Link GeOMe habitat terms to ENVO environmental terms

[jdeck88]

GeOMe has a list of existing habitat types that are marine that we want to map to ENVO environment terms. The current list is: Coral Reef, Estuary, Intertidal, Fouling, Macroalgae, Mangrove, Mud, Continental shelf, Pelagic, Planktonic, River, Rock, Sand, Seagrass

In addition, we want to introduce a broad level of classification of terrestrial habitat (environmental) terms that we can use. At the broadest, this would be: Anthropegenic, desert, forest, grassland, mangrove, shrubland, woodland.

Finally, great if we can create a GeOMe subset in ENVO to help us manage these terms.

[pbuttigieg]

Hi @jdeck88!

As you mention, we can cook up and maintain a subset for your community, similar to how we added NLCD classes for NEON (see #458).

The current list is: Coral Reef, Estuary, Intertidal, Fouling, Macroalgae, Mangrove, Mud, Continental shelf, Pelagic, Planktonic, River, Rock, Sand, Seagrass

We should have many of those in ENVO already, the task would be to check that the definitions work for the GeOMe community. We can create new, related terms if they need different semantics.

In general, it's always better to propose some definitions for the requested terms, to make sure we're on the same page. For example, I'm not clear on what "Fouling" is referring to and what kind of plankton "Planktonic" references.

In addition, we want to introduce a broad level of classification of terrestrial habitat (environmental) terms that we can use. At the broadest, this would be: Anthropegenic, desert, forest, grassland, mangrove, shrubland, woodland.

I think the top levels of the wwfBiome subset or the ncld2011 subset would do the trick. More can be added later if the GeOMe teams need them.

[pbuttigieg]

A first order mapping below. In all cases, the classes are referring to the material entities themselves, rather than the environments around them and determined by their presence. The latter kind of semantics can also be generated if you prefer.

GeOMe term	EnvO class	Comments
Coral Reef	http://purl.obolibrary.org/obo/ENVO_00000150
Estuary	http://purl.obolibrary.org/obo/ENVO_00000045
Intertidal	http://purl.obolibrary.org/obo/ENVO_00000316
Fouling	NULL	Unclear term, requires more input
Macroalgae	NULL	Is this referring to the environment around a collection of macroalgae?
Mangrove	http://purl.obolibrary.org/obo/ENVO_00000057	We also have mangrove biome, if that's more appropriate
Mud	http://purl.obolibrary.org/obo/ENVO_01000001
Continental shelf	http://purl.obolibrary.org/obo/ENVO_00000223
Pelagic	http://purl.obolibrary.org/obo/ENVO_00000208	This assumes you're referring to the marine pelagic zone
Planktonic	http://purl.obolibrary.org/obo/ENVO_01000063	The ENVO class here references planktonic material, which may or may not be ideal.
River	http://purl.obolibrary.org/obo/ENVO_00000022
Rock	http://purl.obolibrary.org/obo/ENVO_00001995
Sand	http://purl.obolibrary.org/obo/ENVO_01000017
Seagrass	NULL	A seagrass bed, I'm assuming?

[jdeck88]

biomes.xlsx
After discussion with the GeOMe group, folks felt that it would be good to adopt the current list of ENVO biome terms wholesale for the habitat field and re-map existing values as needed. The attached biomes list shows the label and the ENVO link.

[jdeck88]

A user provided this definition of fouling in our context: A fouling community is a group of organisms found on artificial hard structure in a marine habitat - docks, boats, jetties, etc. https://en.wikipedia.org/wiki/Fouling_community

[jdeck88]

I went through the entire list of terms that have actually been used as part of GeOMe and it turns out some of what was on our list have not yet been used. Terms that have been used for habitat include only "coral reef, estuary, intertidal, pelagic, planktonic, river, seagrass". Some of these are zones and in one case a material (planktonic). My suggestion is to include these, along with the ENVO biomes list to form the GeOMe habitat list. I've attached the proposed spreadsheet here.

habitats.xlsx

[pbuttigieg]

xref #440

[jdeck88]

@pbuttigieg this is almost complete from the geome perspective... see the habitat spreadsheet i uploaded in the last comment which we are now using to define our list of available habitat descriptions for GeOMe. I would like to still make a subset in ENVO, however, so leaving this issue open. Complete this in Ottawa?

[pbuttigieg]

I think I can get most of this done beforehand. Thanks for the material!

…

On 5 Aug 2017 17:04, "John Deck" ***@***.***> wrote: @pbuttigieg <https://github.com/pbuttigieg> this is almost complete from the geome perspective... see the habitat spreadsheet i uploaded in the last comment which we are now using to define our list of available habitat descriptions for GeOMe. I would like to still make a subset in ENVO, however, so leaving this issue open. Complete this in Ottawa? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#548 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ACK7MvkAtopH4u6o2dFZu1dYFB_8a8Ycks5sVIR_gaJpZM4Op2B_> .