deprecated ENVO:mushroom

[zhengj2007]

@pbuttigieg We used ENVO:mushroom in our annotation. In latest release, the term is deprecated and indicated replaced by: FOODON_00001287
(http://www.ontobee.org/ontology/ENVO?iri=http://purl.obolibrary.org/obo/ENVO_02000072)

However, I searched latest release version of FOODON. I cannot find either 'mushroom' or term ID:FOODON_00001287.

Any suggestion on dealing with the issue?

Thanks,

Jie

[pbuttigieg]

@Public-Health-Bioinformatics: any chance this will be released in FOODON soon?

@zhengj2007 we may have to check that "mushroom" in FOODON is equivalent to what you need. What kind of mushrooms are you dealing with (e.g. wild mushrooms growing in a forest, mushroom products, ...)?

[Public-Health-Bioinformatics]

Ah, so I just cleaned up the deprecated terms last night. I'm happy to move it all over - its just that I'm still not quite sure what the "core" should be - a single .owl file or can it still be based on includes? Happy to move it over and then work on massaging the core together if you'd like?

[pbuttigieg]

@Public-Health-Bioinformatics I think @zhengj2007 just needs a PURL at this stage (correct me if I'm wrong), however, @zhengj2007 could you specify what you mean by mushroom?

[Public-Health-Bioinformatics]

Mushroom purl: http://purl.obolibrary.org/obo/FOODON_00001287
There are many types of mushroom listed underneath that class. None link to NCBI Taxon yet though INDEX FUNGORUM ids are available.

[zhengj2007]

@pbuttigieg We used 'mushroom' to annotate the source of specimen (e.g. parasite isolate) that collected from. So, it is not clear what kind of mushrooms, could be either growing in a forest or farm or lab.

[zhengj2007]

@Public-Health-Bioinformatics I cannot find FOODON: mushroom on the http://www.ontobee.org. So, I cannot import the term from FOODON using ontoFox. Is the ontology on ontobee.org site out-of-date? The available version on the onto is: http://purl.obolibrary.org/releases/2016-03-17/foodon.owl

[Public-Health-Bioinformatics]

Ah I see. I'll ask OntoBee and OntoFox to get FoodOn updated - I just uploaded all the new FoodOn work including this term to https://github.com/FoodOntology/foodon last night, so not surprised OntoBee/OntoFox doesn't see it.

[zhengj2007]

Thanks!

The issue is solved when FOODON: mushroom is available.

[Public-Health-Bioinformatics]

Note, we do have a http://purl.obolibrary.org/obo/FOODON_3306538 wild mushroom (raw) in the subset_siren_import.owl file as a type of food product. I'm just getting feedback about that new import file though.

[cmungall]

what is the relationship to http://purl.obolibrary.org/obo/FAO_0000012 basidiocarp

…

On 7 Mar 2017, at 9:39, jie zheng wrote: Thanks! The issue is solved when FOODON: mushroom is available. -- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: #464 (comment)

[Public-Health-Bioinformatics]

(p.s. if NCBI taxonomy can't do a good job of matching to fungi, then FoodOn could use another ontology's taxonomy terms there.)

[Public-Health-Bioinformatics]

Update: Ontobee now has Foodon loaded. Mushroom is: http://purl.obolibrary.org/obo/FOODON_00001287

[pbuttigieg]

Great! Thanks @Public-Health-Bioinformatics!

I set up the FOODON import for ENVO and added `mushroom environment' in 4ae859d

@zhengj2007 I'll make a release today or tomorrow so you can use mushroom environment to describe the source of your sample (unless you're talking about the actual mushroom tissue, in which case the FOODON term is more appropriate).

The yet-to-be-released ENVO PURL for mushroom environment is: http://purl.obolibrary.org/obo/ENVO_01000929

[zhengj2007]

@pbuttigieg @Public-Health-Bioinformatics Thanks a lot!

[pbuttigieg]

@Public-Health-Bioinformatics, @cmungall asked above:

what is the relationship to http://purl.obolibrary.org/obo/FAO_0000012
basidiocarp

I suppose FOODON will have to tackle this somehow as it's in the FAO space, would this partner with UBERON or are there strange, non-anatomical definitions due to transnational labelling etc?

[Public-Health-Bioinformatics]

@pbuttigieg @zhengj2007 Isn't there a bit of a combination bomb in pairing environment + plant reference with respect to future vocabulary additions? Or is this unavoidable?

[pbuttigieg]

@cmungall and I were discussing this for animal environments (e.g. human guts). It is indeed a combination bomb, so we may create sub-ontologies dedicated to each major taxon for easy imports.

[cmungall]

Uberon covers metazoa, so the FAO strategy would be analogous.

[pbuttigieg]

Closed in this release

[zhengj2007]

@pbuttigieg I think we still need an ENVO:mushroom. The FOODON: mushroom is a subClass of food source. However, I don't think all mushroom can be food since some mushroom are poisonous and can be taken as food. FOODON: mushroom is a mushroom has_role food role. Is it possible to reverse ENVO:mushroom deprecation?

[Public-Health-Bioinformatics]

Ah. This brings up a point we were grappling with in the last few weeks which FoodOn needs improvement on. Not everything is food for everything else, but rather an organism is almost invariably food for some other organism (I'd like to hear the case where this isn't true!).

So to address your concern I was thinking of this move:

1. Top level food source has an equivalency of something like "(nutrient or (part of some organism) and has consumer some organism"

Then underlying food sources can list off the particular organism taxon, part, and the consumer taxon(s) or related groups of consumers (e.g. cow's milk has consumer human infant). Hopefully more general edibles can reference more general groups of consumers rather than having giant lists of consumers for each food.

This would also address allergens insofar as we're not saying ALL humans can eat some food source (e.g. seafood); just that some of them can. More conditionals about allergens could be tacked onto the consumer groups I suppose, like milk as a food product: "is a [milk: UBERON_0001913] and part of some cow and has consumer lactose-tolerant homo sapiens".

[zhengj2007]

@Public-Health-Bioinformatics What you proposed sounds good to me. Thanks!