Biodv is a collection of packages and tools for management and analysis of biodiversity data.
Biodv code and tools, requires the data to be organized in an specific directory and file hierarchy within the current working path (which is defined hera as a “project”). Each sub-directory stores the data in one or more files using the stanza format.
Here is an example of a project sub-directories:
my-project/
taxonomy/
taxonomy.stz
specimens/
taxon-a.stz
taxon-b.stz
synonym-a.stz
...
sources/
biblio.stz
datasets.stz
sources.stz
geography/
geography.stz
Not all sub-directories are required, as they will be created given the needs of each project.
Both tools, and biodv packages look for the database files automatically, so most of the time, a user, or a developer, does not need to know how each file is called, or where is stored.
In biodv data is stored using the stanza format. The stanza format is an structured UTF-8 text file with the following rules:
- Each line containing a field must starts with the field name and separated from its content by a colon ( : ) character. If the field name ends with a new line rather than a colon, the field is considered as empty.
- Field names are case insensitive (always read as lower caps), without spaces, and should be unique.
- A field ends with a new line. If the content of a field extends more than one line, the next line should start with at least one space or tab character.
- A record ends with a line that starts with percent sign ( % ) character. Any character after the percent sign will be ignored (usually %% is used to increase visibility of the end-of-record).
- Lines starting with the sharp symbol ( # ) character are taken as comments.
- Empty lines are ignored.
Here is a simple example of an stanza file containing taxonomic data:
# example dataset
name: Homo
rank: genus
correct: true
%%
name: Pan
rank: genus
correct: true
%%
name: Homo sapiens
parent: Homo
rank: species
correct: true
%%
name: Homo erectus
parent: Homo
rank: species
correct: true
%%
name: Pithecanthropus
parent: Homo
rank: genus
correct: false
%%
name: Sinanthropus pekinensis
parent: Homo erectus
rank: species
correct: false
%%
Stanza file format was inspired by the record-jar/stanza format described by E. Raymond "The Art of UNIX programming" (2003) Addison-Wesley, and C. Strozzi "NoSQL list format" (2007).
Biodv is distributed under a BSD2 license that can be found in the LICENSE file. For a list of authors, see the AUTHORS file.