Reverse edges for causal agents

[cmungall]

Currently you have

A SubClassOf causal-agent-of some D

I recommend switching to

D SubClassOf has-causal-agent some A

Right now you have incorrect inferences - for example, that maize bushy stunt phytoplasma is a causal agent of a rice bacterial disease

You can think of this as analogous to 'true path' rule violations in GO

[austinmeier]

This has been corrected. New relationship exists: has_causal_agent

[cooperl09]

Chris, could you please point me to the location where I can find the BFO references for these relations?

[cmungall]

Should be in ontobee shortly but for now you can open ro in protege https://github.com/oborel/obo-relations

[cooperl09]

Isn't RO deprecated?

[cmungall]

No. OBO_REL is deprecated. See the README

[cooperl09]

Ah yes. So they should have RO Xrefs, rather than BFO?

For example: id: RO:0002608 name: has causal agent def: "Inverse of 'causal agent in'" [] is_a: RO:0002410 ! causally related to inverse_of: RO:0002500 ! causal agent in

and id: RO:0002500 name: causal agent in def: "A relationship between a material entity and a process where the material entity has some causal role that influences the process" [] is_a: RO:0002595 ! causal relation between material entity and a process

[cmungall]

Generally, but some relations such as part of and occurs in have BFO IDs

[cmungall]

Btw, the xref thing is an obo hack. As we get more familiar with Protege we'll see that the Planteome ontologies are using the BFO/RO ObjectProperties directly

[cooperl09]

Agreed

[cooperl09]

Changed relation from 'causal agent of" to "causal agent in" to be consistent with the RO.
Added Dbxref to RO:0002500. causal_agent_in (RO:0002500): - def: "A relationship between a material entity and a process where the material entity has some causal role that influences the process"