Taxonomy Keyword Generator

Tools to produce keyword collections based on taxonomy data.

Initial use case: Generate hierarchical keywords from taxonomy data in order to classify observation photos with a controlled vocabulary for ITPC + XMP metadata. This is currently a simple proof of concept intended for biological taxonomy, but could possibly be applied to other forms of hierarchical classification.

This repo contains working scripts to generate taxonomic trees (in multiple formats) from the following sources:

• iNaturalist observations
• NCBI taxonomy

Installation

pip install git+https://github.com/JWCook/taxon-keyword-gen.git

Usage

iNaturalist

Use case: You want hierarchical keywords for just the taxa you have personally observed on iNaturalist (or based on some other queryable criteria).

First, run an iNaturalist observation query. Select 'Taxon Extras' to include relevant taxonomic ranks, save the output (say, to observations.csv), then run:

taxgen inat export -i observations.csv

NCBI

Use case: You want hierarchical keywords for all of the things

Run:

taxgen ncbi export

This will either download the NCBI taxonomic dump files from the FTP site, or reuse them if they've already been downloaded.

By default, only eukaryotic cellular organisms will be exported, but if you really want to organize all your photos of viruses or bacteria, you can do that too, I guess.

Output

Keywords follow the format taxonomy:<rank>=<taxon>. For example, a complete set of keywords for the common fruit fly would look like:

taxonomy:kingdom=Animalia
  taxonomy:phylum=Arthropoda
    taxonomy:subphylum=Hexapoda
      taxonomy:class=Insecta
        taxonomy:order=Diptera
          taxonomy:suborder=Brachycera
            taxonomy:superfamily=Ephydroidea
              taxonomy:family=Drosophilidae
                taxonomy:subfamily=Drosophilinae
                  taxonomy:genus=Drosophila
                    taxonomy:subgenus=Sophophora
                      taxonomy:species=melanogaster
                        "taxonomy:binomial=Drosophila melanogaster"
                          "taxonomy:common=Common Fruit Fly"

See Also

For working with metadata for individual taxa or observations, see the related tool naturtag.

TODO

If this actually turns out to be useful, there is a lot of room for building on top of this basic PoC, for example:

• Conveniences to make it easier to import generated keywords into popular photo/metadata editing applications that support hierarchical keywords (XnView MP, FastPictureiewer, Lightroom, Daminion, etc.)
  • Add support for FPV keyword synonyms (common name <--> scientific name)
• Improve performance of keyword tree generation
• Unit tests, make the code a bit more presentable, etc.