New predicate request for micro-organisms <=> media

biolink / biolink-model

Schema and generated objects for biolink data model and upper ontology

https://biolink.github.io/biolink-model/

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New predicate request for micro-organisms <=> media #1401

Open hrshdhgd opened 10 months ago

hrshdhgd commented 10 months ago

A clear and concise description of what the request is. I am trying to generate knowledge graphs between micro-organisms and the media they thrive on.

I want to add predicates to the model that represents associations between:
- micro-organisms and medium (grows_in) and vice versa.
- medium and its ingredients (maybe this one already exists: has_part?) but don't know about vice-versa.

What working group (or team) did this request originate from?

The need for representing this type of data originated from the KGHub working group.

Additional information to support this request (optional)

For now I have a PLACEHOLDER going:

subject	edge_label	object	provided_by
NCBITaxon:1955243	biolink:growsIn-PLACEHOLDER	dsmz:1669	bacdive:158156
NCBITaxon:1873457	biolink:growsIn-PLACEHOLDER	dsmz:92	bacdive:139807
NCBITaxon:1848903	biolink:growsIn-PLACEHOLDER	dsmz:1609	bacdive:132461

@cmungall @sierra-moxon @realmarcin

sierra-moxon commented 10 months ago

@hrshdhgd @realmarcin - I went spelunking in RO to see if it had something like "grows in" already. I found two interesting issues that are sort of related to this:

https://github.com/oborel/obo-relations/issues/477 (suggests a new relation for "has exposure medium")
https://github.com/oborel/obo-relations/issues/137 (@diatomsRcool suggests a "grows in[on]" relation for epiphytes)

While neither of these tickets is exactly what we're looking for w/re to "grows on", in the first ticket, @wdduncan suggests using "occurs in" (which already exists in Biolink as well).

Would "part of"/"has part" and "occurs in"/"contains process" work here?

hrshdhgd commented 10 months ago

Awesome, thank you so much @sierra-moxon !!

realmarcin commented 10 months ago

@sierra-moxon thanks for looking into this!

Part_of or occurs_in is not quite it, that could work for habitat/ecosystem though but maybe that is already covered in biolink? But those are somewhat related issues ...

The best relation I have found for now representing growth of an organism in a culture/medium:

is_grown_in from BAO

This reflects the fact that the media are artificial human-generated environments and that there has to be a human initiated process to inoculate the organism into a container with media, resulting in growth. Does that make sense?

sierra-moxon commented 4 months ago

SPOKE team would also like to contribute here.