VERY MUCH UNDER CONSTRUCTION
A script to keep a local set of markdown files in sync with the WFO PlantList taxonomy.
The World Flora Online (WFO) is the international initiative to achieve Target 1 of the Global Strategy for Plant Conservation and provides a global overview of the diversity of plant species. It is the essential tool for conservation planners, policymakers and practitioners at all levels.
The WFO PlantList (WfoPlantList) is a collaborative project within the WFO to maintain a consensus nomenclature and classification of plants to act as a taxonomic backbone for the WFO and other projects.
The WfoPlantList API provides machine readable access to the WfoPlantList so that it can be used in other projects.
This Python script will query the API to create and maintain a set of Markdown text files in sync with the current taxonomy and nomenclature. This means that researchers can work on a local set of notes that are bound to the global consensus view of plant diversity.
The initial intent is for the markdown files to be edited using the Obsidian application, possibly with taxonomically focussed plugins, but any editor or IDE could be used. The local markdown files could be versioned and backed up to GitHub. They could also be published directly to the web or to print via some intermediate application.
This is a taxon based system not a substitute for a specimen based taxonomic editor. Most monographic work starts with specimens and observations and derives a taxonomy. This starts with a taxonomy and populates it with observations. It may be useful for monographic, floristic and other tasks but it is not the ideal tool for alpha taxonomy.
The script can be used in two different modes.
In Monographic Mode the script synchronizes with a complete branch of the classification below a root taxon. The root taxon's ID is specified in a configuration file. This is appropriate for working on a genus, family or other taxon.
In Floristic Mode the user provides a CSV file which contains a list of WFO name IDs. The script then synchronizes files for these taxa only, along with any of their parent taxa. This is appropriate for working on geographically or ecologically restricted projects where a subset of taxa are of interest, possibly spread right across the diversity of plants.
The script is run from the command line. You must be familiar with running simple scripts and manipulating some simple text and CSV files.
You must have Python3 installed on your machine. Type
python3 --version
at the command prompt to see if you have it.
It is possible to download the code from GitHub and install it on your machine but it is far easier to install it and keep it up to date by using the git application. You don't need to know much about git, just the commands here, but we would recommend you become familiar enough to version and backup your own work using git in the long run.