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Using ENVO with MIxS
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. |
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env_broad_scaleshould really focus on the big, contextualising environment. Was the sample from a desert or the tundra? This term should describe an environmental system or an ecosystem, not a process, material, or single object (e.g. a tree) or a group of objects (e.g. a stand of trees). -
env_local_scaleshould include those environmental entities that surround your sample material and are likely to causally influence it. The terms used here should be countable things (e.g. a rock, a snow crystal, a cave, a hydrothermal vent.) -
env_materialshould always refer to the materials that compose your sample or which your entity of interest are surrounded by. These should always be mass/volume nouns (e.g. a mass/volume of "soil", "water", or "tissue") and not terms that refer to countable entities (e.g. a "cuticle", "microbial mat", "tree").
If you need to use a class from another ontology (e.g. a type of tissue material from an anatomy ontology), see "Notes on the use of other ontologies in MIxS environment fields", below.
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] |
Consider a sample of leaf litter taken from the understory of the Amazon rainforest. An appropriate annotation would be:
env_broad_scale : tropical moist broadleaf forest biome [ENVO:01000228]
env_local_scale : understory [ENVO:01000335]
env_medium : plant matter [ENVO:01001121]
If this was a sample of plant matter pooled from several layers of the forest's vegetation, a valid annotation may resemble:
env_broad_scale : tropical moist broadleaf forest biome [ENVO:01000228]
env_local_scale : canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]
env_medium : plant matter [ENVO:01001121]
Consider the following annotation for a water sample from a seasonal thermocline in the well-lit waters of the Atlantic Ocean:
env_broad_scale : oceanic epipelagic zone biome [ENVO:01000033]
env_local_scale : seasonal thermocline [ENVO:01000107]
env_medium : ocean water [ENVO:00002151]
If one is dealing with larger organisms, multiple env_medium terms may be needed. For example, consider a duck paddling in water:
env_medium : pond water [ENVO:00002228]|air [ENVO_00002005]
If needed, request new terms on the ENVO tracker. Please include a definition of the new term (see our guidance on definitions, here), citing relevant sources.
If you plan to add a lot of new terms, please consult this page.
At times, the sampling method used can enrich or deplete certain organisms or otherwise modify the environmental material (env_medium) in the sample. For example, a filtration net dragged through seawater to enrich organisms larger than the spaces in the net weave.
The env_medium field is meant to capture the original material sampled, rather than what subsequently happened to that material during or after sampling. Please add information or links to protocols on the effects of sampling on the original material sampled, to MIxS fields such as:
samp_collect_device
samp_mat_process
size_frac
samp_size
Many MIxS users will be working with microbial communities. We offer the following recommendations for these users:
- When filling in the
env_broad_scalefield, 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_scalefield, attempt to add new, more fine-grained information relative to theenv_broad_scalefield. For example, a MIxS entry that includesenv_broad_scale: village biome [ENVO:01000246]andenv_local_scale: village [ENVO:01000773]is not as useful as one that includesenv_broad_scale: village biome [ENVO:01000246]andenv_local_scale: farm [ENVO:00000078]
- When annotating microbial communities living in or on host organisms, we recommend the following:
- Ensure the taxonomic information of the host (e.g. the NCBI TaxID) is filled out in the MIxS host fields.
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env_broad_scaleentries should reflect the ecosystem the host is found in (e.g. an urban biome [ENVO:01000249] or a tundra biome [ENVO:01000180]) -
env_local_scaleentries should use terms from an ontology such as UBERON or PO to describe the anatomical parts of the host that are most causally influential to the microbial communities sampled (e.g. skin of eyelid [UBERON:0001457] or tepal apex [PO:0025143]) -
env_mediumshould either be a term from the ENVO environmental material hierarchy, or one from the anatomical ontologies relevant to the host organism.
ENVO won't have every term that you need, and we wouldn't import terms from other ontologies that we already interoperate with.
Thus, you can use terms from other OBO ontologies (such as PO and UBERON) in MIxS env_broad_scale, env_local_scale, or env_medium fields, as long as they fit the same logic described in Finding the right terms for each MIxS field.
However, note that some resources in the OBO catalogue are not appropriate for these MIxS fields. For example, OBO's port of the NCBI Taxonomy is not appropriate, as taxonomic information can and should be contained in other MIxS fields. We also do not recommend using ports of thesauri and glossaries such as the NCIT
If you're writing code that needs precise environmental semantics using terms from outside of ENVO, we recommend that you post-compose such semantics using patterns like:
- 'liver ecosystem' = ecosystem [ENVO:01001110] and determined by some liver [UBERON:0002107]
- 'mucus material' = 'environmental material' [ENVO:00010483] and composed primarily of some mucus [UBERON:0000912]