Add IUCN "ecosystem functional groups" to ecosystem hierarchy

[pbuttigieg]

Derived from #1578

Using the source noted here by @timalamenciak

It might be helpful to take T2.2 Deciduous Temperate Forests (pg. 45 of PDF) as an example

And noting #1578 (comment)

Add or - if needed - modify existing ENVO ecosystem classea to include or align with the EFGs in Table 2, accounting for the "ecological traits" as needed.

Ideally, this can be done using a ROBOT spreadsheet template, but @timalamenciak will need clear documentation on how to construct and use these (@cmungall @matentzn )

They can also be added the standard way via protege, although this is less efficient.

[pbuttigieg]

@r0sek perhaps you'd like to assist with marine ecosystems based on #1556 (comment)

[pbuttigieg]

@timalamenciak posted

I think I've got a reasonable handle on the ROBOT template syntax. Just to be clear: we are minting each of the realms, biomes and ecosystem functional groups as instances.

• each realm will be type = biogeographic realm (ENVO:03620000)
• each biome will be type = biome (ENVO:00000428) & part_of = realm_INSTANCE where the realm_INSTANCE is replaced with the instance of the actual realm it is in.
• each ecosystem functional group will be type = ecoregion ENVO:01000276 & part of = biome_INSTANCE where the biome_INSTANCE is replaced with the one it is part_of.

@pbuttigieg response

I think I've got a reasonable handle on the ROBOT template syntax. Just to be clear: we are minting each of the realms, biomes and ecosystem functional groups as instances.

Not unless it's a named place. A tropical rainforest is an ecosystem class, the Amazon Rainforest is an instance.

• each realm will be `type = biogeographic realm (ENVO:03620000)

Not the IUCN "realms". Those we map to astronomical body parts like ENVO:atmosphere with annotation properties. Have to think which ones, but these classes could give examples

http://purl.obolibrary.org/obo/ENVO_01000843 (mapped to the US NLCD)

http://purl.obolibrary.org/obo/ENVO_01001385 (mapped to CMECS, but we can do better now that @r0sek has issued w3ids for CMECS terms)

• each biome will be type = biome (ENVO:00000428) & part_of = realm_INSTANCE where the realm_INSTANCE is replaced with the instance of the actual realm it is in.

Each biome should be a subclass of its corresponding ecosystem ("rainforest" <-subclassOf- "rainforest biome").

See how the biomes are constructed in envo-edit.owl (with differentia "...which is in its climactic successional state") and note their equivalence axioms. Those will be placed in the ENVO:biome branch by inference iff the equivalence axioms are right.

• each ecosystem functional group will be type = ecoregion ENVO:01000276 & part of = biome_INSTANCE where the biome_INSTANCE is replaced with the one it is part_of.

No, most of these will be vanilla ecosystems. Not many are ecoregions, and those are more likely to be instances (if named).

[pbuttigieg]

this is the robot template derived from the one we're using for CMECS, with an example

we would have to update some of the fields, like creator to match dc:creator

@kaiiam created some excellent guidance here, which I think will still work

[pbuttigieg]

Further, we would split EFGs like "Tropical-subtropical lowland rainforest" into

• tropical lowland rainforest
• subtropical lowland rainforest

(note that existing classes may be sufficient, in which case we can map those to the IUCN EFG with annotation properties)

and place each under their most natural superclass (tropical rainforest, subtropical rainforest, resp.)

in that case, we could create a new environmental condition "lowland", paralleling "alpine" etc

I'm assuming the definitions will come from the summaries of EFGs in Part II of the IUCN guide (also attached to this comment, just in case), likely focused on the ecological traits.

[ben-norton]

I did a quick term synthesis.
https://publish.obsidian.md/mbn-notes/Data/Terms/Physical+Geography+Terms

[pbuttigieg]

I did a quick term synthesis.
https://publish.obsidian.md/mbn-notes/Data/Terms/Physical+Geography+Terms

thanks @ben-norton - this shows how much some logical rigour is needed. Many of these definitions aren't very useful to tell one thing from another