NTR: [High-level taxon] community

[pbuttigieg]

Similar to, but probably simpler than, #22 :

It would be good to have some high-level, taxonomically resolved communities to help distinguish flora, fauna, bacteria, archaea, etc.

For example:

'plant community' =def. "An ecological community which is composed of organisms in the Kingdom Plantae."

The axioms could be brought in from NCBITaxon, which uses Viridiplantae We'd use this to axiomatise ENVO terms like vegetated area and vegetated hill https://github.com/EnvironmentOntology/envo/issues/491

[pbuttigieg]

One issue is what rendition of Kingdom (or similar high rank) to use. Perhaps the 7 Kingdom model from Ruggiero et al. 2015 displayed here?

This is not the same as the NCBI Taxonomy. If we go with NCBI for consistency, we should note that this is not an authoritative taxonomy.

[ramonawalls]

@pbuttigieg My plan is to use NCBI and make classes for Archea, Bacteria, Eukaryota, Viridiplantae, and Fungi. Are there any others you need? I consulted with my resident animal ecologist/biodiversity instructor, and he felt that other high level groupings (like Metazoa) are rarely studied as communities. If classes for other clades are needed, we can add those when requested, as long as a good definition of the clade (NCBI or not) is provided.

Going to go ahead and set up a design pattern for these, just to make @kaiiam proud.

[kaiiam]

I believe we had a similar discussion when trying to figure out some of the host types for the GOLD data there were some organismal groupings like fish that are paraphyletic, and can't be pinned down to one NCBItaxon group. I have a list of these examples if you want me to dig it up although I don't know if GOLD will still need them.

@ramonawalls of the examples you gave however, all of these are already represented within NCBITaxon: Archaea , Bacteria, Eukaryota, Viridiplantae, and Fungi.

I presume these types of groupings would better scoped here then in ECOCORE? Under the organism hierarchy in ECOCORE there are a variety of trophic type e.g. autotroph, they also have algae, which I think would be better suited here perhaps?

[kaiiam]

Here are my notes of organismal groupings (from the GOLD paths), which aren't monophyletic clades:

• green algae

There is no obvious class for green algaea unlike brown it's not just one phylogenetic clade. According to the wiki page:

The green algae (singular: green alga) are a large, informal grouping of algae consisting of the Chlorophyta and Charophyta/Streptophyta, which are now placed in separate divisions, as well as the potentially more basal Mesostigmatophyceae, Chlorokybophyceae and Spirotaenia.

• fish

acording to the wiki page:

Fish are a paraphyletic group: that is, any clade containing all fish also contains the tetrapods, which are not fish. For this reason, groups such as the "Class Pisces" seen in older reference works are no longer used in formal classifications.

Hence there is no one NCBItaxon class there are several: including Actinopterygii, Hyperotreti, Hyperoartia etc. There is a FOODON fish, which gives a good definition of how humans commonly refer to fish.

• invertebrate

There is no single clade for invertebrates, NCBITaxon metagenomes hierarchy has invertebrate metagenome.

• coral

No single clade to describe group.

• Protists and Protozoa

Neither are proper phylogenetic clades. We have Protozoa in Vaccine Ontology.

• reptiles

Reptilia are not a monophyletic clade there are three main groups Crocodylia (crocodyles), Lepidosauria (lizards), and Testudines which we think of as reptilia. The highest common ancestor Sauria also includes birds.

• Spiralia

Spiralia are an unranked group including annelids and molluscs.

[ramonawalls]

I believe we had a similar discussion when trying to figure out some of the host types for the GOLD data there were some organismal groupings like fish that are paraphyletic, and can't be pinned down to one NCBItaxon group. I have a list of these examples if you want me to dig it up although I don't know if GOLD will still need them.

Let us wait to see if there is a need for them.

@ramonawalls of the examples you gave however, all of these are already represented within NCBITaxon: Archaea , Bacteria, Eukaryota, Viridiplantae, and Fungi.

That is why I chose those ones. :)

I presume these types of groupings would better scoped here then in ECOCORE? Under the organism hierarchy in ECOCORE there are a variety of trophic type e.g. autotroph, they also have algae, which I think would be better suited here perhaps?

I think taxonomic groupings fit better here, functional groupings in ECOCORE. Algae is going to move here.

[kaiiam]

Sounds good, I'm interested to see what kind of pattern this will be. Would we want a Robot Template that has multiple slots for different NCBITaxon terms to make something like the union of them? e.g. fish = Actinopterygii, Hyperotreti, Hyperoartia ....

Or are you thinking of something more along the lines of X community? Could this do both?

[ramonawalls]

I think it actually needs to be X collection of organisms because there are times when the "community" will only have a single species in it. Then at the data level, it can be decided if it is an ecological community or a population.

[ramonawalls]

Postponing this for the next release, since there is not an urgent demand.

[kaiiam]

Just speculating here that perhaps in the future these X collections of organism terms or something similar could be used to help solidify the NBCITaxon hierarchy, used for the organism descriptions in NCBI. Just a though xref to the envo issue about it here.