About BASIS
BASIS is an acronym for Biological And Systematic
Information System. It is a stand-alone relational database system
for PC's written in FoxPro for Windows 2.6.
BASIS was designed as a general database/cataloguing program to facilitate the
compilation, integration, and retrieval of systematic, biological, and
bibliographic information for arthropods at and below the family level on a
world or regional basis. A major feature of BASIS is that it automatically
compiles and formats conventional taxonomic catalogues as WordPerfect, RTF or
HTML documents based on the entered data and numerous user-selected options.
Additional queries enable retrieval of different types and levels of
information. Efficiency of data entry is maximized by data carry-over options
for many of the fields and by many pick lists for entry of highly repetitive
types of information. All but one of the pick lists can be customized by users
for their own particular requirements. Most record screens have a 'filed notes'
and a 'printed notes' memo field. The printed notes field is for information to
be outputted as part of a catalogue or a listing whereas the filed notes field
is for any other stored data. An append option enables users to append any ASCII
text (e.g., optically scanned descriptions, keys, abstracts) into either the
printed or filed notes field.
The latest version of BASIS consists of ten data tables as illustrated in
the figure of BASIS linking relationships.
There are four core tables and six
supplementary tables as follows:
Core Tables
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- Supplementary Tables
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Use of all or any of the supplementary data tables is completely optional, as
are most fields in any table so that a user has great flexibility in
determining the scope of the database/catalogue to be developed.
Four of the BASIS data tables can be considered 'core' to the system because
they comprise: 1) the nomenclatural backbone necessary to arrange names within
a taxonomic hierarchy under the rules of Zoological Nomenclature, and 2) the
bibliographic references that are necessary to validate all supplementary
information attached to taxon names, such as distribution, hosts, and biology
of species. The four core tables are:
References
References contains the individual citations of all publications that
validate any of the information contained in the other data tables. Each
publication is designated by a unique 'citation code' that is generated
automatically by the program. The citation code is formed from the names of
the first three authors, year of publication, and letter for multiple publications.
A choice of two screens allows entry of reference data in two formats - 'journal'
or 'book'. In addition to standard bibliographic data, fields are available to
enter the language of publication and the language(s) of any summaries. Pick lists
assist rapid, consistent entry of full journal titles and languages of publication.
The printed and filed notes field can be used for such purposes as appending
abstracts or content keywords, or giving translations of publication titles.
Citations
Citations is linked to References through the unique publication
citation code and to Genera and Species through the valid name of
the taxon. This table contains, in the form of individual citation code records,
a list of all the publications that cite a particular genus or species, whether
by its valid name or some junior synonym. The citation code is entered using a
pick list and fields are available so that a user can add 'keyword' descriptors,
page numbers of the publication relevant to the taxon, and whether or not the
citation record should be included under Citations and/or References in catalogue
output. The keyword descriptor option enables users to summarize the contents of
any publication that includes the taxon, and can be entered from a user-customizable
pick list.
Genera
Genera is linked to Citations through the citation code, and to
two of the supplementary data tables, Remarks and Keys, through
the valid name of the genus. This table contains the nomenclatural data necessary
to organize genera and subgenera within subtribes, tribes and subfamilies of a
particular family. Rapid data entry is assisted by a pick list of all previously
entered generic names and a data field carry-over option. A critical component
of this table is a two letter 'status code'. The status code defines the
status of any name cited in a publication relative to the currently accepted
valid name of the genus under the rules of the International Code of Zoological
Nomenclature. For example, 'SJ' is the status code for 'junior synonym' and 'RN'
is the status code for 'replacement name'. The status codes are entered using a
picklist in which each code is explained. A status code is necessary for each
record in order for the program to properly organize synonymy and generate
correct catalogue output. Genera also includes optional information on the
type species of the genus, including whether or not the name is a junior synonym
and, if so, the name of the senior synonym. The method of type designation
(e.g., subsequent designation) is entered using a picklist. Three sets of
author/year/letter fields are used to validate (i.e. reference) different
types of included data, such as the citation of a subsequent type designation.
The printed notes field is used to include miscellaneous information that the
user may want to be outputted as part of a catalogue. The filed notes field can
be used to append ASCII files (e.g., optically scanned descriptions).
Species
Species linking relationships are similar to Genera, but the table
is linked additionally to Common Names, Distribution, and First
and Second Level Associates through the valid name of the species. This
table contains the nomenclatural data necessary to organize species and subspecies
within genera. Field structure and options to assist rapid data entry are similar
to those described for Genera. An advantage of BASIS is that users do not
have to place author names in parentheses where required because the cataloguing
program handles this automatically based on the cited name, currently accepted
valid name, and status code entered for each record. Information that can be
stored in Species includes data on the type specimen(s) of each name, sexes
originally described, and whether or not illustrations were included. The optional
type-specimen information includes type category (e.g., holotype, syntype),
method of designation (e.g., original, subsequent), sex/stage (e.g., female,
nymph), museum depository acronym (e.g., USNM), type number (if applicable),
and type locality. All but the type number and type locality can be entered using
pick lists.
BASIS currently has six tables linked to one or both of Genera and Species
through the valid name of the taxon. These tables can be considered 'supplementary'
because whether or not they are used depends entirely on the developer of the
database. The purpose of these tables is to organize all known information associated
with a valid genus or species name. A linked table could be developed for any type
of information that can be associated with a valid species or genus name and the
six tables currently available are not necessarily exhaustive. The six supplementary
tables are:
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Remarks is linked to both Genera and Species through the valid
name of the taxon. This table consists of five memo fields that are used to organize
up to five different types of general information about a taxon, such as biology,
geographic range, economic importance, nomenclatural or taxonomic issues, etc. The
user provides a descriptive title for each field used, which is included as part
of a catalogue.
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Keys is linked to both Genera and Species through the valid
name of the taxon. Linked to genus Keys stores the references of all published
keys to the species of a genus; linked to species Keys stores the references
of all keys in which the species was included (either as a valid name or as a synonym).
The author, year and letter of the reference can be filled in automatically using a
pick list that is based on entered References records, and optional fields
are provided for the sex/stage (e.g., adult, female) keyed and the name used
in the key if different from the valid name. The printed notes field enables entry
of information on the geographical coverage (e.g., Nearctic region) or
biological scope (e.g., pests of apples) of the key. The filed notes field
can be used to append the key as ASCII text.
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Common names is linked to Species through the valid name of the
species. It contains the records of all common names that have been used for
species throughout the world. In addition to a field for the common name are
optional fields to record the language of the common name, where it is used,
and one or more published references to the name. A language picklist and
country picklist can be used to enter relevant data. Printed and filed notes
permit entry of general comments.
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Distribution is linked to Species through the valid name of the
species. It contains the records of all localities from which a species is
recorded. Distribution can be recorded at three levels: biogeographic realm,
country, and subpolitical unit (state, province, etc.). A single pick list can
be used to enter up to three levels of information at one time. The pick list
includes seven biogeographic realms (Afrotropical, Antarctic, Australasian,
Nearctic, Neotropical, Oriental and Palaearctic), about 160 'countries', and
about 425 states or provinces of larger countries. Islands or island groups
are often treated as 'countries'. Included with BASIS is an 86 page 'distribution
standard' that includes an alphabetical list of all the country and subpolitical
names entered in the pick list and maps that show the location of all realms,
countries, and subunits. Fields are available so that the user can indicate
whether any country or subpolitical unit record is doubtful and whether the
record is new or previously published. If the record is new, acronyms of one
or more museums that contain the validating specimens can be entered; if
previously published, one or more publication references can be entered to
validate the record. Pick lists are available to enter both types of validation data.
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First Level Associates is linked to Species through the valid
name of the species. This table permits storage of the scientific name of any
direct biological associate of the species, including hosts, foes
(e.g., parasites, predators), pollen sources, etc. A data carry-over
option and pick lists simplify entry of the order, family, genus, species,
subspecies and author fields of the associate. Additional fields allow
definition of the type of relationship between the associate and linked
species (e.g., host), the type of action of one on the other
(e.g., ectoparasite), and the site or sites affected (e.g., pupa),
with data entry through pick lists. As for Distribution, associate
records can be designated as doubtful and records validated either through
museum acronyms that indicate the location of specimens or citation codes
that reference a previous publication.
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Second Level Associates is linked to First Level Associates
through a concealed, program-generated code. This table permits storage of
the scientific name of any taxon that is associated with the linked species
indirectly through the first level associate. Examples of indirect associations
include hyperparasites or the name of the plants consumed by different hosts
of a parasite. Field structure is the same as for First Level Associates.
Locating and unraveling the nomenclatural and associated biological,
distributional, and bibliographic information that comprises what we know
about taxa can involve a huge investment of time and effort. BASIS provides
a mechanism to assist the efficient, consistent, and accurate entry,
organization and storage of taxonomic and associated information. At the push
of a button, BASIS also eliminates the arduous task of compiling the information
into an organized, easily readable summary - a taxonomic catalogue. BASIS
automatically compiles and formats conventional taxonomic catalogues/checklists
as WordPerfect, RTF or HTML documents depending on user preference. Catalogues
can be generated for an entire family or for one or any number of species,
subgenera, genera or subfamilies within a family on a world basis or for one
or any number of countries or subpolitical units. Users can also select which
of the supplementary data tables and Remarks memo fields, and in what
order, should be outputted as part of a catalogue. Users can also specify many
of the fields in the core and supplementary data tables to be outputted. Finally,
users can also customize formatting by selecting bold or italic fonts for reference
output, and bold or italics and/or upper case or lower case for headings. Because
of the ease and speed of catalogue generation users of BASIS should plan to
increase their printer paper budget!
For more information about BASIS contact
Gary Gibson.
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