Change to has_input hierarchy

[cmungall]

The RO has_input hierarchy has some legacy that needs cleaned up

Note that GO is moving to exclusively using has_primary_input in BP as all GO biological processes are programmed objectives. But if someone wants to incorporate GO in a combined ontology or KG alongside Rhea axiomatization the participants of catalytic activities would use the weaker relation

original comments from @pgaudet, responses are mine

1.   ‘has direct input’ has a curator note “This is likely to be obsoleted.”
   

We should remove the direct/indirect distinction

2.   ‘has ligand’ is inconsistent with GO’s usage of has input, since ligands are not inputs (at least not receptor ligands)
   

propose obsoletion

3.   ‘has primary input’ -> ok for GO
   

yes

4.   ‘results in breakdown of’, which has 2 children:
   

we can get rid of many of these when GO stops is-a overloading

5.   ‘results in catabolism of’: GO does not use this; we use ‘has primary input’. Note that we could not use that either, since it’s not a primary input
   

yes, this relation predates the primary distinction

6.   ‘results in disassembly of’: GO uses this relation; which has another parent, ‘results in changes to anatomical or cellular > structure’ (which is also the parent of ‘results in organization of’) >> so this branch in GO/RO is:
   

• GO: x organization// RO: results in organization of x
  • GO: x assembly// RO: results in assembly of x
  • GO: x disassembly// RO: results in disassembly of x
    Note that these are not primary inputs.

These should be made primary inputs, but we will have no need of these relations when we stop is-a overloading

7.   ‘results in remodeling of’: this is a child of ‘results in organization of’; other ‘developmental relations’: ‘results in development of’, ‘results in growth of’, ‘results in morphogenesis of ‘ ‘results in maturation of’ (etc), are direct children of , ‘results in changes to anatomical or cellular structure’ (but not of ‘has input; not sure why this is the case)
   

same

8.   Note that ‘transports or maintains localization of’, which we used to use for transporters, is a child of ‘results in changes to anatomical or cellular structure’, but not of ‘has input’, I wonder if GO is inconsistent with RO here? Certainly transported substrates are participants (inputs and outputs) in RHEA reactions.
   

it shouldn't be under development

[wdduncan]

Before obsoleting, we should put together a list of impacted ontologies.

[pgaudet]

Is there an easy way to address @wdduncan 's request?
When I look in ontobee I see terms not used in ontologies, just loaded. Also, how would we know these are not used for annotations?

[pgaudet]

In GO we email some email list, and people who may be impacted by changes in the ontology can comment before the obsoletion/term changes take place. Does RO have a way to communicate with people using it?

[balhoff]

According to discussion about #818, we need to obsolete 'has direct input' ('has direct output' is already obsoleted). But it is used in a number of property chains related to 'myristoylates', 'phosphorylates', etc. Can these all be changed to simply use 'has input'?

[pgaudet]

Can we also move 'has ligand' out of this branch? We have discussed this relation for GO-CAM, and ligands are activators, not inputs (ie, substrates).
I see two options:

1. move it up directly under 'has participant'
2. (maybe better, but more work): move it under the 'has small molecule regulator' branch, but this would need to be broadened, since ligands can be proteins, not just small molecules.

Thanks, Pascale

[citmejia]

Hello,

I agree that 'has ligand' has to be moved out of the branch, because 'has participant' and 'has input' both are relations held between a process and a continuant, but the definition of "has ligand' is a relation held between a receptor and a chemical entity. The two proposals of pgaudet have the same issue: those are properties between a process and a continuant. In short: 'has ligand' relates two continuants, but its superproperties relate a process to a continuant.

Can we also move 'has ligand' out of this branch? We have discussed this relation for GO-CAM, and ligands are activators, not inputs (ie, substrates). I see two options:

1. move it up directly under 'has participant'
2. (maybe better, but more work): move it under the 'has small molecule regulator' branch, but this would need to be broadened, since ligands can be proteins, not just small molecules.

Thanks, Pascale

[pgaudet]

@balhoff Could you implement this ?