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The Acacia Biodiversity Database Management System


Overview

Welcome to Acacia Biodiversity Database Management System, an interactive data entry, querying, and editing system based on the Acacia generic conceptual schema for taxonomic databases. It combines the automated use of scientific names and synonyms in a species checklist with user-friendly access to geographical data and common knowledge data (morphological descriptors, genomics, ecology, vernacular names, economic uses, structured notes and conservation status) about the species. All these data can be cross-indexed to a citation list. The design and standard permits rapid customization to suit any taxonomic group.

Operating Requeriments

Minimum operating requirements for running the Acacia DBMS are:

A Java™ 2 Runtime Environment is an optional requirement for running the interactive keys applet.

Menu Options

Search

The "Search" form allows to query the database by Phylum/Division, Class, Order, Family, Genus, Species, Species epithet, Continent, Region, Country, State/Province, Habitat, Vernacular name, Use, Conservation status, Morphological descriptor, or Genetic sequence.

The "Quick Browse" option allows to browse through species, genera, families, higher taxa, descriptive, genetic, and geospatial data for which taxa are recorded in the database. This is particularly useful for exploratory application by casual users with only a superficial knowledge of the database contents.

Tabular query results can be downloaded as spreadsheets in MS-Excel format or comma separated values text files (CSV).

Edit/Browse

This option allows to look at and search data for each data class used in the database (Descriptors, Distribution, Habitats, Higher Taxa, Notes, Taxa, Synonyms, Resources, Uses, Vernacular Names, Conservation Status, Genome, Bibliography, Metadata), as well as to add or edit data relating to a particular named species (if the database has not been installed in read-only mode), using the phpMyEdit MySQL table editor and PHP code generator.

Tabular data for each data class can be downloaded as spreadsheets in MS-Excel format or comma separated values text files (CSV). For some particular data classes, other, more specific, formats are also available. So, bibliographic citations can be exported to BibTeX format, morphological descriptive data can be exported to DELTA format, genetic sequences data can be exported to FASTA format, and geographic distribution data can be exported to KML format.

Keys

This option provides access to interactive identification keys from descriptive data coded in DELTA format, using the NaviKey Java applet.

To generate interactive keys, it is first required to export descriptive data to DELTA format by clicking the link on the bottom of the "Descriptors" table.

Maps

This option allows species distribution maps to be generated on the fly, based on georeferenced records stored in the database. Localities are plotted using the OpenLayers JavaScript library.

Another plot option is available from a link on the bottom of the "Distribution" table accessible from the Edit/Browse menu. Clicking this link creates a text file in KML format which can be saved to disk for later use, or opened for plotting with Google Earth.

Statistics

This option displays statistical information about the currently selected database, including the number of taxa and taxonomic names, descriptors and descriptors types, genetic sequences, conservation categories, bibliography, and data dictionaries entries.

Copyright

Acacia Biodiversity Database Management System Copyright © 2004-2014 Mauro J. Cavalcanti. The source code is available here under the GNU General Public Licence 3.

Contact

Comments, suggestions, and bug reports can be emailed directly to:

Mauro J. Cavalcanti
E-mail: maurobio (at) gmail (dot) com
Home page: http://sites.google.com/site/maurobio


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