Causal relations: New relations and changes to some existing relations

Hello,

The GO editors have worked on some causal relations that were either undefined or missing. We propose the following changes:

Changes to term hierarchy:

[x] 'is small molecule regulator of' - moved from subclass of 'participates in' to subclass of 'capable of regulating'
[x] 'is small molecule inhibitor of' - moved from subclass of 'participates in' to subclass of 'capable of negatively regulating'
[x] 'is small molecule activator of' - moved from subclass of 'participates in' to subclass of 'capable of positively regulating'

New terms added

[x] 'constitutively upstream of':
def: p is constitutively upstream of q iff p is causally upstream of q, p is required for execution of q or a part of q, and the execution of p is approximately constant.
Added: in subset: valid for GO-CAM
Added: in subset: valid for GO annotation extension GO-CAM
[x] 'removes input for'
def: p removes input for q iff p is causally upstream of q, there exists some c such that p has_input c and q has_input c, p reduces the levels of c, and c is rate limiting for execution of q.
Added: in subset: valid for GO-CAM
Added: in subset: valid for GO annotation extension GO-CAM
[x] 'indirectly causally upstream of':
def: p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q.
[x] indirectly regulates (NEW)
def: p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q.

Changes in definitions

[x] enables
Was not defined in RO
Added def: c enables p iff c is capable of p and c acts to execute p.
[x] causally related to
old def: This relation groups causal relations between material entities and causal relations between processes.
Updated def to: A relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause. Source: https://en.wikipedia.org/wiki/Causality
[x] causal relation between processes
old def: p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q.
Updated def to: p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q.
[x] causally upstream of or within
old def: p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q.
Updated def to: p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q.
[x] causally upstream of
old def: p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain
Updated def to: p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q.
[x] causally upstream of, negative effect
No definition in RO
Updated def to: p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q.
[x] causally upstream of, positive effect
No definition in RO
Updated def to: p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q.
Removed comment 'holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y'
[x] immediately causally upstream of
old def: p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q.
Updated def to: p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q.
removed 'requires discussion' status
[x] directly provides input for
old def: p1 directly provides input for p2 iff there exists some c such that p1 has_output c and p2 has_input c
Updated def to: p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c
[x] regulates
old def: process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2.
Updated def to: p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q.
Removed comment 'We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit'
removed curation status 'pending final vetting'
[x] negatively regulates
old def: Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 decreases the frequency of initiation of P2 or the magnitude or rate of output of P2.
Updated def to: p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q.
[x] positively regulates
old def: process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2.
Updated def to: p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q.
[x] directly regulates
old def: Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2.
Updated def to: p directly regulates q iff p is immediately causally upstream of q and p regulates q.
[x] directly negatively regulates
old def: Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2.
Updated def to: p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q.
[x] directly positively regulates
old def: Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2.
Updated def to: p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q.

oborel / obo-relations

Causal relations: New relations and changes to some existing relations #630