Change logical definitons for children of 'signaling receptor activity'

[pgaudet]

These use 'has input', which is wrong WRT GO-CAM modeling guidelines.

We need to use either 'has small molecule activator activity' for small molecules, such that the logical definition would be:
signaling receptor activity
and 'has small molecule activator' some chemical enttiy

However for protein-activated receptors, such as insulin receptor, I dont know which RO relation we can use (or maybe we need to create one?)

from OLS:

@cmungall @thomaspd @ukemi @vanaukenk Any suggestions?

Thanks, Pascale

[pgaudet]

Options:

1. Create a new parent for ‘has small molecule regulator’ (+ activator/inhibitor children), 'has regulator'/'activator'/'inhibitor'
2. Rename ‘has small molecule regulator’ & children to 'has regulator'/'activator'/'inhibitor'
   '
   Impacted terms:

'BMP receptor activity'
'C-C motif chemokine 2 receptor activity'
'GPI-linked ephrin receptor activity'
'ICAM-3 receptor activity'
'activin receptor activity'
'activin receptor activity, type I'
'activin receptor activity, type II'
'apelin receptor activity'
'apolipoprotein A-I receptor activity'
'boss receptor activity'
'brain-derived neurotrophic factor receptor activity'
'cell adhesion receptor activity'
'cholecystokinin receptor activity'
'ciliary neurotrophic factor receptor activity'
'ephrin receptor activity'
'epidermal growth factor receptor activity'
'erythropoietin receptor activity'
'fibroblast growth factor receptor activity'
'galanin receptor activity'
'gastrin receptor activity'
'glial cell-derived neurotrophic factor receptor activity'
'granulocyte colony-stimulating factor receptor activity'
'granulocyte macrophage colony-stimulating factor receptor activity'
'growth hormone secretagogue receptor activity'
'growth hormone-releasing hormone receptor activity'
'hepatocyte growth factor receptor activity'
'insulin receptor activity'
'insulin-like growth factor receptor activity'
'interleukin-1 receptor activity'
'interleukin-1, type I, activating receptor activity'
'interleukin-1, type II, blocking receptor activity'
'interleukin-10 receptor activity'
'interleukin-11 receptor activity'
'interleukin-13 receptor activity'
'interleukin-15 receptor activity'
'interleukin-16 receptor activity'
'interleukin-17 receptor activity'
'interleukin-17A receptor activity'
'interleukin-18 receptor activity'
'interleukin-19 receptor activity'
'interleukin-2 receptor activity'
'interleukin-20 receptor activity'
'interleukin-21 receptor activity'
'interleukin-22 receptor activity'
'interleukin-24 receptor activity'
'interleukin-25 receptor activity'
'interleukin-26 receptor activity'
'interleukin-27 receptor activity'
'interleukin-3 receptor activity'
'interleukin-33 receptor activity'
'interleukin-4 receptor activity'
'interleukin-5 receptor activity'
'interleukin-6 receptor activity'
'interleukin-7 receptor activity'
'interleukin-8 receptor activity'
'interleukin-9 receptor activity'
'leukemia inhibitory factor receptor activity'
'macrophage colony-stimulating factor receptor activity'
'neuropeptide Y receptor activity'
'oncostatin-M receptor activity'
'orexin receptor activity'
'pancreatic polypeptide receptor activity'
'parathyroid hormone receptor activity'
'peptide YY receptor activity'
'pituitary adenylate cyclase-activating polypeptide receptor activity'
'placental growth factor receptor activity'
'platelet-derived growth factor alpha-receptor activity'
'platelet-derived growth factor beta-receptor activity'
'platelet-derived growth factor receptor activity'
'prolactin receptor activity'
'protein tyrosine kinase collagen receptor activity'
'secretin receptor activity'
'semaphorin receptor activity'
'stem cell factor receptor activity'
'transforming growth factor beta receptor activity'
'transforming growth factor beta receptor activity, type I'
'transforming growth factor beta receptor activity, type II'
'transforming growth factor beta receptor activity, type III'
'transmembrane histidine kinase cytokinin receptor activity'
'transmembrane receptor histidine kinase activity'
'transmembrane receptor protein kinase activity'
'transmembrane receptor protein phosphatase activity'
'transmembrane receptor protein serine/threonine kinase activity'
'transmembrane receptor protein tyrosine kinase activity'
'transmembrane receptor protein tyrosine phosphatase activity'
'transmembrane-ephrin receptor activity'
'urokinase plasminogen activator receptor activity'
'vascular endothelial growth factor receptor activity'

[thomaspd]

My observations are: 1) there aren't too many impacted terms, and 2) not all of the terms listed above would be addressed by the proposed solution (e.g. 'transmembrane receptor protein kinase activity'). Logical definitions based on PRO or some other way to group proteins into classes seems overly complicated for handling this number of terms, which we could handle, at least for the time being, by just asserting them to be children of signaling receptor activity (which is probably already the case, so job done :) ).

As an added consideration, I'm concerned that having a new relation, which would be equivalent to a property chain that involves a directly_regulates relation, could potentially lead to incorrect inferences, since GO-CAM uses those in many contexts, not just for receptor ligands.