[Obo-envo] food and organism parts

[Chris M. <cj...@fr...>]

I think this deserves elevating to list discussion. There is ongoing  
concern and confusion on what to do with food and bits of organisms.

Ideally food, animal parts and derivatives can be described  
compositionally, possibly recursively, using simpler classes; for  
example:

termite gut = gastrointestinal_tract that part_of termite
ear gunk = bodily_substance that derived_from ear
bird feces = feces that excreted_from bird
wool = fiber that derived_from (fur that part_of Ovis)
armpit sweat = sweat that located_in armpit

cheese = substance that derived_from milk
blue cheese = cheese that has_part penicilin
spoiled blue cheese = blue_cheese that has_quality spoiled
bone meal = bones that has_quality crushed and has_role animal_food  
and has_role fertilizer

These compositions can easily be made at ontology development time  
(this is true in general of oboedit, protege etc), or they can be  
made at annotation time (phenote makes this simple). That part is easy.

However, the hard part is where we find the simpler terms to use in  
order to compose the more complex terms.

Let's take anatomical entities first. If all host environments were  
human then this problem would be solved, we would simply use classes  
from the FMA. If host environments were also located in fruitflies,  
zebrafish, mice, frogs we'd still be in the clear. But this is not  
the case.

Take termite gut. It may be tempting to take the closest terms from a  
species specific AO, eg the fly anatomy. But this would be wrong.

Note that CARO will not help us here, as CARO has stalled at the high  
upper level and goes no more specific than organ.

I see no alternative here other than to simply bite the bullet and  
start the bottom-up creation of a species-neutral anatomical  
ontology. It doesn't have to be huge - only as large as is needed for  
annotation. It doesn't have to be as rigorous as the FMA (as that  
would bring the whole enterprise to a halt). It does have to have  
clear definitions (otherwise we may as well use free text). At some  
point in the future development could and should be handed off to the  
appropriate people - but these people don't have funding yet!

We can then use the simple classes in this ontology (and others) to  
make more complex classes such as ear gunk or bird feces.

It isn't so important whether the descriptions are pre- or post-  
composed. For those who don't have the informatics capacity to deal  
with post-composition we can have an application ontology off to the  
side of ENVO.

We face a similar problem with food. Ideally we would use some  
external food ontology. This would presumably have to meet some  
minimal requirements, such as for example a basis in biology/ 
chemistry rather than culture or culinary arts. I don't know exactly  
what those requirements are, it depends on the questions we want to  
ask and useful ways of clustering data for the purposes of discovery.

For example, before arguing about what to do with terms like "peanut  
butter and jam sandwich" we should think about what questions the  
ontology should be able to answer:

- what are the parts? (bread, peanut butter, jam)
-- recursively? (sugar content, oil viscosity, ubiquinone content)
- what is it derived from? (legume, fruit, cereal)
-- means of derivation (preservation, grinding, leavening)
- does it spoil easily?
-- what does it decompose into?
- is it industrially prepared?

presumably some of these are important, otherwise we can dispense  
with this issue and have a single term "food" and ignore all other  
distinctions.

Once we have prioritized these and come up with realistic scenarios  
we should have a better idea how to proceed.

I think then our course of action will fall somewhere between two  
extremes:

1) collect somewhere off to the side of ENVO an unorganized list of  
food terms on an as-needed basis, with a view to eventually handing  
this off or merging with the food ontology. Or if the food ontology  
never transpires, gradually adding N+S conditions to the classes and  
classifying mostly automatically.

2) post-composition of all food descriptions. This could be from an  
ultra-minimalist list from the multi-species anatomy ontology:

  organism substance
   blood
   milk
  portion of tissue
  oil


Then we can compose descriptions easily using existing ontologies:  
RO, PATO, GO, ... + a taxonomy.

We can really go to town and specify the N+S conditions for a PBJ  
sandwich based on mereological constraints (PBJ must be surrounded_by  
a bilayer of white bread) and derivation relations (PBJ derived_from  
peanut, oil, substance derived_from fruit+pectin). But this probably  
wouldn't be the best use of our time.

The middle ground is to have a minimal food ontology containing the  
basics, such as bread, preserved food etc, and allowing people to  
post-compose descriptions to the extent which they feel worthwhile.

There is also the issue of what is a food and what isn't. I don't  
think 'food' is such a good top level. There's organic matter and  
it's derivatives. Some substances have roles as foods for some  
organisms (or cultures), other substances are toxic to other  
organisms. We can do this with a has_role relation.