Add processes "combustion" and "oxidation"

[l-emele]

Description of the issue

We have some classes with words like combustion or combustible in the label. Examples are combustion fuel, internal combustion vehicle and combustion turbine (as synonym for gas turbine). Additionally we have quite a lot of classes where we use combustion in the definition. So we should define it.

Combustion is special kind of oxidation process. But I think we also need the oxidation process itself to describe e.g. the process in a fuel cell.

Ideas of solution

Potential class structure:

• process
  • oxidation
  • combustion

Workflow checklist

• [ ] I discussed the issue with someone else than me before working on a solution
• [ ] I already read the latest version of the workflow for this repository
• [ ] The goal of this ontology is clear to me

I am aware that

• [ ] every entry in the ontology should have a definition
• [ ] classes should arise from concepts rather than from words

[Vera-IER]

I would prefer "redox reaction" instead of "oxidation", because oxidation is always a part of a redox reaction. For the definitions I actually like the ones from wikipedia:

Redox (reduction–oxidation) reaction is a type of chemical reaction in which the oxidation states of atoms are changed. Redox reactions are characterized by the actual or formal transfer of electrons between chemical species, most often with one species (the reducing agent) undergoing oxidation (losing electrons) while another species (the oxidizing agent) undergoes reduction (gains electrons).

Combustion is a high-temperature exothermic redox chemical reaction between a fuel (the reductant) and an oxidant (usually atmospheric oxygen).

But we would need to make them arestotelian, if you also like them.

[l-emele]

I am fine with redox reaction, but we should include then oxidaten as alternative term. Regarding the definition, @jannahastings might help with her ChEBI background.

[jannahastings]

This looks good to me! We may want to look at the definitions used in REX, e.g. http://www.ontobee.org/ontology/REX?iri=http://purl.obolibrary.org/obo/REX_0000405.

[l-emele]

I am fine with this definition from REX.

[Vera-IER]

Me too. So the definitions would be:

Redox reaction: A redox reaction is a process in which the oxidation of one reactant is coupled to the reduction of a second reactant. Combustion: Combustion is a redox reaction between a fuel (the reductant) and an oxidant (usually atmospheric oxygen).

[l-emele]

Combustion: Combustion is a redox reaction between a fuel (the reductant) and an oxidant (usually atmospheric oxygen).

With that definition, reacting hydrogen in a fuel cell would be a combustion. Do we all agree that the fuel cell process is a combustion? If not, we have to include something in the definition of combustion that separates it from the fuel cell process.

I am neutral in this question, but we should find a consensus.

[Vera-IER]

For describing fuel cells I would add the subclass "electrochemical reaction". REX also has this subclass, but they don't have a definition for it. A definition (slightly changed from wikipedia) could be: An electrochemical reaction is a process that describes the overall reactions of individual redox reactions being separated but connected by an external electric circuit and an intervening electrolyte.

[l-emele]

How would you change the combustion definition that it excludes the electrochemical reaction?

[Vera-IER]

We could include some words to the definition: Combustion: Combustion is an exothermic redox reaction between a fuel (the reductant) and an oxidant (usually atmospheric oxygen) which is initiated by a ignition source.

[sfluegel05]

So far we got:

• redox reaction: A redox reaction is a process in which the oxidation of one reactant is coupled to the reduction of a second reactant. (synonym: oxidation)
• combustion: Combustion is an exothermic redox reaction between a fuel (the reductant) and an oxidant (usually atmospheric oxygen) which is initiated by an ignition source.
• electorchemical reaction: An electrochemical reaction is a process that describes the overall reactions of individual redox reactions being separated but connected by an external electric circuit and an intervening electrolyte.

Does everybody agree with this?

[Vera-IER]

I agree with the definitions. I think its better to delete the synonym oxidation for redox reaction, because a redox reaction is the combination of an oxidation and a reduction.

[l-emele]

We now define redox reaction using oxidation but do not yet have a definition for oxidation itself (which the issue was originally about).

[Vera-IER]

I understood that the aim is to describe the combustion process as well as the process inside a fuel cell. The concept of redox reaction is something like a helping term to describe them. If you think that the definiton of redox reaction from REX ist not understandable without oxidation, we could add some explaining words: redox reaction: A redox reaction is a process in which the oxidation (process of loosing electrons) of one reactant is coupled to the reduction (process of gaining electrons) of a second reactant.

[l-emele]

I am not a chemist. How would you call such simple reactions?

• 2 H2 + O2 = 2 H2O
• C + O2 = CO2

I would call such reaction simply "oxidation".

[Vera-IER]

I would call these reactions redox reactions. They are often called oxidation because the old definition of oxidation from early chemistry was simply a reaction with oxygen. With modern chemistry they generalised the definition of oxidation using the concept of the electrons moving from one reactant to the other. I would prefer to go with the modern definition of redox reaction :-)

[l-emele]

They are often called oxidation because the old definition of oxidation from early chemistry was simply a reaction with oxygen.

That's exactly why oxidation as alternative term is here useful. My impression is that a lot of energy modellers do not care about what happens exactly with the electrons on molecular level. They simply need to describe that oxygen reacts with some other atom or molecule and forming a new molecule that contains oxygen and hence call this oxidation.

[Vera-IER]

Okay let's put it as an alternative term then. Even if I think they are no synonyms it might be helpful if someone searches for oxidation he will be "redirected" to redox reaction.

[l-emele]

Actually, we can have both: We can define the oxidation process as part of the redox reaction process and use the oxidation as alternative terms for both theredox reaction processand theoxidation process`. Then a user of the ontology could see that the term oxidation is ambiguous.

As example: We did something similar for wind turbine and wind rotor where we defined a class wind turbine and a second class wind rotor and the latter having also the alternative term wind turbine.

[Vera-IER]

Ok, good idea!

[l-emele]

Do you have a suggestion for a definition of the oxidation half reaction?

[Vera-IER]

Oxidation is a process that describes the loss of electrons of an atom, an ion, or of certain atoms in a molecule and is a part of a redox reaction.

[l-emele]

Okay, sounds good. Shall we for completeness also include the reduction?

[Vera-IER]

Yes. We can define it in an analogue way: Reduction is a process that describes the gain of electrons of an atom, an ion, or of certain atoms in a molecule and is a part of a redox reaction.

[l-emele]

So to some up what we've agreed so far:

• A redox reaction is a process in which the oxidation of one reactant is coupled to the reduction of a second reactant. (alternative term: oxidation)
• Combustion is an exothermic redox reaction between a fuel (the reductant) and an oxidant (usually atmospheric oxygen) which is initiated by a ignition source.
• An electrochemical reaction is a process that describes the overall reactions of individual redox reactions being separated but connected by an external electric circuit and an intervening electrolyte.
• Oxidation is a process that describes the loss of electrons of an atom, an ion, or of certain atoms in a molecule and is a part of a redox reaction.
• Reduction is a process that describes the gain of electrons of an atom, an ion, or of certain atoms in a molecule and is a part of a redox reaction.

Redox reaction, electrochemical reaction, oxidation and reduction are all processes. But can we be more specific? I think all of these are transformations: A transformation is a process that transforms one or more inputs into at least one output.

Maybe we should define chemical reaction as class in between: A chemical reaction is a transformation that changes the changes the chemical properties of the input. Then our class structure would become:

• process
  • transformation
  • chemical reaction
    • redox reaction
    • combustion
    • oxidation
    • reduction
    • electrochemical reaction

[Vera-IER]

I like the idea of adding a class chemical reaction and grouping them. REX has the following defintion of chemical reaction: A chemical reaction is a process involving the interconversion of chemical species. With that definition the class would fit better under process. But we can also change the definition so that it fits under transformation: A chemical reaction is a transformation that involves the interconversion of chemical species.

Both solutions sound good to me.

[l-emele]

I would definitely prefer the later, else we have to extend the definition to distinguish from a transformation. So I think, we are ready for implementation:

• process => already existing class
  • transformation => already existing class
  • chemical reaction: A chemical reaction is a transformation that involves the interconversion of chemical species.
    • redox reaction: A redox reaction is a process in which the oxidation of one reactant is coupled to the reduction of a second reactant. (alternative term: oxidation)
    • combustion: Combustion is an exothermic redox reaction between a fuel (the reductant) and an oxidant (usually atmospheric oxygen) which is initiated by a ignition source.
    • oxidation: Oxidation is a process that describes the loss of electrons of an atom, an ion, or of certain atoms in a molecule and is a part of a redox reaction.
    • reduction: Reduction is a process that describes the gain of electrons of an atom, an ion, or of certain atoms in a molecule and is a part of a redox reaction.
    • electrochemical reaction: An electrochemical reaction is a process that describes the overall reactions of individual redox reactions being separated but connected by an external electric circuit and an intervening electrolyte.

I am off for the next couple of days, I can't implement. Who wants to implement? @sfluegel05 or @Vera-IER ?

[sfluegel05]

I can do the implementation