QuickAdd NCBI Taxonomy

This script was written to help my self get a grip with the Obsidian API as well as improve my personal "Cool stuff i come across in my job" wiki.

My day job as a Bioinformatician, working in ToLA and alongside GRIT at Sanger on the DTOL project, involves exposure to a number of organisms which are just fascinating to read up on or in many cases to not read up on. For these organisms, I make a note to find extra information that would be useful to know during the assembly/curation phases, this might include karyotype information, existence of B chromosomes, duplication rates and more. This script goes towards generating notes with essential taxonomic information, used in conjunction with Obsidian, can eventually generate a web of linked notes connecting various species, clades and/or phyla.

This script was heavily based on another QuickAdd script found HERE written by Christian B. B. Houmann

Future Plans

If there is enough interest I will create a full plugin to make use of the entirety of the NCBI API.

Installation

This follows the same steps as other QuickAdd scripts.

Step 1: Move the files

Move the quick-add-ncbi.js script to your obsidian vault script folder and the template to y0ur templates folder.

The template is already set out for all the data you can get back from ncbi.

Step 2: Create the Macro

Go to Obsidian Settings > QuickAdd
Click Manage Macros
Give your macro a name, e.g. "Taxon API"
Click Configure on the macro
Under User Scripts, select the "ncbi" script and click Add
Click Template
- Click on the cog next to Untitled Template Choice
- Choose the ncbi template you copied across or use your own.
- Enable File Name Format and use {{VALUE:scientificName}} as the file name. The scientificName value takes the latin name of the organism
- Decide on any other settings, such as the folder to create movie notes in
Close all the popup modals and go back to the Settings > QuickAdd screen
In the dropdown next to the Add Choice button choose Macro
- Give your command a name like "Taxon" then click Add Choice
- Click the cog next to your Taxon macro and choose the "Taxon API" macro you just created
- Toggle the lightning bolt icon which will make this macro available from your main command palette

Step 3: Create a note

Launch the command palette with CMD + P (or your preferred hotkey)
Type "Taxon" (i.e. the name of your macro command)
Enter a scientific name
You should automatically see a new note open with your template pre-filled

Example

In my case running this on the little known Tihpia femorata we get:

# Tiphia femorata

## Taxonomic Data
### TaxID:: 330862
### RankOfQuery:: species
### Lineage:: [[Eukaryota]], [[Metazoa]], [[Ecdysozoa]], [[Arthropoda]],
                [[Hexapoda]], [[Insecta]], [[Pterygota]], [[Neoptera]],
                [[Endopterygota]], [[Hymenoptera]], [[Apocrita]], [[Aculeata]],
                [[Tiphioidea]], [[Tiphiidae]], [[Tiphiinae]], [[Tiphia]], [[]]

## Genetic Code
### GeneticCode:: 1
### MitoGeneticCode:: 5