Organisms

Source

We're using NCBI taxonomies to annotate biological organisms (including virus).

How is the information accessed?

We're accessing the information from within the MBDB using their REST API (opens in a new tab). In particular, we're using the "taxon_suggest" endpoint for searching for taxonomy ids, and then extracting the information associated with each taxonomy id using the "taxon" endpoint.

I can't find the organism I used, what should I do.

Depending on which taxa (level) information are unavailable for you should do one of the two following things

The specific strain I used is not available

We want to have the information as precise as possible, and therefor would like to have the information to the strain level, especially if this is known to be critical to the obtained results (in which case have a look at the instructions below). Otherwise, it can be specified to the species level of precision.

The species, genus, etc.

Deposition genetic information to one of the sources that the NCBI taxonomy draws it's information from is required. The NCBI taxonomy draws it's information from several sources under The International Nucleotide Sequence Database Collaboration (INSDC). Links to the deposition system that is most appropriate for you can be found here (opens in a new tab).

Fields available

id

The id prefix is taxid:.

Description: NCBI taxid of the organism (e.g. 9606) to the lowest possible taxonomic rank (e.g. species)
Required: yes
Type: string (keyword)

title

Description: Name of organism associated with the taxid (e.g. Mycobacterium phage PurpleHaze_DEM1
Required: yes
Type: object (Title)
Contains: see Vocabulary title

rank

Description: The taxonomic level the taxid is associated with (e.g. SPECIES)
Required: yes
Type: string (keyword)