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EnvironmentOntology / envo

A community-driven ontology for the representation of environments
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Termite gut #802

Open tnn111 opened 5 years ago

tnn111 commented 5 years ago

"Termite gut P1 segment microbial communities" anyone?

Not sure how to do that one.

pbuttigieg commented 5 years ago

Perhaps a class like "microbiome of the termite gut's P1 segment"?

Note the this would reference the environment the communities are in (the communities are a necessary part of a biome), but not only the communities themselves.

kaiiam commented 5 years ago

Cross link to #672.

@tnn111 I can answer your question as I'm currently working on creating envo terms for the JGI/EBI biomes.

My understanding of the terms:

root > Host-associated > Arthropoda > Digestive system > Gut > P3 segment
root > Host-associated > Arthropoda > Digestive system > Hindgut > P1 segment
root > Host-associated > Arthropoda > Digestive system > Hindgut > P3 segment

is that they must be sourced from the description given in this paper Cellulolytic Systems in Insects (Arthropoda include termites).

Where they describe the five segments of the termite hindgut (from front to back): ileum (P1), enteric valve (P2), paunch (P3), colon (P4, this region is sub-divided into P4a and P4b in some cases), andrectum (P5).

Similarly for according to this paper Internal ornamentation of the first proctodeal segment of the digestive tube of Syntermitinae (Isoptera, Termitidae) in a logical extension of whats described in the other paper those 5 segments are refereed to as proctodeal segments which gives us the root > Host-associated > Arthropoda > Digestive system > Gut > Proctodeal segment

Also I think the Gut > P3 segment and Hindgut > P3 segment refer to the same thing.

pbuttigieg commented 5 years ago

Thanks @kaiiam - so you'll be able to create the ENVO class for this region? I think we should go for an informative name like "termite ileum microbiome" with a synonym like "microbiome of the P1 segment of the termite gut"

Does UBERON have a relevant class for this anatomical entity?

tnn111 commented 5 years ago

Thanks. It’d be nice to have classes for this.

Do all Arthropoda have the P1 and P3 segments?

I’m going through a lot of these annotations to get a better idea of what is there and that is one I can’t find a good answer for in ENVO as it is now.

On Jun 14, 2019, at 9:31 AM, Kai Blumberg notifications@github.com wrote:

Cross link to #672 https://github.com/EnvironmentOntology/envo/issues/672.

@tnn111 https://github.com/tnn111 I can answer your question as I'm currently working on creating envo terms for the JGI/EBI biomes.

My understanding of the terms:

root > Host-associated > Arthropoda > Digestive system > Gut > P3 segment root > Host-associated > Arthropoda > Digestive system > Hindgut > P1 segment root > Host-associated > Arthropoda > Digestive system > Hindgut > P3 segment is that they must be sourced from the description given in this paper Cellulolytic Systems in Insects https://www.annualreviews.org/doi/10.1146/annurev-ento-112408-085319 (Arthropoda include termites).

Where they describe the five segments of the termite hindgut (from front to back): ileum (P1), enteric valve (P2), paunch (P3), colon (P4, this region is sub-divided into P4a and P4b in some cases), andrectum (P5).

Similarly for according to this paper Internal ornamentation of the first proctodeal segment of the digestive tube of Syntermitinae (Isoptera, Termitidae) http://zoobank.org/9861480D-4CBF-4B33-B08A-80F10E3C9D6F in a logical extension of whats described in the other paper those 5 segments are refereed to as proctodeal segments which gives us the root > Host-associated > Arthropoda > Digestive system > Gut > Proctodeal segment

Also I think the Gut > P3 segment and Hindgut > P3 segment refer to the same thing.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/EnvironmentOntology/envo/issues/802?email_source=notifications&email_token=ABMXPRXK2T5YUEBIKTSRJN3P2PBUZA5CNFSM4HYEYZP2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODXXJOQA#issuecomment-502175552, or mute the thread https://github.com/notifications/unsubscribe-auth/ABMXPRQN23JLXQZE7ICE573P2PBUZANCNFSM4HYEYZPQ.

diatomsRcool commented 5 years ago

seems like the actual microbial community should be in PCO?

pbuttigieg commented 5 years ago

@tnn111

I’m going through a lot of these annotations to get a better idea of what is there and that is one I can’t find a good answer for in ENVO as it is now.

Keep the requests coming! We'll often have to import semantics from other interoperating ontologies to make sure things fit. ENVO grows based on user needs.

@diatomsRcool

seems like the actual microbial community should be in PCO?

See https://github.com/EnvironmentOntology/envo/issues/805#issuecomment-502735084

kaiiam commented 5 years ago

@tnn111

Do all Arthropoda have the P1 and P3 segments?

I'm not sure, but by having a class such as @pbuttigieg is suggesting termite ileum microbiome be subclass to arthropoda digestive system associated microbiome we cover these cases without stating all Arthropoda have the P1 and P3 segments.

If necessary classes such as arthropoda ileum microbiome could be created later.

Uberon has ileum, however I cannot find classes for paunch or Proctodeal segment. paunch is a related_synonym in rumen but that refers to the rumen of a ruminant animal. So I don't think this class is appropriate for termites. I'll add these to my list of UBERON requests.

pbuttigieg commented 5 years ago

Thanks @kaiiam, could you cross-link the issues on the UBERON tracker to this issue?

cmungall commented 5 years ago

If you add a ticket in uberon I will take care of it.

Didn't realize we were making "X microbiome" classes?

kaiiam commented 5 years ago

If you add a ticket in uberon I will take care of it.

@cmungall Thanks! I have several uberon issue to post, I will post all of them and as @pbuttigieg suggest cross link accordingly.

Didn't realize we were making "X microbiome" classes?

@cmungall I though this was the general plan which we'd discussed this in our previous email exchanges recall the example I gave the example of a microbiome term:

marine abyssal plain microbiome

Definition:

An oceanic microbiome which is determined by an abyssal plain.

hasNarrowSynonym (EBI label): Abyssal plane Axioms

hasDbXref: https://www.ebi.ac.uk/metagenomics/api/v1/biomes/root:Environmental:Aquatic:Marine:Oceanic:Abyssal%20plane

Axioms: determined by some [abyssal plain](http://purl.obolibrary.org/obo/ENVO_00000244) part of some [marine abyssal zone biome](http://purl.obolibrary.org/obo/ENVO_01000027)