#121 Terms request for Event/Reaction representation in Reactome
The following paper (https://doi.org/10.1093/database/bau060 - section 'Event (reaction) CV names') lists and proposes terms missing in existing CV/ontologies for Event types in Reactome. My questions: are some of them already matching to existing SBO terms? Can the others be integrated within SBO?
I am listing below the terms (in capital letters) with the definitions (in italic) mentionned in the paper. I also give my suggestions of mapping if there are existing terms in SBO that seems to match them.
Any thoughts are welcome, thanks!
Vasundra
TRANSFORMS TO ?
Transformation of entities is the default category for Reactome events, i.e. all reactions are considered to be transformations unless they can be assigned to another specified class of reaction.
BINDS TO: Match with SBO:0000177 non-covalent binding?
If there are more input entities than output entities, the event is classed as a binding event. The test applied to determine binding can also be useful for verifying stoichiometric balance; at least one input entity should become a component of (one of) the output entities, or one of the input entities should include more entities as an output than it did as an input.
DISSOCIATES TO: Match with SBO:0000180 dissociation?
If more output molecules are present than inputs, the event is a dissociation event. This can be tested by determining that at least one of the output entities is a component of an input entity or that an output complex reduces in size (to distinguish this class from certain transformation reactions).
POLYMERIZES TO: Could it be either children of SBO:0000210 - addition of a chemical group or children of SBO:0000177 - non-covalent binding?
Polymerization can be seen as a specialized form of a binding event. Polymerization events have their own reaction class in the Reactome data-model and are therefore easy to identify.
DEPOLYMERIZES TO: Could it be a children of SBO:0000211 - removal of a chemical group?
TRANSFERS TO: Could it be a children node of SBO:0000185 - transport reaction? Or are transfers to and transport reaction similar?
TRANSLOCATES FROM: Could it be a children node of SBO:0000185 - transport reaction?
Transport with no identified transporter or passive movement between compartments, Translocation can be identified by comparing the compartment of molecular entities as inputs with their compartment as an output. If the entity is unchanged but associated with a different molecular compartment, this is a translocation event.
TRANSPORTS: Could it be a children node of SBO:0000185 - transport reaction?
*Transport mediated by a known transporter
Transport that requires a transporter uses a different phrasing. The extra requirement is that there is a protein entity named as catalyst. *
EXCHANGES: Could it be a children node of SBO:0000185 - transport reaction?
*Antiporter reactions, Here, different entities are exchanged in opposite directions across a membrane, mediated by an exchanger protein. *
CO-TRANSPORTS: Could it be a children node of SBO:0000185 - transport reaction?
*Cotransporters (also called symporters) couple the movement of one or more entities with another entity(ies) in the same direction. *
ACTIVATED ?
*Activation reactions can be identified as events where the input and output entities are the same with no change of compartment. *
REGULATES ?
Regulation, where an entity has a modulatory effect on an event.
Related
Discussion
Anonymous
Thank you Vasundra. Many of those terms are already in SBO, but some would indeed be welcome additions. SBO terms are nouns, not verbs. I think the difference comes from the fact that despite its name, Reactome is not a reaction database but a physical entityffunction database (initialy gene product - its original name was the "Genome Knowledge Base"). So the terms characterise a gene product or a chemical compound. But we can draw equivalences.
TRANSFORMS TO ? seems to be SBO:0000167 - biochemical or transport reaction. But if it is the root term, it could just be SBO:0000375 - process
I woud suggest that DEPOLYMERIZES TO is mapped to a new term "depolymerization", initially child of SBO:0000182 - conversion. It is a bit more than the removal of a chemical group.
TRANSFERS TO is our current term transport, that we need to rename "translocation" ... and create children "transport", "active transport", "passive translocation", "exchange", "co-transport", "anti-transport" etc.
ACTIVATED is just weird (because of the single compartment clause), but would be SBO:0000643 - stimulated
REGULATES is SBO:0000019 - modifier
Hi Nicolas, Vasundra,
I have the following definitions and proposed changes for the terms that you both have been discussing.
Kindly let me know if you have any feedback on the proposed definitions before I create the terms.
I will create new terms
(Parent term: SBO:0000182 - conversion)
A chemical reaction involving two or more molecules combining to form a larger molecule with repeated structural units.
(Parent term: SBO:0000182 - conversion)
A chemical reaction in which a large molecule with repeated structural units, breaks into its constituent parts.
(Parent term: SBO:0000185 - transport reaction)
A biochemical process involving the simultaneous transport of two substances across a membrane via a protein or protein complex.
I will change
SBO:0000185 - transport reaction to SBO:0000185: translocation reaction
(Parent term: SBO:0000167 - biochemical or transport reaction)
and create child terms to translocation
We already have a term for exchange reaction (SBO:0000627). Did you have a different definition in mind ?
For Anti-transport, do you mean antiport as defined here. If not, how would you define it?
Best,
Varun
[adding Vasundra to the discussion. I think the initial mail only went to SF]
On 20/01/18 23:49, Varun Kothamachu wrote:
I think we might need to start mentioning that we are talking about transmembrane translocation here.
translocation
==== transmembrane active transport
==== transmembrane passive diffusion
Because we will have other types of translocation, e.g. between nucleus and cytoplasm.
This is different. This is a pseudo reaction, used for FBA. We could perhaps be more precise in the name.
Indeed, I think we need:
symporter-mediated transport
https://en.wikipedia.org/wiki/Symporter
antiporter-mediated transport
https://en.wikipedia.org/wiki/Antiporter
NB, they are both a type of cotransporter.
https://en.wikipedia.org/wiki/Cotransporter
But I do not think we need to reconstruct gene ontology just yet. What is important is to know if the reactions are both going in the same direction (e.g. the stoichiometries of all reactants on the same side have the same sign, except for the side-substrates)
--
Nicolas LE NOVERE, Babraham Institute, Babraham Campus Cambridge, CB22 3AT
Tel: +441223496433 Mob:+447833147074
orcid.org//0000-0002-6309-7327 http://lenoverelab.org/
Related
Term request: #121
Posting on behalf of Vasundra:
Hi Varun and Nicolas,
I believe a feedback from Reactome people would be useful for the rest.
Hi Vasundra,
I have created new terms for polymerisation (SBO:0000652) and de-polymerisation (SBO:0000653).
For co-transport we now have the term SBO:0000654 which is currently described for 2 substances. I am not aware of examples of co-transport being used for more than 2 substances. Could you share some examples ?
Will wait for more responses on the other terms.