GOOS EOV semantics

[pbuttigieg]

Linked to #904

[kaiiam]

@pbuttigieg I noticed that some of the imports your adding here for the concentration of pattern are CHEBI atom terms e.g.

http://purl.obolibrary.org/obo/CHEBI_28073 # chromium atom
http://purl.obolibrary.org/obo/CHEBI_28112 # nickel atom
http://purl.obolibrary.org/obo/CHEBI_28659 # phosphorus atom

Following our discussion of using atom vs molecular entity terms, I emailed the CHEBI team and they suggested we use the molecular entity terms. Hence I think we should be consistent and not use these atom terms here.

[cmungall]

@kaiiam - can you provide more details? (IMHO it's good to do this via tickets on the respective ontology tracker)

It would be good to get a definitive answer with scientific justification for the choice. We need to clearly document this across multiple OBO ontologies that need to represent things at the level of elements (@diatomsRcool @matentzn @bpeters42)

As it happens, I think the molecular entity choice is a good one, because it groups ions, and sometimes these forms are more physiologically relevant.

However, it would be good if the choice we made scientifically rather than just 'this seems to give us the inferences we need'

This part of chebi has always confused me, we have a has-part between the molentity and the atom. This implies to me that the molentity is molecule with multiple atoms but this is now what we want here...

see:

[kaiiam]

@cmungall I don't want to overwhelm this PR with this issue could you move the discussion to #977. I've ported this over, please continue this discussion there.

[pbuttigieg]

Following our discussion of using atom vs molecular entity terms, I emailed the CHEBI team and they suggested we use the molecular entity terms. Hence I think we should be consistent and not use these atom terms here.

@kaiiam I'm not sold on this yet

Edit 2020-07-14: Getting closer to some sort of resolution over at #977
Edit 2020-08-03: Resolved on using molecular entities where possible, atoms (or axioms built around atoms) for isotopes.

[pbuttigieg]

Odd error in the Travis Build:

dosdp-tools --table-format=csv --template=./patterns/chemical_concentration.yaml --outfile=modules/chemical_concentration.tmp.owl --obo-prefixes=true generate --infile=modules/chemical_concentration.csv

Unrecognized argument: --table-format=csv

Unrecognized argument: --template=./patterns/chemical_concentration.yaml

Unrecognized argument: --outfile=modules/chemical_concentration.tmp.owl

Unrecognized argument: --obo-prefixes=true

Makefile:543: recipe for target 'modules/chemical_concentration.owl' failed

make: *** [modules/chemical_concentration.owl] Error 1

Could be a misfire as the PR check passed

[matentzn]

@pbuttigieg ping me if this persists.. Maybe its spurious but Reviewing your logs, something slightly different is run in both cases (same command, different output)

[pbuttigieg]

Status and comments:

Biogeochemistry

These are often shorthands for commonly held / jargony associations

• Oxygen
• Nutrients
• Inorganic carbon
• Transient tracers
• Nitrous oxide
• Stable carbon isotopes
• Dissolved organic carbon
• Particulate matter

Physics

Some of these labels will be changed for semantic clarity (e.g. "sea ice" is actually about the variability of sea ice)

• Sea state
• Ocean surface stress
• Sea ice
• Sea surface height
• Sea surface temperature
• Subsurface temperature
• Surface currents
• Subsurface currents
• Sea surface salinity
• Subsurface salinity
• Ocean surface heat flux

Biology and Ecosystems

These are conceputally confounded - we'll abstract the true variables from the targets of observation for clarity

• Phytoplankton biomass and diversity
• Zooplankton biomass and diversity
• Fish abundance and distribution
• Marine turtles, birds, mammals abundance and distribution
• Hard coral cover and composition
• Seagrass cover and composition
• Macroalgal canopy cover and composition
• Mangrove cover and composition
• Microbe biomass and diversity (*emerging)
• Invertebrate abundance and distribution (*emerging)

Other

• Ocean colour
• Ocean Sound

[kaiiam]

Sea surface salinity
Subsurface salinity

@pbuttigieg I created salinity in PATO PATO:0085001 see this commit, the term hasn't been released yet but when it does I was thinking we could use it to create terms like liquid water salinity and or sea water salinity using the Entity Attribute DOSDP. Xref #883. Were you planning on doing something like that the the sea surface and subsurface salinity terms?

[matentzn]

I think it's released in PATO

[kaiiam]

I think it's released in PATO

Great thanks @matentzn I see it was in the v2021-04-14 release hence not yet showing up on OLS, should be able to import it soon.

[pbuttigieg]

Merging this as is so it doesn't become a Gordian Knot - will open a new PR for the remainder and further edits

Looks like the merge will work, will revert if not