algae as a community rather than organism

[diatomsRcool]

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]

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

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On Wed, Feb 6, 2019 at 1:16 PM diatomsRcool ***@***.***> 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? — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#97>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AADGOZj4lPj-djpdw_yW46x717jPXblBks5vK0Y1gaJpZM4amH8Q> .

[diatomsRcool]

good point

[ramonawalls]

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]

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

[jhammock]

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]

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]

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

[cmungall]

a PR would be ideal...

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On Fri, Aug 2, 2019 at 1:39 PM diatomsRcool ***@***.***> wrote: ok, I assume that requires an issue submitted here https://github.com/geneontology/go-ontology? — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#97?email_source=notifications&email_token=AAAMMOKPDDZQ3XDO4QPOCULQCSLQTA5CNFSM4GUYP4IKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD3OZFJQ#issuecomment-517837478>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAAMMONCSH5BPZXCXN4XGG3QCSLQTANCNFSM4GUYP4IA> .

[diatomsRcool]

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

• cyanobacteria
• dinophyceae
• cryptophytes
• euglenozoa
• haptophytes
• rhodophytes
• stramenopiles
• chlorophytes

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

[jhammock]

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.