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EnvironmentOntology / envo

A community-driven ontology for the representation of environments
http://www.environmentontology.org
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Tropical forest biome #805

Open tnn111 opened 5 years ago

tnn111 commented 5 years ago

Need a "tropical forest biome" for "tropical forest soil microbial communities". Or any suggested alternatives?

pbuttigieg commented 5 years ago

In the WWF scheme we've aligned to, this class would work for tropical rainforests :

http://purl.obolibrary.org/obo/ENVO_01000228

If it's a mixed or coniferous tropical forest, there are a few relates classes nearby that may work, depending on where your sample originates from.

diatomsRcool commented 5 years ago

I kind of feel like the communities themselves should go in PCO....

pbuttigieg commented 5 years ago

I kind of feel like the communities themselves should go in PCO....

Yes, there is a microbial community class there which @kaiiam will be coordinating with ENVO's "microbiomes". There's a lot of misuse and fuzziness of these terms. Some notes here: https://github.com/PopulationAndCommunityOntology/pco/issues/70

In this case, however, I think we're dealing with the environment of these communities, as specified in MIxS.

pbuttigieg commented 5 years ago

I kind of feel like the communities themselves should go in PCO....

Yes, there is a microbial community class there which @kaiiam will be coordinating with ENVO's "microbiomes". There's a lot of misuse and fuzziness of these terms. Some notes here: https://github.com/PopulationAndCommunityOntology/pco/issues/70

In this case, however, I think we're dealing with the environment of these communities, as specified in MIxS.

diatomsRcool commented 5 years ago

Ah! Ok.

ddooley commented 5 years ago

On the topic of biome description in MixS, is someone compiling notes on how to satisfy MixS environmental biosample reporting using ENVO and other ontologies? If so I'd appreciate that. A few years ago I grabbed a number of ENVO related terms to cover some MixS categories but it wasn't a thorough scan. Notes on how to describe different "slots" using ontology would be great.

pbuttigieg commented 5 years ago

@ddooley we put this together on our website quite some time back: http://environmentontology.org/annotation-guidelines

MIxS 5 is a little different in that you have more freedom in what to add to each slot, as long as you're 'zooming in' to the sample itself.

cmungall commented 5 years ago

@ddooley welcome any and all tickets pertaining to how to use ENVO for sample annotation. I made a project to organize the tickets: https://github.com/orgs/EnvironmentOntology/projects/1