organismal abundance terms for CSM datasets

[kaiiam]

@ramonawalls we'll need to make some PCO style terms to cover Chris' NFCC_Benthic_Biomonitoring organismal abundance data. A preview of the taxonomic descriptions mapping to his abundance data is as follows

header	order	family	genus	species
ACENTR	Ephemeroptera	Baetidae	Acentrella	spp.
BAETIS	Ephemeroptera	Baetidae	Baetis	spp.
DIPHAG	Ephemeroptera	Baetidae	Diphetor	hageni

The data itself are counts of these organisms. Thus I'm thinking we could perhaps use a DOSDP or ROBOT Template that to make X (NCBITaxon) aggregates/counts/enumerations/collections etc.

One similar example I was able to find was from the Malaria Ontology: measure relating to enumeration of aggregate of arthropods, which is rooted under the OBI:information content entity hierarchy, which is under generically dependent continuant.

Would we instead want these terms to be rooted under something like PCO:collection of organisms? If so perhaps we could do something like the following as a DOSDP where X = the input NCBITaxon term?

Label: collection of X

Def: A collection of organisms that consist of two or more X obtained as a result of a specimen collection process.

equivalence axiom

'collection of organisms'
 and ('has member' some X)
 and ('has member' min 2 X)

Would we also want these terms to be something like output of some specimen collection process?

[ramonawalls]

I think rather than defining these as collections of organisms, we should make a trait (using count from PATO) that inheres in some collection of organisms. This is a generic enough trait that it could be housed in PCO or ECOCORE as a term for 'organism count' or organism abundance'. I will make an issue for a new term.

[kaiiam]

Ok sounds like a plan, would we still want to have a DOSDP with an equivalence axiom by which to create these types of terms?

[ramonawalls]

On further thought, you are right that we will still need to have taxon-specific collections of organisms in which the trait inheres. @kaiiam Please do go ahead and create the DOSDP that you described in your initial comment, and I will create the trait term in PCO.

Are there any cases where the count is 1? In that case, it can't really inhere in a collection of organisms, and we will need to adapt to that situation. I think in PCO I will say that an organism count can inhere in a collection of organisms or a single organism.

[ramonawalls]

See PopulationAndCommunityOntology/pco#86

[kaiiam]

Are there any cases where the count is 1?

Yes these types of count data can includes abundance values of 0 and 1, hence I think maybe collection of organisms (which specifies >1 organism) might not be quite right. I do like the idea of having organism abundance terms be qualities/traits that inhere in something from PCO. Since PCO:object aggregate only has collection of organisms as subclass, I'm not sure what else we'd have organism abundance terms inhere in.

I don't see a suggested parent term in pco 86. Is this intended to be in the quality hierarchy? Are you think of rooting it at something like PATO:amount?

If we say organism count(s) can inhere in a collection of organisms or a single organism would that be a problem for count data where some organisms are observed at 0 abundance? I know this is quite common in these types of data.

[kaiiam]

Picked up here: xref BiodiversityOntologies/bco#115