definition of environmental system/environment

[cmungall]

The definition of environmental system could be improved, to be more useful to domain scientists:

https://www.ebi.ac.uk/ols/ontologies/envo/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FENVO_01000254

Def: A system which has the disposition to environ one or more material entities. [ http://dx.doi.org/10.1186/2041-1480-4-43 ]

What does it mean to environ a material entity?

There is a comment that says:

_ In ENVO's alignment with the Basic Formal Ontology, this class is being considered as a subclass of a proposed BFO class "system". The relation "environed_by" is also under development. Roughly, a system which includes a material entity (at least partially) within its site and causally influences that entity may be considered to environ it. Following the completion of this alignment, this class' definition and the definitions of its subclasses will be revised._

In the > 7 years since this was written there is still no BFO system class, and there is no environed_by/environs relation in ENVO

(I added 'system' to RO as a placeholder, but so far ENVO is the only ontology to use this, and it confuses people to have classes in RO. We can consider adding to COB)

The referenced paper has more information:

We propose that an environment (synonymous with an environmental system [ENVO_01000254]) is a certain sort of system which has the disposition to environ, that is to contain within its BFO:site [BFO_0000029] and causally integrate, some BFO:material entity. Examples of environments range from rainforests to gut lumens to the interiors of virally infected cells. As described below, the subclasses of environmental system will reference environment-types familiar to most biologists.

I think it would be useful to include the examples.

Note also there is a subclass "ecosystem" An environmental system which includes both living and non-living components.

However, many of the direct subclasses of environmental system have both living and non-living components, so by this definition they should be moved under ecosystem?

I have a number of (non-disjoint) proposals:

Proposal 1: change definition

I propose the definition should exclude all abstract BFO terms ("material entity", "disposition"). It can still use technical terms an environmental scientist would understand.

Merriam Webster has a good definition:

the complex of physical, chemical, and biotic factors (such as climate, soil, and living things) that act upon an organism or an ecological community and ultimately determine its form and survival

To accommodate the planetary use case we can add a hedge that the complex is capable of acting on an organism/community

Adding this and making the definition more conformant with OBO, I propose:

A combination of physical objects, materials, and living entities (or their parts) that act upon an organism or an ecological community and ultimately determine its form and survival

Proposal 2: rename back to 'environment'

Rename 'environmental system' back to 'environment', make it a direct subclass of material entity

potentially: deprecate 'system' from RO

Proposal 3: differentiate ecosystem from environment

I would make ecosystem part of environment. For example:

_The part of an environment consisting of living and non-living components linked via nutrient cycles and energy flows _ [ISBN:978-0-534-42066-6]

However, this is more complex and may be better served as a separate ticket, as it is also tied with the ecosystem vs biome distinction (https://docs.google.com/document/d/15gp6RyMZrYskRSDonB7y8kkw9E3a8wHuqcdRDt_blhU/edit#)

[ddooley]

RO is deprecating "system" and there won't be a replacement term within OBO foundry for now.

This means in addition that we need a new parent for "environmental system" and deprecation likely affects definition.

Here are the related issues: OBOFoundry/COB#206 and oborel/obo-relations#607

[pbuttigieg]

We can modify the definition somewhat. System will be retained, with an ENVO class created. Ecosystems are types of environmental systems. Some direct subclasses of the latter should be moved to ecosystem.