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soilfoodwebontology / sfwo

The Soil Food Web Ontology is a formal conceptual model of soil trophic ecology.
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Taxon different from organism #90

Closed Archilegt closed 1 year ago

Archilegt commented 1 year ago

From the ongoing discussions contributed by Nicolas, Anton, David, and I: We agree in that we need a "Taxon different from organism" thing introduced in the next SFWO version. Taxa denoted with names are not organisms but groups of organisms. An organism is often understood as an individual instance (specimen) that can be assigned to a taxon if it is identified. This meaning also differs from the use of the Organism class in DarwinCore, which includes aggregates (e.g., a wolf pack) (see http://rs.tdwg.org/dwc/terms/Organism). Currently, there is no standard way to represent the fact that an individual organism is an individual of a taxon(omic class). A solution is to represent a "taxon is a subclass of collection of organisms", and an "individual organism is member of a taxon". PCO has "taxon as collection of organisms" (http://purl.obolibrary.org/obo/PCO_0000059) and that probably is as good as it can get.

This is needed to make the class Nematoda.all being an "equivalent class" of the class NCBITaxon:Nematoda, which is currently not possible because of the Taxon=organism thing. This in turn is needed because Nematoda.all means "all Nematoda" and "all Nematoda" is the meaning of "Nematoda" itself. Keeping Nematoda.all as a convenience container for trophic groups requires: Nematoda.all "has exact synonym" Nematoda.

A derived issue is the fact that "Nematoda.zooparasites 'has member' Nematoda" is considered misleading. It sounds like there are also other taxa in Nematoda.zooparasites and that Nematoda is just one member of this trophic group. A taxo-trophic group entity like Nematoda.zooparasites 'is a' member of the taxonomic group Nematoda and simultaneously 'is a' member of the zooparasite trophic group. Conversely, Nematoda and zooparasite 'has member' Nematoda.zooparasites. This is happening because currently, from the ontology point of view, Nematoda -> (single) organism, Nematoda.all -> collection of organism. Nematoda (and other taxa) has (have) to be changed to a collection of organisms to start fixing the logic.

Maybe we should encourage other ontologies to tackle this Taxon problem. See discussions in the PCO (https://github.com/BiodiversityOntologies/bco/issues/112) and BCO (https://github.com/BiodiversityOntologies/bco/issues/112) issue trackers.

I guess that I am expected to provide the main input on the Taxon definition and how we are going to model it. I cannot work on this within the next three weeks. I am only posting the issue to capitalise on the discussions that took place in the comments on the SFWO manuscript, as suggested by Nicolas.

nleguillarme commented 1 year ago

As mentioned by @Archilegt, PCO has a class "taxon as collection of organisms" (http://purl.obolibrary.org/obo/PCO_0000059) which is a subclass of "collection of organisms"

Similarly, BCO has a class "Taxon" (http://rs.tdwg.org/dwc/terms/Taxon) which is also a subclass of "collection of organisms".

I guess we could import taxonomic classes from the NCBITaxon ontology as subclasses of "taxon as collection of organisms" and use the "member of" property to link an organism to its taxon.

Then we would have to rewrite the logical definitions of diet classes as follows: bacterivore = eats some ('member of' some Bacteria)

Archilegt commented 1 year ago

Hi, @nleguillarme. It seems that this is a good solution. Let's try it out and hope that nothing breaks. One positive thing is that BCO has DarwinCore class "Taxon" (http://rs.tdwg.org/dwc/terms/Taxon) as a reference, as you mentioned. Why? Because the definition and the example are well-redacted, and the example clearly refers to an unambiguous taxonomic treatment, e.g., the taxon as understood by some author(s) in a given publication. This is how we want things to be, also for future developments of the EUdaphobase Taxonomy Ontology.

Definition | A group of organisms (sensu http://purl.obolibrary.org/obo/OBI_0100026) considered by taxonomists to form a homogeneous unit. -- | -- Examples | The genus Truncorotaloides as published by Brönnimann et al. in 1953 in the Journal of Paleontology Vol. 27(6) p. 817-820.
nleguillarme commented 1 year ago

Concerning the implementation, I plan to import both BCO:Taxon and PCO:'taxon as collection of organisms' in the SFWO and state that both classes are equivalent.