rsc-ontologies / rxno

Name Reaction Ontology

RXNO: reaction ontologies

RXNO is the name reaction ontology. It contains more than 500 classes representing organic reactions such as the Diels–Alder cyclization.

MOP is the molecular process ontology. It contains the underlying molecular processes, for example cyclization, methylation and demethylation.

Both ontologies are stored as .obo and .owl files, both of which can be read by Protege (http://protege.stanford.edu/).

You can browse the terms here: http://www.ebi.ac.uk/ols/ontologies/rxno and here: http://www.ebi.ac.uk/ols/ontologies/mop

Instructions for adding new reactions

To add new reactions to RXNO follow the instructions below using the flowcharts provided in the documentation folder:

1. Determine the "skeleton" using the skeleton flowchart.
2. Go through the reaction flowchart to find the correct parent class for the new reaction that you would like to add.

Steps for release

1. You will need to obtain a tool to convert OBO to OWL (or vice versa if you're editing the OWL), for example ROBOT, which is available here: http://robot.obolibrary.org/
2. java -jar robot.jar convert --input rxno.obo --output rxno.owl
3. java -jar robot.jar convert --input mop.obo --output mop.owl
4. (currently optional for various reasons) Check that the resulting files don't violate DL: java -jar robot.jar validate-profile --input rxno.owl --profile DL --output dl.txt
5. java -jar robot.jar validate-profile --input mop.owl --profile DL --output dl.txt

Colin Batchelor

2020-06-08

rxno's Issues

Term request: Coordination polymerisation

Preferred term label

Coordination polymerisation

Synonyms or alternative term labels

Ziegler-Natta-Polymerisation

Textual definition

Coordination polymerisation is a form of polymerization that is catalyzed by transition metal salts and complexes, i.e. a Ziegler-Natta catalyst.
(https://en.wikipedia.org/wiki/Coordination_polymerization)

Suggested parent term

Chain polymerisation

Examples

Attribution

0000-0003-1869-463X

Other comments

RXNO neither reports a date nor a data_version in OBO

It would be useful for reproducibility purposes to include both of a date and data_version field at the top of the RXNO OBO file

Uniqueness of synonyms

I'm not sure if this is a bug or is unintentional, but there are three 
duplicate synonyms in the RXNO ontology.  These are "Huisgen reaction" and 
"Huisgen cycloaddition" that are synonyms of both RXNO:0000018 and 
RXNO:0000269, and "Gattermann reaction" which is a synonym of both RXNO:0000022 
and RXNO:0000139.  This many-to-one mapping makes it impossible to map the 
string "Huisgen reaction" to a single RXNO concept. I'm not sure if this is a 
design constraint, but it would be a very convenient property.

Revealingly, the same ambiguity appear to exist on wikipedia:
http://en.wikipedia.org/wiki/1,3-Dipolar_cycloaddition
http://en.wikipedia.org/wiki/Azide_alkyne_Huisgen_cycloaddition

Original issue reported on code.google.com by [email protected] on 22 Jul 2011 at 9:58

Addition of nitroxide exchange reaction, Baeyer pyridine synthesis, Corey-Kim oxidation, Corey-Suggs oxidation, Corey-Schmidt oxidation, Albright-Goldman oxidation, Rubottom oxidation & IBX oxidation to RXNO

Addition of 8 more reactions:

1. nitroxide exchange reaction (RXNO:0000663)
   Def.: Nitroxide exchange reactions are based on thermal C–O bond homolysis of alkoxyamines, which leads to transient carbon-centred radicals and persistent nitroxide radicals. Usually these carbon centred radicals are quickly trapped by the nitroxide radicals and reform the alkoxyamines.
   Parent class: functional group modification (RXNO:0000011)

2. Baeyer pyridine synthesis (RXNO:0000664)
   Def.: The conversion of pyran or pyrone (pyranone) derivatives to the corresponding pyridine derivative.
   Parent class: functional group modification (RXNO:0000011)

3. Corey-Kim oxidation (RXNO:0000665)
   Def.: Oxidation of primary and secondary alcohols via their alkoxysulfonium salts. Upon the addition of base, the salt rearranges intramolecularly to aldehydes and ketones, respectively.
   Parent class: functional group oxidation (RXNO:0000012)

4. Corey-Suggs oxidation (RXNO:0000666)
   Def.: Oxidation of primary and secondary alcohols to aldehydes and ketones, respectively, through the use of pyridinium chlorochromate (PCC).
   Parent class: functional group oxidation (RXNO:0000012)

5. Corey-Schmidt oxidation (RXNO:0000667)
   Def.: Oxidation of primary and secondary alcohols to aldehydes and ketones, respectively, through the use of pyridinium dichromate (PDC).
   Parent class: functional group oxidation (RXNO:0000012)

6. Albright-Goldman oxidation (RXNO:0000668)
   Def.: A particularly mild oxidation method in which, for example, dimethyl sulfoxide and acetic anhydride can be used as oxidizing agents to selectively produce aldehydes from primary alcohols without further oxidation to carboxylic acids. Analogously, secondary alcohols can be oxidized to form ketones.
   Parent class: functional group oxidation (RXNO:0000012)

7. Rubottom oxidation (RXNO:0000669)
   Def.: The Rubottom oxidation is a useful, high-yielding chemical reaction between silyl enol ethers and peroxy acids to give the corresponding α-hydroxy carbonyl product.
   Parent class: functional group oxidation (RXNO:0000012)

8. IBX oxidation (RXNO:00006673)
   Def.: Oxidation of alcohols to the corresponding carbonyl product using 2-iodoxybenzoic acid (IBX) as oxidizing agent.
   Parent class: functional group oxidation (RXNO:0000012)

revert MIREOT style import of GO's "protein trimerization" in #36

In #36 GO's "protein trimerization" was imported into MOP as a subclass of trimerization (MOP:0000715). This will most likely lead to issues downstream if MOP and GO are to be combined and protein trimerization being defined thus as a subclass of trimerization in MOP and also a subclass of protein complex oligomerization in GO.

Cyclic relationship in RXNO_0000580

Hi,

There looks to be a cyclic relationship in RXNO_0000580, where RXNO_0000580 is a subClass of itself:

<!-- http://purl.obolibrary.org/obo/RXNO_0000580 -->

    <owl:Class rdf:about="http://purl.obolibrary.org/obo/RXNO_0000580">
        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/RXNO_0000140"/>
        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/RXNO_0000580"/>

Please could you take a look?

Many thanks,
Rebecca

switching to ODK for the maintanance of RXNO & MOP

There are a lot of open issues (e.g.: #37, #30, #28, #27) that could be resolved better with a repository structure and workflow as layed out by the Ontology Development Kit (ODK). Switching to an ODK workflow would not just make the development and maintanance of RXNO & MOP much easier and less error prone, but would also ensure these two to adhere to the OBO Foundry principles, as most of them are checked for in the quality control checks implemented in ODK.

As we already use RXNO in NFDI4Chem and plan on using / contributing more to it, I started working on the ODK migration in our NFDI4Chem fork, documenting it in its wiki. I have talked about migrating a repo to ODK in general with @matentzn in late 2021 and I will follow the inofficial "how to video" he shared with me as the basis.
An important part of this is addressing the fact that MOP and RXNO are hosted and maintained in the same repository. It seems to me, that creating a repo for MOP would be best, but for now I will go for having an ODK folder structure for each (RXNO & MOP) within the existing rxno repo.

The following TODOs are the needed steps I have identified. Constructive feeback to these steps is very welcome :)

TODOs:

• write documentation on how to set up a VM for the plattform independent use of an ODK workflow
• blocked by #27
• create editor files for both ontologies in src folder
• migrate RXNO to an ODK workflow
  • seed repo folder structure with templates
  • export lists of terms with ROBOT|export from recent rxno.owl to be used as input for the building of import modules
  • somehow copy existing RXNO terms including all annotations and axioms into new rxno-edit.owl (using ROBOT filter probably)
  • find out if rxno.makefile is needed for the import module build
• migrate MOP to an ODK workflow
  • seed repo folder structure with templates
  • export lists of terms with ROBOT|export from recent rxno.owl to be used as input for the building of import modules
  • somehow copy existing MOP terms including all annotations and axioms into new mop-edit.owl (using ROBOT filter probably)
  • find out if mop.makefile is needed for the import module build
• test the workflow by making a proper release and adjusting the metadata YAML for the purls to resolve

Term shift: RAFT; ARTP, NMP

I suggest to shift the terms

• MOP:atom-transfer radical polymerisation
• MOP:nitroxide-mediated polymerisation
• MOP:reversible addition-fragmentation chain transfer polymerisation

into the requested #53 Reversible-deactivation radical polymerization (see https://en.wikipedia.org/wiki/Reversible-deactivation_radical_polymerization)

All three are distinct from living radical polymerisations.

Connect ROMP to living polymerisation

Please connect
MOP:ring-opening metathesis polymerisation

also to
MOP:living polymerisation

besides
MOP:ring-opening polymerisation

See:
https://en.wikipedia.org/wiki/Living_polymerization
https://en.wikipedia.org/wiki/Ring-opening_metathesis_polymerisation

how to use BFO:process profile & maybe discard using it

MOP reuses the BFO class "process profile" (BFO_0000144) as parent class for 'Baldwin-disfavoured profile' (MOP:0000774) & 'Baldwin-favoured profile' (MOP:0000773). These classes are also the only ones reusing the not resolvable BFO relation "process profile of".
In order to harmonize with OBO, I propose to rework these two classes.
More on how an attribute can be assigned to a process, see

• OBOFoundry/COB#53
• OBOFoundry/COB#65

Addition of 16 missing reactions to RXNO

Addition of 16 reactions:

1. Kabachnik-Fields reaction (RXNO:0000676)
   Def.: A three-component condensation reaction in which primary or secondary amines react with a carbonyl compound (aldehyde or ketone) and a dialkyl phosphonate (also called dialkyl phosphite) to form an alpha-aminophosphonate.
   Parent class: molecular skeleton joining reaction (RXNO:0000000) & molecular dehydration reaction (MOP:0000628)

2. Baekeland-Manasse-Lederer reaction (RXNO:0000677)
   Def.: A polymerisation reaction in which phenol and formaldehyde react together in a chain reaction to form a phenol formaldehyde resin (also infrequently called phenoplast).
   Parent class: polymerisation reaction (RXNO:0000246)

3. Aston-Greenburg rearrangement (RXNO:0000678)
   Def.: The rearrangement of an alpha-haloketone into an ester with a tertiary alpha-carbon atom by intramolecular migration of an alkyl or aryl group.
   Parent class: rearrangement step (RXNO:0000025)

4. Baddeley isomerization (RXNO:0000679)
   Def.: The rearrangement/migration of alkyl groups in polyalkylbenzenes or polynuclear aromatic compounds in the presence of anhydrous aluminum chloride or the mixture of protonic acid and Lewis acid.
   Parent class: rearrangement step (RXNO:0000025)

5. Fukuyama reduction (RXNO:0000680)
   Def.: The reduction of a thioester to an aldehyde by a silyl hydride in the presence of catalytic amounts of palladium.
   Parent class: functional group reduction (RXNO:0000037)

6. Dötz reaction (RXNO:0000681)
   Def.: A three component cyclization of an aromatic or vinylic alkoxy pentacarbonyl chromium carbene complex, an alkyne and carbon monoxide to give a Cr(CO)3 coordinated phenol.
   Parent class: ring formation reaction step (RXNO:0000005)
   Synonym: Wulff-Dötz reaction

7. Kulinkovich reaction (RXNO:0000682)
   Def.: The formation of a substituted cyclopropanol by reaction of a carboxylic ester with a Grignard reagent (carrying a hydrogen atom in the beta-position) in the presence of a titanium(IV) alkoxide as catalyst. A modified cyclopropanol product can be generated by addition of a terminal alkene as a further reactant.
   Parent class: ring formation reaction step (RXNO:0000005)

8. Kulinkovich-de Meijere reaction (RXNO:0000683)
   Def.: The formation of a substituted cyclopropylamine by reaction of an amide with a Grignard reagent (carrying a hydrogen atom in the beta-position) in the presence of a titanium(IV) alkoxide as catalyst.
   Parent class: ring formation reaction step (RXNO:0000005)

9. Kulinkovich-Szymoniak reaction (RXNO:0000684)
   Def.: The formation of a substituted primary cyclopropylamine by reaction of a nitrile with a Grignard reagent (carrying a hydrogen atom in the beta-position) in the presence of a titanium(IV) alkoxide as catalyst.
   Parent class: ring formation reaction step (RXNO:0000005)

10. cyclotrimerization (RXNO:0000685)
    Def.: The formation of a trimer by cycloaddition of three unsaturated compounds (e.g. alkynes, alkenes, nitriles or mixtures of these). Usually, the reaction requires a metal catalyst.
    Parent class: ring formation reaction step (RXNO:0000005) & cycloaddition (MOP:0000562)
    => not added to RXNO because it fits better in the scope of MOP and will be added there, see #34

11. Jacobsen epoxidation (RXNO:0000686)
    Def.: Chiral (salen)manganese(III)-catalyzed asymmetric epoxidation of alkenes. In addition to the catalyst, stoichiometric amounts of an oxidant (e.g. sodium hypochlorite) are required.
    Parent class: ring formation reaction step (RXNO:0000005) & epoxidation (MOP:0000671)
    Synonym: Jacobsen-Katsuki epoxidation

12. Shi epoxidation (RXNO:0000687)
    Def.: Organocatalytic enantioselective epoxidation of trans- and tri-substituted olefins using a fructose derived chiral ketone catalyst and potassium peroxomonosulfate or H2O2 as an oxidant.
    Parent class: ring formation reaction step (RXNO:0000005) & epoxidation (MOP:0000671)

13. Asinger reaction (RXNO:0000688)
    Def.: A multicomponent reaction (A-4CR) in which 3-thiazolines (2,5-dihydro-1,3-thiazoles) or mixtures of several 3-thiazolines are synthesized from elemental sulfur, an alpha-substitutable ketone or aldehyde, another carbonyl component and ammonia.
    Parent class: ring formation reaction step (RXNO:0000005) & thiacycle synthesis (RXNO:0000348)
    Synonym: Asinger thiazoline synthesis & Asinger-4 component reaction (A-4CR)

14. haloform reaction (RXNO:0000689)
    Def.: Cleavage of methyl ketones (i.e. oxidative demethylation) with halogens (or hypohalites) in the presence of a base to give a carboxylic acid and haloform (trihalomethane).
    Parent class: end-of-chain chain shortening (RXNO:0000105) & halogenation (MOP:0000550)
    Synonym: Einhorn reaction & Lieben reaction

15. Atherton-Todd reaction (RXNO:0000690)
    Def.: The conversion of dialkyl phosphites (dialkyl phosphonates) to dialkyl chlorophosphates using tetrachloromethane and a base (usually a primary, secondary or tertiary amine).
    Parent class: functional group oxidation (RXNO:0000012) & halogenation (MOP:0000550)
    Synonym: AT reaction

16. Baeyer diarylmethane synthesis (RXNO:0000691)
    Def.: Synthesis of diarylmethane derivatives using an aldehyde and an aromatic compound at low temperature in an acidic medium.
    Parent class: molecular skeleton joining reaction (RXNO:0000000) & molecular dehydration reaction (MOP:0000628)

17. silyl deprotection (RXNO:0000692)
    Def.: A hydroxyl group deprotection in which an silyl ether group is transformed into a hydroxy group.
    Parent class: hydroxy group deprotection (RXNO:0000430)

improve versioning scheme of RXNO & MOP

At the moment the versions of RXNO and MOP are declared in the ontology metadata using:
<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/mop/releases/2022-02-01/mop.owl"/> &
<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/rxno/releases/2021-12-16/rxno.owl"/>
Unfortunately these IRIs are not resolvable as there are no releases other than the files in the root dir.

TODOs:

• switch to ODK setup with proper release artefacts in the long run
• think about manually making GitHub releases to resolve to or a release folder in the root dir
  • edit OBO registry YAML to make the versionIRIs resolvable
• add owl:versioninfo and maybe a comment/documentation to the recent release process

add license for the repo

This repo has no license at the moment.
MOP and RXNO are licensed under CC-BY 4.0.

I'm not sure what the proper OA license would be for the repo. RO uses CC-0 and OBI, IAO and CHEMINF have also no license for the repo. I guess the most important part is having the release artefacts licenced, but I think it would be in the best interest of open science to also declare an open licence for the repo. This would be easier to reuse documentation and other supplementary data in here in other research contexts, like workshops etc.

Addition of Miyaura borylation, Corey-Winter elimination, Tsuji-Wilkinson decarbonylation & Corey-Seebach reaction to RXNO

Addition of 4 more reactions:

1. Miyaura borylation (RXNO:0000659):
   Def.: A chemical reaction that allows the generation of boronates from vinyl or aryl halides with the cross-coupling of bis(pinacolato)diboron under basic conditions.
   Parent class: molecular skeleton joining reaction (RXNO:0000000)

2. Corey-Winter elimination (RXNO:0000660)
   Def.: A chemical reaction for the stereoselective synthesis of an olefin from a 1,2-diol.
   Parent class: molecular skeleton elimination reaction (RXNO:0000123)

3. Tsuji–Wilkinson decarbonylation (RXNO:0000661)
   Def.: The Tsuji–Wilkinson decarbonylation reaction is a method for the decarbonylation of aldehydes and some acyl chlorides.
   Parent class: end-of-chain chain shortening (RXNO:0000105)

4. Corey-Seebach reaction (RXNO:0000662)
   Def.: A chemical reaction in which ketones are synthesized from formaldehyde or other aldehydes, involving a temporary repolarization of a carbonyl group.
   Parent class: functional group modification (RXNO:0000011)

Term request: Reversible-deactivation polymerisation

Preferred term label

Reversible-deactivation polymerisation 

Synonyms or alternative term labels

RDP

Textual definition

RDP is a form of polymerization propagated by chain carriers, some of which at any instant are held in a state of dormancy through an equilibrium process involving other species. Despite having some common features, RDP is distinct from living polymerization which requires a complete absence of termination and irreversible chain transfer. 
(https://en.wikipedia.org/wiki/Reversible-deactivation_polymerization)

Suggested parent term

Chain polymerisation

Examples

Attribution

0000-0003-1869-463X

Other comments

Import CHEBI terms into MOP and RXNO editor files via a seperatly maintained module

For a better maintainability the editor files for both ontologies (mop-edit.owl and rxno-edit.owl) should each have their own CHEBI import module. These CHEBI import modules would have to be maintained in the repo as well. As proposed in #40 this is best done with the ODK workflow.

Ontology alignment with wikipedia

I recently came across the RXNO ontology by following
the identifiers link from the Wikipedia page on Diels Alder
http://en.wikipedia.org/wiki/Diels%E2%80%93Alder_reaction
Indeed, an ontology for reactions is precisely what the
community needs (even MeSH terms don't cover reactions).

However, I was then disappointed by the limited degree
of cross-referencing between wikipedia and RXNO.
For example, Neither the Suzuki reaction/coupling
page nor the Negishi coupling page contain reaction
boxes.

To make the cross-referencing process easier, it would
be convenient if RXNO could introduce concepts matching
those currently used by wikipedia's classification and
organization of reactions.  For example, "condensation
reactions" or "cycloaddition".  This way these wikipedia
pages could also contain a reaction box pointing out to
RXNO, but also encode in the ontology the fact that Diels-Alder
is an example of a cycloaddition reaction in RXNO, a
relationship non-semantically encoded by wikipedia.

Original issue reported on code.google.com by [email protected] on 20 Jul 2011 at 8:58

add subclass axioms in MOP based on rdfs:comment annotations

There seem to be a couple of classes in MOP (e.g. silylation) that have rdfs:comment annotations in the form of has_participant CHEBI:XXXXX.
It might be good to get a list of these using ROBOT or rdflib to add the subclassOf axiom that express this.

N-demethylation

I am working on an ontology dealing with an N-demethylation reaction. Would it be correct to describe N-demethylation as a demethylation (MOP:0001364) that occurs at a nitrogen atom of the substrate, or is there more to it? Thanks.

Term request: Living anionic polymerization

Preferred term label

Living anionic polymerization 

Synonyms or alternative term labels

Living anionic polymerization 

Textual definition

Living anionic polymerisation involves no formal termination step. The chains will remain active indefinitely unless there\s\s
is inadvertent or deliberate termination or chain transfer.  
(https://en.wikipedia.org/wiki/Anionic_addition_polymerization#Living_anionic_polymerization)

Suggested parent term

Anionic polymerisation AND living polymerisation

Examples

Attribution

0000-0003-1869-463X

Other comments

Addition of trimerization, cyclotrimerization & protein trimerization to MOP

Addition of 3 missing reactions:

1. trimerization (MOP:0000715)
   Def.: The formation of a trimer from three molecular subunits.
   Parent class: molecular process (MOP:0000543)

2. cyclotrimerization (MOP:0000716)
   Def.: The formation of a trimer by cycloaddition of three unsaturated compounds (e.g. alkynes, alkenes, nitriles or mixtures thereof). A metal catalyst is usually required for this type of reaction.
   Parent class: cycloaddition (MOP:0000562) & trimerization (MOP:0000715)
   Source: https://doi.org/10.1002/anie.200700802

3. protein trimerization (GO:0070206) - Import from Gene Ontology
   Def.: The formation of a protein trimer, a macromolecular structure consisting of three noncovalently associated identical or nonidentical subunits.
   Parent class: trimerization (MOP:0000715)
   Source: http://purl.obolibrary.org/obo/GO_0070206

note:

• also added "dc:date" to the ontology header

mop.obo & mop.owl are out of sync

When producing mop.obo from mop.owl using ROBOT convert, we can see that these two are out of sync for longer time. We happened to notice this while doing PR #21.

OBO Purl is wrong

Hi @colinbatchelor,
the IRI provided in RXNO is http://purl.obolibrary.org/obo/rxno.obo.owl which resolves to http://ontologies.berkeleybop.org/
but it should be http://purl.obolibrary.org/obo/rxno.owl which resolves to https://raw.githubusercontent.com/rsc-ontologies/rxno/master/rxno.owl, right?

harmonize MOP object properties with RO

There are object properties (aka relations) reused in MOP that are defined in BFO. As the OBO community uses the BFO2.0 classes only version these relations are not being resolved via their IRI. In order to be compliant with the OBO principles these relations should thus be replaced by RO equivalents.
The following relations need to be changed in MOP (individual issues need to be made for each):

• “has dispositions at all times” (BFO_0000162) should be changed to “has disposition” (RO_0000091)
• ‘has participant’ (BFO_0000057) should be changed to ‘has participant’ (RO_0000057)
  • its sup-properties 'has participant beginning to exist' (BFO_0000077) & 'has participant ceasing to exist' (BFO_0000078) should be changed to something suitable in the ‘has participant’ branch of RO, or a term request should be made
    • a possible candidate for 'has participant ceasing to exist' might be "has primary input" (RO_0004009)
    • a possible candidate for 'has participant beginning to exist' might be "has primary output" (RO_0004008)
• “occurent part of” & its inverse (BFO_0000117 & BFO_0000132) should be changed to “occurent part of” (RO_0002012) and “has occurent part” (TXPO_0002523), but see also the open issue to pull the later into RO

Ensure named direct children of carbon-carbon coupling reaction become planned processes

Best way of doing this is to add has_specified_product axioms---that means they 
will shift to becoming children of molecular skeleton joining reaction.

Original issue reported on code.google.com by [email protected] on 7 Feb 2014 at 5:38

Addition of Groebke-Blackburn-Bienaymé reaction, Baeyer oxindole synthesis, Leimgruber-Batcho indole synthesis, decarboxylative cross-coupling & Balsohn alkylation to RXNO

Addition of 5 reactions:

1. Groebke-Blackburn-Bienaymé reaction (RXNO:0000670)
   Def.: A three-component reaction (3CR) of a heterocyclic amidine, an aldehyde, and an isocyanide, resulting in a cyclic compound with imidazo[1,2-a] heterocycle as the core structure.
   Parent class: fused-ring-system formation (RXNO:0000052)

2. Baeyer oxindole synthesis (RXNO:0000671)
   Def.: The preparation of oxindole/indolin-2-one from 2-nitrophenylacetic acid by reduction of the nitro group and subsequent dehydration.
   Parent class: fused-ring-system formation (RXNO:0000052)

3. Leimgruber-Batcho indole synthesis (RXNO:0000672)
   Def.: Condensation of a formamide acetal with a derivative of o-nitrotoluene to yield an enamine intermediate that subsequently undergoes reductive cyclization to give the corresponding indole.
   Parent class: indole synthesis (RXNO:0000395)

4. decarboxylative cross-coupling (RXNO:0000674)
   Def.: A chemical reaction in which a carboxylic acid (or its salt) reacts with an organic (alkyl or aryl) halide to form a new carbon-carbon bond with concomitant loss of CO2. In addition, the reaction requires a metal catalyst, a base and an oxidizing agent.
   Parent class: cross-coupling (RXNO:0000603)

5. Balsohn alkylation (RXNO:0000675)
   Def.: A carbon-carbon coupling reaction between an arene and an alkene to give a substituted arene. The reaction is catalysed by a Lewis acid.
   Parent class: carbon-carbon coupling reaction (RXNO:0000002)

Add "ligand exchange reaction" to MOP

We would like to add the "ligand exchange reaction" to MOP because of the relevance of the term (especially but not exclusively for inorganic chemistry).

Label: "ligand exchange reaction"
has_exact_synonym: ligand substitution reaction
Definition: A ligand exchange reaction is a molecular process, in which one or more ligands around a metal ion are replaced by other ligands without changing the oxidation state of the metal atom. (Source: https://doi.org/10.1093/oso/9780195301007.003.0005)

Question parent class:
Where to subsume this new reaction is unsure. It could be inserted under "coordination" (MOP:0000797) or “formation of covalent bond with group” (MOP:0000566). Since a ligand exchange in the broadest sense is also a substitution, an entry under "substitution reaction" (MOP:0000790) would also be conceivable.
But the definitions of these possible classes are not entirely appropriate for this. To postpone the exact subsumption we propose to use "molecular process" (MOP:0000543) as parent for now.

term requested by: http://orcid.org/0000-0002-4378-6061

Missing reaction SMARTS

I notice that when I go to this page for the Diels-Alder reaction it has "[C:1]=[C:2][C:3]=[C:4].[C:5]=[C:6]>>[C:1]1[C:2]=[C:3][C:4][C:5][C:6]1" listed as a synonym.

I see that these SMARTS strings (or maybe SMIRKS, I'm very unclear on the difference) were removed from this repo four years ago and wanted to ask why. Were these SMARTS strings not very good representations of the reactions in question?

More duplicate pruning

Many thanks for your recent efforts to obsolete duplicates. Three duplicates remain.
The current rxno.obo file contains identical definitions of CHEBI:29224 and CHEBI:33855.
More serious though is that RXNO:0000596 is used for both Combes quinoline synthesis on line 6407, and for Conrad-Limpach cyclisation on line 6416.

Many thanks in advance,
Roger

Re #wikichem - Protecting groups

Furthur to the discussion on IRC a reminder to consider adding protecting
group information, for example a list of functional groups that will NOT be
affected by a reaction, or even as suggested by Norm a list of protecting
schemes.

Original issue reported on code.google.com by [email protected] on 28 Jul 2009 at 5:13

Term request: Stable-radical-mediated polymerization

Preferred term label

Stable-radical-mediated polymerization

Synonyms or alternative term labels

SRMP; Stable-radical-mediated polymerization

Textual definition

Stable-radical-mediated polymerization (SRMP) or stable-free-radical-mediated polymerization (SFRP) is a special type of controlled radical polymerization or Reversible-deactivation radical polymerisation. In SRMP, radical polymerization is controlled, i.e. the average molecular weight of the resulting polymer is specifically influenced by adding a stable radical to the reaction mixture. 
(https://de.wikipedia.org/wiki/Stable_Free_Radical_Polymerization)

Suggested parent term

Reversible-deactivation radical polymerisation #53

Examples

Attribution

0000-0003-1869-463X

Other comments

import MOP directly into RXNO

At the moment MOP is not directly imported into RXNO but only classes of it are imported.
This can lead to inconsitencies, e.g:

• cycloaddition is for example subsumed under cyclisation in RXNO but not so in MOP.
• there is a conflict between the classes polymerisation (MOP:0000629) & polymerisation reaction (RXNO:0000246) (or their respective subclasses), since both classes express the same chemical reaction type/mechanism but are subsumed under different parent classes ('molecular process' resp. 'carbon-carbon coupling reaction)

In order to maintain MOP and RXNO better, I therefore propose to import MOP directly into RXNO and resolve any conflicting issues.

Term request: Reversible-deactivation radical polymerisation

Preferred term label

Reversible-deactivation polymerisation 

Synonyms or alternative term labels

RDRP; controlled radical polymerization 

Textual definition

the prerequisite of a successful RDRP is fast and reversible activation/deactivation of propagating chains. There are three types of RDRP; namely deactivation by catalyzed reversible coupling, deactivation by spontaneous reversible coupling and deactivation by degenerative transfer (DT) 
(https://en.wikipedia.org/wiki/Reversible-deactivation_radical_polymerization)

Suggested parent term

Chain polymerisation

Examples

Attribution

0000-0003-1869-463X

Other comments

processual entity (BFO_0000007) has been merged with process (BFO_0000015)

There is no 'processual entity' in BFO 2.0 anymore (see also BFO-ontology/BFO#37).

Thus I propose to reflect this change in MOP as well, as this only means to pull up 'process' a level and make it the parent of 'process profile'. Just like it is done in RXNO.

harmonize RXNO object properties with RO

There are object properties (aka relations) reused in RXNO that are defined in BFO. As the OBO community uses the BFO2.0 classes only version these relations are not being resolved via their IRI. In order to be compliant with the OBO principles these relations should thus be replaced by RO equivalents.
The following relations need to be changed in RXNO (individual issues need to be made for each):

• “has dispositions at all times” (BFO_0000162) should be changed to “has disposition” (RO_0000091)
• ‘has participant’ (BFO_0000057) should be changed to ‘has participant’ (RO_0000057)
  • its sup-properties 'has participant beginning to exist' (BFO_0000077) & 'has participant ceasing to exist' (BFO_0000078) should be changed to something suitable in the ‘has participant’ branch of RO, or a term request should be made
    • a possible candidate for 'has participant ceasing to exist' might be "has primary input" (RO_0004009)
    • a possible candidate for 'has participant beginning to exist' might be "has primary output" ([RO_0004008]
    • the remaining relations ('deprotects', 'protects', 'has specified product', 'has specified reactant', 'has_catalyst' and 'has_intermediate' need to be correctly subsumed then as well
• (http://purl.obolibrary.org/obo/RO_0004008))
• “has_part" and "part_of" should be replaced with "ro:has part" (BFO_0000051 ) & "ro:part of" (BFO_0000050)

Migrate this repo to github

https://docs.google.com/document/d/1NfaeHWdZ7BcnaGFfh09X63L4LL7VG_8RNCrLyNdZ8wk/
edit#

Original issue reported on code.google.com by [email protected] on 17 Aug 2015 at 10:54

Add obofoundry topic to repo metadata

The OBO Foundry has recently created a topics page at https://github.com/topics/obofoundry. It would be great if you could add the obofoundry topic to your repository, since it's currently listed as active in the OBO Foundry. If you're not sure how to do that, follow the instructions here. The main issue for this task is at OBOFoundry/OBOFoundry.github.io#1538 in case you want some more context or to join the larger discussion.

FENTON!

RXNO:0000266 has a terminological rather than an ontological definition and 
needs attention.

Original issue reported on code.google.com by [email protected] on 25 Feb 2014 at 11:02

Term request: Living cationic polymerization

Preferred term label

Living cationic polymerization 

Synonyms or alternative term labels

Living cationic polymerization  

Textual definition

Living cationic polymerization is a living polymerization technique involving cationic propagating species.[1][2] It enables the synthesis of very well defined polymers (low molar mass distribution) and of polymers with unusual architecture.
(https://en.wikipedia.org/wiki/Living_cationic_polymerization)

Suggested parent term

Cationic polymerisation AND living polymerisation

Examples

Attribution

0000-0003-1869-463X

Other comments