biolink-model
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biolink
New predicate request for micro-organisms <=> media
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 | relation | 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
@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?
@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?
