Loading and saving data

There is no widely-adopted standard format for taxonomic data. Taxonome can handle the two formats below, but if your data is in another format, you’ll need to convert it, or write some code to tell taxonome how to load it.

See also

Reading specific data sources

CSV files

CSV is a simple, common format for many sorts of data, and can easily be created by any spreadsheet program. Taxonome can load taxa from CSV files which include scientific names, and optionally also the authorities for those names. Other columns will be read as information on the species.

Taxonome can also save data to CSV files for further analysis (e.g. plotting data).

Taxonome understands three main structures of CSV files:

• Taxa records: Each row refers to one taxon (by name).
• Synonym records: Each row refers to one name, and contains both that name, and the accepted name which it matches. Accepted names may appear with the same name for both parts, or can be taken from the relevant fields of their synonyms.
• Individual records: Each row refers to one individual specimen, sighting, population, or similar, of a particular taxon. A taxon name may appear on one or more rows.

In all cases, the authorities for the scientific names can be in a separate column, present within the names column, or absent.

See also

API reference for the taxonome.taxa.file_csv module.

Taxonome JSONlines files

Taxonome defines a more flexible file format. This can handle things like a list of measured heights for each species in a dataset.

See also

Module taxonome.taxa.file_jsonlines

API referenec for the file_jsonlines module.

JSON.org

Overview of JSON data format.