, such as scarification techniques, light regimes, hormone treatments, media mixes, etc.

ArcGIS\SQL Connector

This module provides a linkage between BG-BASE and ArcGIS mapping software from ESRI. SQL and either XML or tab-delimited files are used to facilitate the synchronization of geo-referenced data between the two systems. Synchronization intervals are controlled by a user-defined scheduler, which may be configured to run every few minutes or longer. Please note that this module should only be considered for use by sites with extensive in-house GIS experience and expertise. This module may also be used if you simply wish to mirror your BG-BASE data to a SQL database.

HTML (Web) Module

BG-BASE users can now export their data in such a way that their institutional collections form part of a 'virtual collection' shared with other BG-BASE sites around the world. Web users can then search for collections (of taxa, of living plants, of herbarium or museum specimens, of references, etc.) held in a particular BG-BASE site as well as any other BG-BASE site that has exported data in a similar fashion. This is all done through a single Web search form - the Web user does not need to go to separate Web pages; everything can be controlled from any BG-BASE site's search form. Information does not need to be merged into a central repository - this is truly a distributed database. This module was created by Dr. Martin Pullan at Royal Botanic Garden Edinburgh.

Visit the multisite search page to search in collections around the world. The data available from this page are extracted from the on-line Living Collections and conservation databases at BG-BASE sites.

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