Env fields (broad and local)

[only1chunts]

Current term details

Term name - broad-scale environment field
Term ID - MIXS:0000012 
Definition - 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. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html

Suggested update(s)

Definition - 

The definition needs to be updated to include the narrow synonym "biome" as well as a link to the ENVO documentation about how to use the field https://github.com/EnvironmentOntology/envo/wiki/ENVO-annotations-for-MIxS-v5

Current term details

Term name - local scale environment field
Term ID - MIXS:0000013
Definition - 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. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: 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]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html

Suggested update(s)

Definition - 

The definition needs to be updated to include the link to the ENVO documentation about how to use the field https://github.com/EnvironmentOntology/envo/wiki/ENVO-annotations-for-MIxS-v5, and to include mention of the possibility to use anotomical ontologies for environments relating to a host

[pbuttigieg]

The definition needs to be updated to include the narrow synonym "biome"

The key issue here is that "biome" is not a direct synonym of the broad scale environment. It is either a narrow or related synonym - if we can't express that, we should remove biome.

The synonyms suggested for env_local_scale also need update:

• "habitat" is incorrect and should be removed
• "feature" is fuzzy, so should be a "related synonym" or be removed

include mention of the possibility to use anotomical ontologies for environments relating to a host

Or other OBO ontologies that interoperate with ENVO. This prevents us from needing to unnecessarily inflate ENVO. We cover this in the wiki page noted below (this section)

as well as a link to the ENVO documentation about how to use the field https://github.com/EnvironmentOntology/envo/wiki/ENVO-annotations-for-MIxS-v5

We can create a new wiki page for MIxS v6. This would greatly shorten the definition field.

[pbuttigieg]

@only1chunts

We can create a new wiki page for MIxS v6. This would greatly shorten the definition field.

We've created a generic "Using ENVO with MIxS" wiki page here, which we'll update whenever MIxS does. Please use this in all the relevant ENVO fields.

[lschriml]

Could 'biome' be added back to EnvO ?

On Mon, Feb 8, 2021 at 11:47 AM Pier Luigi Buttigieg < @.***> wrote:

The definition needs to be updated to include the narrow synonym "biome"

The key issue here is that "biome" is not a direct synonym of the broad scale environment. It is either a narrow or related synonym - if we can't express that, we should remove biome.

include mention of the possibility to use anotomical ontologies for environments relating to a host

Or other OBO ontologies that interoperate with ENVO. This prevents us from needing to unnecessarily inflate ENVO. We cover this in the wiki page noted below (this section https://github.com/EnvironmentOntology/envo/wiki/ENVO-annotations-for-MIxS-v5#notes-on-the-use-of-other-ontologies-in-mixs-environment-fields )

as well as a link to the ENVO documentation about how to use the field https://github.com/EnvironmentOntology/envo/wiki/ENVO-annotations-for-MIxS-v5

We can create a new wiki page for MIxS v6.

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[only1chunts]

update the definition to include a link to https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS

[pbuttigieg]

@lschriml ENVO still has biome and its subterms, which the documentation in the link above explains. The biome branch is the recommended source of terms for env_broad_scale.

The MIxS field should not be reverted back to biome : the loose community usage of the term and lack of any MIxS validation make that a lost cause.

[lschriml]

@pbuttigieg - understood. Thank you Pier !!

en_broad_scale definition: Report the major environmental system the sample or specimen came from. The system(s) identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. in the desert or a rainforest). We recommend using subclasses of EnvO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS

expected value: The major environment type(s) where the sample was collected. Recommend subclasses of biome [ENVO:00000428]. Multiple terms can be separated by one or more pipes.

value syntax: {termLabel} {[termID]}

example: oceanic epipelagic zone biome [ENVO:01000033] for annotating a water sample from the photic zone in middle of the Atlantic Ocean

[lschriml]

env_local_scale and env_medium

also updated in MIxS core, new MIxS-Food, MIMAG, MISAG and MIUVIG