Greenhouse gas

[GoogleCodeExporter]

CHEBI models "greenhouse gas" as a role:

http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:76413

Individual molecules such as water have "has_role" relationships to the "role" 
of greenhouse gas

This seems odd - I would model gas as either a phase (quality?) or a material 
entity at the level of some aggregate of molecules.

In either case, it seems that ENVO should have something to say about 
greenhouse gases, greenhouse effects, etc, and this should be coordinated with 
CHEBI

Original issue reported on code.google.com by cmung...@gmail.com on 14 Jan 2014 at 1:16

[GoogleCodeExporter]

Agreed. 

We have "water vapour" ENVO:01000266 as an environmental material with def: 
"Water vapour is a vapour which is the gas phase of water." 
"water" ENVO:00002006 has a def that pins it to liquid water. 
Rendering states of matter as qualities (e.g. gaseous, liquid, solid, 
plasmatic) may be a good approach since classes such as "gas" won't really sit 
well in the material hierarchy.

Thus water vapour has_quality gaseous and has the disposition (rather than the 
role) to act as a greenhouse gas. 
Could this work?

Original comment by p.buttig...@gmail.com on 14 Jan 2014 at 5:04

• Added labels: ****
• Removed labels: ****

[GoogleCodeExporter]

Also, I don't think the environmental material hierarchy is redundant with 
CHEBI's classes. When CHEBI says water, it means H2O, but I think ENVO means an 
environmental material that is primarily composed of CHEBI:water as there are 
few environments with volumes of pure water in them. Thoughts?

Original comment by p.buttig...@gmail.com on 14 Jan 2014 at 5:14

• Added labels: ****
• Removed labels: ****

[GoogleCodeExporter]

I agree with your analysis.

does this suggest:

 * envo:new ! environmental aggregate of H2O in any phase
  * ENVO:01000266 ! (environmental) (portion of) water vapor
  * ENVO:00002006 ! (environmental) (portion of) water

with the two child nodes defined using the parent as genus and PATO as 
differentiae.

Is there a sensible name for the parent?

We could omit it and just link the siblings by a phase_of relation

mass nouns:

Barry likes "portion of X" for mass nouns. I am less keen as having this as the 
primary label, but we could at least have this as an exact synonym.

implicit "environment" context:

Of course, not all portions of water/vapour are environmental materials (e.g. 
water on uninhabited planets). Strictly speaking we should prefix some of our 
labels with "environmental". OR we should work with CHEBI to come up with an 
ontology of chemical aggregates that can be applied to any planet. Maybe this 
is going too far, the def of environmental material is dispositional "Material 
in or on which organisms *may* live".

greenhouse gas:

I think modeling greenhouse gas as a disposition is logically valid. But we 
don't have any disposition classes at the moment. Sometimes I prefer to cut to 
the chase and model the process first (i.e. the greenhouse *effect*). We can 
then say has_disposition only 'greenhouse effect'. Or we can shortcut the 
disposition and say 'water vapour' has-disposition-that-is-realized-as 
'greenhouse effect', and 'greenhouse gas' equivalent to vapour and 
has-disposition-that-is-realized-as some'greenhouse effect'.

We don't have any process classes at the moment, but I think they will be 
required at some stage.

Original comment by cmung...@gmail.com on 14 Jan 2014 at 8:57

• Added labels: ****
• Removed labels: ****

[GoogleCodeExporter]

"I think modeling greenhouse gas as a disposition is logically valid."

Along the lines of 

x is portion of greenhouse gas = def. x is portion of gas & x has disposition 
greenhouse effect

Or some such? (If something like this is right, then I don't think it can be 
said clearly without the 'portion of' prefix.)
BS

Original comment by ifo...@gmail.com on 16 Jan 2014 at 8:25

• Added labels: ****
• Removed labels: ****

[GoogleCodeExporter]

Yes, I think that's right. So it seems we need somewhere a process hierarchy 
for atmospheric processes and the like. This is certainly outside my expertise, 
and I wonder if there are already efforts out there we can connect to.

Original comment by cmung...@gmail.com on 16 Jan 2014 at 9:15

• Added labels: ****
• Removed labels: ****

[pbuttigieg]

@cmungall we should come back to this as this will be important for SDGIO and we now have the process branch in the ontology.

CHEBI's chemical roles have been imported, but is it valid to use "has role" with these? They're not really BFO:roles. Could we then say:
atmospheric water vapour 'has role' some greenhouse gas?

It seems a shame not to link to CHEBI on this, but I'm not sure how to use the CHEBI:role robustly.