CHEMROF: Chemical Entities Mixtures Reactions Ontological Framework

This project provides a LinkML schema/datamodel to represent chemical entities and other related entities.

It also includes as a proof of concept:

small database of entities conforming to the model
a translation of this database to an ontology (OWL TBox)

Core Datamodel

Some example classes and their instances:

Atoms:
- Elements: nickel atom, carbon atom, ...
- Monoatomic Ions: copper(2+), ...
- Isotopes: carbon-14, carbon-12, ...
- Fully Specified Atoms: Helium-4(2+), ...
Molecules:
- Enantiomers: L-serine
- Racemic Mixtures: thalidomide, ...

Note that in a chemical ontology like CHEBI, concepts such as "nickel atom" are treated as classes. In this primary chemrof representation, they are instances, but can be later translated to OWL classes.

Schema

The schema and overall framework uses LinkML

Browse the schema here: http://chemkg.github.io/chemrof
See the yaml source in the src/schema directory

Schema Organization

The main division is between:

ChemicalEntity - essentially things you can write a formula/inchi for, and
GroupingClass - generalizations/sets of chemical entities

This distinction may be hard to grasp if you are coming from an OBO realist ontologist philosophical perspective, but this in fact allows us to serve a much wider variety of use cases than a strict OBO-style approach. At the same time we can generate an OBO-style ontology from this representation

Example

Enantiomers are mirror-image stereoisomers.

The Enantiomer class represents a chemical entity that has a form (e.g L/D) specified.

Racemic mixtures are compounds with equal amounts left and right-handed enantiomers.

SchemaExample Data (Turtle)Example Data (YAML)

racemic mixture:
  aliases:
    - racemate
    - racemic mixture of enantiomers
  is_a: precise chemical mixture
  description: >-
    a chemical compound that has equal amounts of left- and right-handed enantiomers of a chiral molecule. An example is Thalidomide
  slot_usage:
    has left enantiomer:
      required: true
      range: enantiomer
    has right enantiomer:
      required: true
      range: enantiomer
    chirality agnostic form:
      recommended: true
      required: false
      range: molecule
    IUPAC name:
      pattern: "^rac-"
  defining_slots:
    - has left enantiomer
    - has right enantiomer
  exact_mappings:
    - CHEBI:60911
    - NCIT:C103198
    - wdeschema:E47
    - wd:Q467717
    - goldbook:R05025
  see_also:
    - https://github.com/ebi-chebi/ChEBI/issues/3245

ChemicalEntity:InChI%3D1S%2FC13H10N2O4%2Fc16-10-6-5-9%2811%2817%2914-10%2915-12%2818%297-3-1-2-4-8%287%2913%2815%2919%2Fh1-4%2C9H%2C5-6H2%2C%28H%2C14%2C16%2C17%29%2Fs3
        a chem:RacemicMixture ;
        rdfs:label "thalidomide" ;
        chem:chebi_iri obo:CHEBI_9513 ;
        chem:chirality_agnostic_form ChemicalEntity:InChI%3D1S%2FC13H10N2O4%2Fc16-10-6-5-9%2811%2817%2914-10%2915-12%2818%297-3-1-2-4-8%287%2913%2815%2919%2Fh1-4%2C9H%2C5-6H2%2C%28H%2C14%2C16%2C17%29 ;
        chem:has_left_enantiomer ChemicalEntity:InChI%3D1S%2FC13H10N2O4%2Fc16-10-6-5-9%2811%2817%2914-10%2915-12%2818%297-3-1-2-4-8%287%2913%2815%2919%2Fh1-4%2C9H%2C5-6H2%2C%28H%2C14%2C16%2C17%29%2Ft9-%2Fm0%2Fs1 ;
        chem:has_right_enantiomer ChemicalEntity:InChI%3D1S%2FC13H10N2O4%2Fc16-10-6-5-9%2811%2817%2914-10%2915-12%2818%297-3-1-2-4-8%287%2913%2815%2919%2Fh1-4%2C9H%2C5-6H2%2C%28H%2C14%2C16%2C17%29%2Ft9-%2Fm1%2Fs1 .

```yaml id: "ChemicalEntity:InChI%3D1S%2FC13H10N2O4%2Fc16-10-6-5-9%2811%2817%2914-10%2915-12%2818%297-3-1-2-4-8%287%2913%2815%2919%2Fh1-4%2C9H%2C5-6H2%2C%28H%2C14%2C16%2C17%29%2Fs3" type: "RacemicMixture" label: "thalidomide" chebi_iri: "CHEBI:9513" chirality_agnostic_form: "ChemicalEntity:InChI%3D1S%2FC13H10N2O4%2Fc16-10-6-5-9%2811%2817%2914-10%2915-12%2818%297-3-1-2-4-8%287%2913%2815%2919%2Fh1-4%2C9H%2C5-6H2%2C%28H%2C14%2C16%2C17%29" has_left_enantiomer: "ChemicalEntity:InChI%3D1S%2FC13H10N2O4%2Fc16-10-6-5-9%2811%2817%2914-10%2915-12%2818%297-3-1-2-4-8%287%2913%2815%2919%2Fh1-4%2C9H%2C5-6H2%2C%28H%2C14%2C16%2C17%29%2Ft9-%2Fm0%2Fs1" has_right_enantiomer: "ChemicalEntity:InChI%3D1S%2FC13H10N2O4%2Fc16-10-6-5-9%2811%2817%2914-10%2915-12%2818%297-3-1-2-4-8%287%291

``````

OWL (TBox)

<owl:Class rdf:about="https://w3id.org/chemrof/ChemicalEntity/InChI%3D1S%2FC13H10N2O4%2Fc16-10-6-5-9%2811%2817%2914-10%2915-12%2818%297-3-1-2-4-8%287%2913%2815%2919%2Fh1-4%2C9H%2C5-6H2%2C%28H%2C14%2C16%2C17%29%2Fs3">
    <owl:equivalentClass>
        <owl:Class>
            <owl:intersectionOf rdf:parseType="Collection">
                <rdf:Description rdf:about="https://w3id.org/chemrof/RacemicMixture"/>
                <owl:Restriction>
                    <owl:onProperty rdf:resource="https://w3id.org/chemrof/chirality_agnostic_form"/>
                    <owl:someValuesFrom rdf:resource="https://w3id.org/chemrof/ChemicalEntity/InChI%3D1S%2FC13H10N2O4%2Fc16-10-6-5-9%2811%2817%2914-10%2915-12%2818%297-3-1-2-4-8%287%2913%2815%2919%2Fh1-4%2C9H%2C5-6H2%2C%28H%2C14%2C16%2C17%29"/>
                </owl:Restriction>
            </owl:intersectionOf>
        </owl:Class>
    </owl:equivalentClass>
    <owl:equivalentClass>
        <owl:Class>
            <owl:intersectionOf rdf:parseType="Collection">
                <rdf:Description rdf:about="https://w3id.org/chemrof/RacemicMixture"/>
                <owl:Restriction>
                    <owl:onProperty rdf:resource="https://w3id.org/chemrof/has_left_enantiomer"/>
                    <owl:someValuesFrom rdf:resource="https://w3id.org/chemrof/ChemicalEntity/InChI%3D1S%2FC13H10N2O4%2Fc16-10-6-5-9%2811%2817%2914-10%2915-12%2818%297-3-1-2-4-8%287%2913%2815%2919%2Fh1-4%2C9H%2C5-6H2%2C%28H%2C14%2C16%2C17%29%2Ft9-%2Fm0%2Fs1"/>
                </owl:Restriction>
                <owl:Restriction>
                    <owl:onProperty rdf:resource="https://w3id.org/chemrof/has_right_enantiomer"/>
                    <owl:someValuesFrom rdf:resource="https://w3id.org/chemrof/ChemicalEntity/InChI%3D1S%2FC13H10N2O4%2Fc16-10-6-5-9%2811%2817%2914-10%2915-12%2818%297-3-1-2-4-8%287%2913%2815%2919%2Fh1-4%2C9H%2C5-6H2%2C%28H%2C14%2C16%2C17%29%2Ft9-%2Fm1%2Fs1"/>
                </owl:Restriction>
            </owl:intersectionOf>
        </owl:Class>
    </owl:equivalentClass>
    <rdfs:subClassOf rdf:resource="https://w3id.org/chemrof/RacemicMixture"/>
    <rdfs:label>thalidomide</rdfs:label>
</owl:Class>

Note that a class "Enantiomer" does not really make sense at an OBO level where all chemical entities are classes; it is a metaclass.

Mappings

SSSOM

Example mappings:

subject_id	subject_label	predicate_id	object_id	match_type	subject_source
chemrof:bond_type_enum#covalent	covalent	skos:exactMatch	gc:NormalBond	skos:exactMatch	https://w3id.org/chemrof
chemrof:bond_type_enum#aromatic	aromatic	skos:exactMatch	gc:AromaticBond	skos:exactMatch	https://w3id.org/chemrof
chemrof:element_metallic_classification#Metallic	Metallic	skos:exactMatch	damlpt:Metallic	skos:exactMatch	https://w3id.org/chemrof
chemrof:nanostructure_morphology_enum#nanotube	nanotube	skos:exactMatch	CHEBI:50796	skos:exactMatch	https://w3id.org/chemrof
chemrof:periodic_table_block_enum#s-block	s-block	skos:exactMatch	CHEBI:33674	skos:exactMatch	https://w3id.org/chemrof
chemrof:Enantiomer	enantiomer	skos:exactMatch	SIO:010777	skos:exactMatch	https://w3id.org/chemrof

Derived artefacts

Currently the main derived artefacts of interest are:

With care, you also see:

OWL -- note this should be read as a meta-ontology by OBO people

Comparison with CHEBI and Wikidata

TODO