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EcologicalSemantics / ecocore

An ontology of core ecological entities
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algae as a community rather than organism #97

Open diatomsRcool opened 5 years ago

diatomsRcool commented 5 years ago

Right now, algae is in ecocore as a subclass of organism. Should this be moved to be a subclass of collection of organisms? It's hard to say because "algae" can refer to many cells of one species or many cells of multiple species. In the lab, a culture or strain of algae is treated kind of like an organism - as the unit of experimentation. One cell is called an "algal cell". Algae is plural. Alga is singular. Some times a seaweed is called an alga, but its not clear that these are truly multicellular organisms. @ramonawalls do you have any thoughts?

cmungall commented 5 years ago

not sure we should have a class with this as primary label. We should enumerate all the correct classes and include alga(e) as related synonyms

On Wed, Feb 6, 2019 at 1:16 PM diatomsRcool notifications@github.com wrote:

Right now, algae is in ecocore as a subclass of organism. Should this be moved to be a subclass of collection of organisms? It's hard to say because "algae" can refer to many cells of one species or many cells of multiple species. In the lab, a culture or strain of algae is treated kind of like an organism - as the unit of experimentation. One cell is called an "algal cell". Algae is plural. Alga is singular. Some times a seaweed is called an alga, but its not clear that these are truly multicellular organisms. @ramonawalls https://github.com/ramonawalls do you have any thoughts?

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diatomsRcool commented 5 years ago

good point

ramonawalls commented 5 years ago

Ditto what Chris said. What is the use case for including this term? That should determine whether we need to define it as an organism, collection of organisms, or something else.

diatomsRcool commented 5 years ago

The use case is making assertions about algivores, planktivores, etc. Being able to say that an algivore eats algae.

jhammock commented 5 years ago

We have gotten datasets mentioning algae as a food class. I think I've seen it as a habitat class too- though I think that's usually subcategories of algae by growth habit or environmental context. Encrusting, filamentous, benthic...

cmungall commented 5 years ago

How about a union class. See http://purl.obolibrary.org/obo/go/imports/go-taxon-groupings.owl

We could make this more part of the ncbitaxon release as an extension module. Seems this may be a better place than ecocore?

diatomsRcool commented 5 years ago

ok, I assume that requires an issue submitted here https://github.com/geneontology/go-ontology?

cmungall commented 5 years ago

a PR would be ideal...

On Fri, Aug 2, 2019 at 1:39 PM diatomsRcool notifications@github.com wrote:

ok, I assume that requires an issue submitted here https://github.com/geneontology/go-ontology?

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diatomsRcool commented 5 years ago

I will do a PR, but I would like feedback on the taxonomic groups I include. How about:

Some of these are partially autotrophic, partially heterotrophic. There are some judgement calls in here. @jhammock

jhammock commented 3 years ago

For habitat and trophic purposes the precise trophic mode of the algal taxon hasn't been relevant in my experience, so that doesn't worry me. I think that list is pretty comprehensive. In our classification we've got one node possibly not covered: Glaucophytes.