ENVO annotations for MIxS v5

General notes and guidance

The Minimum Information about any (x) Sequence (MIxS) is a checklist from the Genomic Standards Consortium. This checklist features three mandatory fields for environmental description using ENVO classes.

This guidance is relevant to version 5 of the MIxS checklist, available as an XLSX document, here

Field name	Full name	Description	Comments
env_broad_scale	broad-scale environmental context	In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?).	We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428
env_local_scale	local environmental context	In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen.	Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale
env_medium	environmental medium	In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling	Please use one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483.

The valid format includes the term label, followed by a space, and then the term's ID in CURIE format.

Format (single term)	Format (multiple terms)
termLabel [termID]	termLabel [termID]\|termLabel [termID]\|termLabel [termID]

Example: single term	Example: multiple terms
tropical moist broadleaf forest biome [ENVO:01000228]	canopy [ENVO:00000047]\|herb and fern layer [ENVO:01000337]

Annotating a sample from the Amazon rainforest consider:

tropical moist broadleaf forest biome [ENVO:01000228]

Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider:

oceanic epipelagic zone biome [ENVO:01000033]

Annotating a pooled sample taken from various vegetation layers in a forest consider:

canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]

Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider:

ocean water [ENVO:00002151]

Annotating a duck on a pond consider:

 pond water [ENVO:00002228]|air [ENVO_00002005]

If needed, request new terms on the ENVO tracker. Please include a definition of the new term, citing relevant sources.

Many MIxS users will be working with microbial communities. We offer the following recommendations for these users:

When filling in the env_broad_scale field, it's tempting to assume that macroscale environments do not matter to the microbial assemblage sampled. Nonetheless, we strongly encourage these larger scale systems (e.g. urban biomes or subtropical desert biomes) to be identified, in addition to any smaller scale features. These annotations will be instrumental for leveraging data in global analyses and for microbial biogeography. Keep in mind, users can always include any smaller-scale environments using the multi-term format noted above.
When filling in the env_local_scale field, attempt to add new, more fine-grained information relative to the env_broad_scale field. For example, a MIxS entry that includes env_broad_scale: village biome [ENVO:01000246] and env_local_scale: village [ENVO:01000773] is not as useful as one that includes env_broad_scale: village biome [ENVO:01000246] and env_local_scale: farm [ENVO:00000078]