Proposed ENVO simple layer

[cmungall]

As part of the NEON/NMDC collaboration we have been mapping NEON terms to ENVO. The team needed a concept "deciduous forest", and the closest they could find was "area of deciduous forest", so this was used.

However, this leaves us in an odd position. If we look at the placement of "area of deciduous forest" in comparison to other more specific "deciduous forest" terms:

We see that they are in completely separate branches. We would like all terms we use to be in a single is-a/part-of hierarchy, such that we can do standard ontology operations such as provide faceted browsing, roll up terms for analyses, etc.

The two branches here also surfaces a number of other unusual decisions.

• "tropical broadleaf forest biome" is not classified under biome, despite the name (UPDATE fixed via logical defs)
• "biome" is an ecosystem, yet "terrestrial biome" is not a "terrestrial ecosystem" (UPDATE fixed via logical defs)
• none of the terms under "forest ecosystem" are a part of the biosphere, which seems like an accidental omission (UPDATE not yet fixed)
• none of the terms under "forest ecosystem" have is-a or part-of relationships to planet or astronomical body part (UPDATE partially fixed)
• we have duplicative concepts like "tropical broadleaf forest" and "tropical broadleaf forest biome" with little guidance on when to choose one over the other for annotation
• there is at least one case of a deciduous forest classified under coniferous forest
• the general design patterns and classification rules are not clear. Observe how the the tropical branch differs from the the temperate one.

In tropical, we have "tropical {...} broadleaf forest IS_A tropical broadleaf forest":

But this is inconsistent with "temperate {...} broadleaf forest PART_OF temperate broadleaf forest":

It would be useful if we could somehow tease apart the core concepts in ENVO independent of whether something is considered an area, an ecosystem, a biome, or an astronomical body part. For annotating sample sources and many other applications of users would appreciate something that looks more like anatomy ontologies, GO, etc, with less duplication of concepts, where the core concepts are in one hierarchy and follow standard classification patterns.

In this classification we would have a general concept like "forest", and then we would have a fairly consistent lattice of sub-types (no part-ofs) for the various ways a forest can be classified: tropical vs temperate, needle vs broad leaf, deciduous vs non-deciduous...

We would reserve parthood for things that are clearly composition - a forest is made of trees, a canopy is part of a forest, the forest is part of the terrestrial composition of the earth, etc

Then for groups that need to distinguish area vs ecosystem vs biome vs feature, these could be added as separate branches; however, the simple core could still be extracted and it would form a coherent consistent core.

[wdduncan]

I notice that ENVO has a forest ecosystem term. Should deciduous forest be a subclass of that?

On a more general note, I agree with you that we need design patterns that avoid defining things as immaterial entity.

[cmungall]

@wdduncan thanks for your comments!

notice that ENVO has a forest ecosystem term. Should deciduous forest be a subclass of that?

The essence of my proposal is that we would like to see a class hierarchy that organized something like this

• forest
  • deciduous forest
    • temperate deciduous needleaf forest
    • ...

We are neutral as to whether these are conceived of as ecosystems, biomes, whatever. This would also work for us

• forest ecosystem
  • deciduous forest ecosystem
    • temperate deciduous needleaf forest ecosystem
    • ...

Note that for brevity I am only showing one path here but this could potentially be a lattice.

The main point of my proposal is that the concepts annotators need should be in one hierarchy, rather than the concept of "decidous forest" being in one hierarchy, "temperate deciduous needleaf forest ecosystem" being in another, etc.

On a more general note, I agree with you that we need design patterns that avoid defining things as immaterial entity.

To be clear, I am not proposing that we avoid adding immaterial entities. I would prefer to see the use cases for these clearly articulated, but I trust these use cases exist.

We just need to capture the base concepts in a single hierarchy.

Right now, an annotator who is looking to annotate a "deciduous forest" concept is likely to pick "area of deciduous forest" (this has indeed happened for NEON annotation). This means that our annotations are a pick and mix of different branches, and roll-up queries don't work as expected - e.g. annotations to "deciduous forest" do not roll up to "forest ecosystem", and annotations to "temperate deciduous needleaf forest ecosystem" do not roll up to "deciduous forest".

[wdduncan]

@cmungall I agree with your reasoning about the advantages of a single hierarchy.

To be clear, I am not proposing that we avoid adding immaterial entities. I would prefer to see the use cases for these clearly articulated, but I trust these use cases exist.

I didn't think you were. This is my opining ;)

Perhaps my use of 'avoid' sounded to strong. Here is all I meant.

It seems to me that immaterial entities (and ICEs) generate a number of these shadow issues. Consider (for example) how we would represent the northern hemisphere or Eastern Europe. Such entities invite the use immaterial entity (especially amongst the more philosophically/BFO minded developers .... I think I may still be included in this group). This, in turn, increases the chance of creating shadow hierarchies.

It would be better (again my opinion) if the default stance was to classify things as material entities, and use immaterial entity only when a clear and motivating case can be made.

[kaiiam]

After a long querying and manual filtering exercise of terms from the environmental system, environmental zone, layer, and astronomical body part hierarchies, filterning it into a around 1164 terms in ~100 categories. I found the following. Shown below are the 28 most problematic concepts which are only or mostly found in some combination of biome, layer, environmental zone, ecosystem, (or others), but not in the astronomical body part hierarchy, which is the closest current hierarchy to the single branch with the bulk of terms. I think cleaning up all terms associated with these concepts would help with the vision of a single hierarchy for curators.

ENVO Parent	Category
ecosystem	bog
layer	canopy
geographic feature and ABP	cut
ecosystem	ecotone
Various	estuarine
ecosystem	farm
layer	floor
Various	forest
layer	front
Various	grassland
Various	marine
ecosystem	marsh
ecosystem	meadow
ecosystem	mire
various geographic feature, biome and layer	neritic
environmental zone	oasis
various ecosystem and ABP	palsa
Various: biome and layer	pelagic
ecosystem	plantation
environmental zone	plate
environmental zone	scrubland
biome	shrubland
Various	swamp
Various	tidal/tide
Various	tundra
Various: layer, environmental zone	vegetation
Various	wetland
Various	woodland

[cmungall]

OAK report here:

envo-ldef-rpt.tsv.txt

I have exerted a subset of it here:

• this is based on simple lexical patterns (the axiomatization is too inconsistent to drive this)
• id and label show the "atomic concept" (if id is null the atomic concept cannot be found)
• further columns represent "derived concepts"

id	label	environment	ecosystem	biome	area	num_concepts
ENVO:01001357	desert		ENVO:01001780	*ENVO:01000179/GEN	+ENVO:00000097/DF	4
None	freshwater	ENVO:01000306	ENVO:01001789	ENVO:00000873		3
None	aquatic	ENVO:01000317	ENVO:01001787	ENVO:00002030		3
ENVO:01000206	temperate	ENVO:01001705		ENVO:01001831		3
None	marine	ENVO:01000320	ENVO:01001788	ENVO:00000447		3
ENVO:01000205	subtropical	ENVO:01001702		ENVO:01001832		3
ENVO:01000204	tropical	ENVO:01001701		ENVO:01001830		3
ENVO:01000238	polar	ENVO:01001703		ENVO:01000339		3
ENVO:01000251	subpolar	ENVO:01001704		ENVO:01001834		3
None	alpine tundra		ENVO:01001371	ENVO:01001505	ENVO:03400001	3
None	grassland		ENVO:01001206	ENVO:01000177	ENVO:00000106	3
None	cropland		ENVO:01001244	ENVO:01000245	ENVO:01000892	3
None	woodland		ENVO:01001245	ENVO:01000175	ENVO:00000109	3
None	tundra		ENVO:01001370	ENVO:01000180	ENVO:00000112	3
ENVO:01000431	mixed forest			*ENVO:01000198/GEN	ENVO:01000855	3
ENVO:00002010	saline water	ENVO:01000307				2
ENVO:00002149	sea water	ENVO:01000321				2
ENVO:00002019	brackish water	ENVO:01000322				2
ENVO:00005791	sterile water	ENVO:01001042				2
ENVO:00002012	hypersaline water	ENVO:01001043				2
ENVO:00001998	soil	ENVO:01001044				2
ENVO:00002007	sediment	ENVO:01001048				2
ENVO:00010505	aerosol	ENVO:01001052				2
UBERON:0015474	axilla skin	ENVO:08000001				2
PATO:0001429	acidic	+ENVO:01000315/DF				2
PATO:0001430	alkaline	ENVO:01000316				2
UBERON:0002416	integumental system	ENVO:2100004				2
UBERON:0000022	feather	ENVO:2100006				2
ENVO:00005801	rhizosphere	ENVO:01000999				2
UBERON:0001555	digestive tract	ENVO:01001033				2
UBERON:0001474	bone element	ENVO:01001306				2
UBERON:0001062	anatomical entity	ENVO:2100000				2
UBERON:0000160	intestine	ENVO:2100002				2
ENVO:01000112	polymetallic nodule		ENVO:01001629			2
None	swamp		ENVO:00000233		ENVO:01001208	2
None	wetland		ENVO:01001209		ENVO:00000043	2
None	forest		ENVO:01001243	ENVO:01000174		2
None	polar tundra		ENVO:01001625		ENVO:03400002	2
None	terrestrial		ENVO:01001790	ENVO:00000446		2
ENVO:01000143	marine reef			ENVO:01000029		2
ENVO:01000122	marine hydrothermal vent			+ENVO:01000030/DF		2
ENVO:00000015	ocean			ENVO:01000048		2
ENVO:01000150	marine subtidal rocky reef			+ENVO:01000050/DF		2
ENVO:01000161	marine sponge reef			+ENVO:01000123/DF		2
ENVO:01001802	subtropical moist broadleaf forest			*ENVO:01000226/GEN		2
ENVO:00000021	freshwater lake			ENVO:01000252		2
ENVO:01000297	freshwater river			ENVO:01000253		2
None	gramanoid or herbaceous vegetation				ENVO:01000888	1
None	lichen-dominated vegetation				ENVO:01000889	1
None	moss-dominated vegetation				ENVO:01000890	1
None	pastureland or hayfields				ENVO:01000891	1
None	woody wetland				ENVO:01000893	1
None	emergent herbaceous wetland				ENVO:01000894	1