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Class: SmallMolecule

A small molecule as a chemical entity: a ligand, drug, substrate, cofactor, metal ion, lipid, detergent, sugar or crystallization additive, with its structure and identifiers. The counterpart of Protein and NucleicAcid for everything in a sample that is not a biopolymer. One SmallMolecule record is shared by every Sample that contains it, through SampleComponent. Facts about a particular preparation - how much was added, what it was added for, what it is bound to - stay on SampleComponent and SampleComponentInteraction.

URI: lambda:SmallMolecule

classDiagram class SmallMolecule click SmallMolecule href "../SmallMolecule/" NamedThing <|-- SmallMolecule click NamedThing href "../NamedThing/" SmallMolecule : chebi_id SmallMolecule : chemical_class SmallMolecule --> "0..1" ChemicalClassEnum : chemical_class click ChemicalClassEnum href "../ChemicalClassEnum/" SmallMolecule : cross_references SmallMolecule --> "*" DatabaseCrossReference : cross_references click DatabaseCrossReference href "../DatabaseCrossReference/" SmallMolecule : description SmallMolecule : id SmallMolecule : inchi SmallMolecule : inchikey SmallMolecule : molecular_formula SmallMolecule : molecular_weight_theoretical SmallMolecule --> "0..1" QuantityValue : molecular_weight_theoretical click QuantityValue href "../QuantityValue/" SmallMolecule : pdb_ligand_id SmallMolecule : small_molecule_name SmallMolecule : smiles SmallMolecule : title

Inheritance

Slots

Name Cardinality and Range Description Inheritance
small_molecule_name 0..1 recommended
String		 Name as ChEBI, the depositor or the supplier gives it (e direct
chebi_id 0..1
Uriorcurie		 ChEBI identifier as a CURIE (CHEBI:30616) direct
pdb_ligand_id 0..1
Uriorcurie		 wwPDB Chemical Component Dictionary code as a CURIE (pdb direct
chemical_class 0..1
ChemicalClassEnum		 Broad chemical kind: ion, lipid, detergent, carbohydrate, nucleotide, direct
molecular_formula 0..1
String		 Molecular formula (e direct
smiles 0..1
SmilesString		 SMILES string for the structure direct
inchi 0..1
String		 IUPAC InChI string for the structure direct
inchikey 0..1
String		 InChIKey hash of the InChI, the 27-character form used for exact-structure lo... direct
molecular_weight_theoretical 0..1
QuantityValue		 Mass computed from the formula, typically in daltons direct
cross_references *
DatabaseCrossReference		 Cross-references to databases other than those named by chebi_id and pdb_liga... direct
id 1
Uriorcurie		 Globally unique identifier as an IRI or CURIE for machine processing and exte... NamedThing
title 0..1
String		 A human-readable name or title for this entity NamedThing
description 0..1
String		 A detailed textual description of this entity NamedThing

Usages

used by used in type used
Dataset small_molecules range SmallMolecule
SampleComponent small_molecule_id range SmallMolecule

Comments

  • Use the ChEBI CURIE for the id wherever one exists (CHEBI:30616 for ATP, CHEBI:29105 for zinc(2+)). Where ChEBI has no entry use ChEMBL, PubChem or DrugBank, or the wwPDB Chemical Component Dictionary code (pdb.ligand:ATP), which every ligand in a deposited structure has. Reserve lambda-prefixed ids for compounds with no entry anywhere, such as a hit from an in-house screening library.
  • A peptide is a Protein, however short. A modified nucleotide that is part of a strand is described on the NucleicAcid. A free nucleotide such as ATP, or a free amino acid, is a SmallMolecule.

Identifier and Mapping Information

Valid ID Prefixes

Instances of this class should have identifiers with one of the following prefixes:

  • CHEBI

  • chembl.compound

  • pubchem.compound

  • drugbank

  • pdb.ligand

  • lambda

Schema Source

  • from schema: http://w3id.org/lambda/

Mappings

Mapping Type Mapped Value
self lambda:SmallMolecule
native lambda:SmallMolecule
related mmCIF:_chem_comp, mmCIF:_pdbx_entity_nonpoly

LinkML Source

Direct

name: SmallMolecule
id_prefixes:
- CHEBI
- chembl.compound
- pubchem.compound
- drugbank
- pdb.ligand
- lambda
description: 'A small molecule as a chemical entity: a ligand, drug, substrate, cofactor,
  metal ion, lipid, detergent, sugar or crystallization additive, with its structure
  and identifiers. The counterpart of Protein and NucleicAcid for everything in a
  sample that is not a biopolymer. One SmallMolecule record is shared by every Sample
  that contains it, through SampleComponent. Facts about a particular preparation
  - how much was added, what it was added for, what it is bound to - stay on SampleComponent
  and SampleComponentInteraction.'
comments:
- Use the ChEBI CURIE for the id wherever one exists (CHEBI:30616 for ATP, CHEBI:29105
  for zinc(2+)). Where ChEBI has no entry use ChEMBL, PubChem or DrugBank, or the
  wwPDB Chemical Component Dictionary code (pdb.ligand:ATP), which every ligand in
  a deposited structure has. Reserve lambda-prefixed ids for compounds with no entry
  anywhere, such as a hit from an in-house screening library.
- A peptide is a Protein, however short. A modified nucleotide that is part of a strand
  is described on the NucleicAcid. A free nucleotide such as ATP, or a free amino
  acid, is a SmallMolecule.
from_schema: http://w3id.org/lambda/
related_mappings:
- mmCIF:_chem_comp
- mmCIF:_pdbx_entity_nonpoly
is_a: NamedThing
attributes:
  small_molecule_name:
    name: small_molecule_name
    description: Name as ChEBI, the depositor or the supplier gives it (e.g., 'ATP',
      'heme b', 'n-dodecyl beta-D-maltoside'). Recommended, not required, so that
      a record seeded from an identifier alone can be enriched later.
    from_schema: http://w3id.org/lambda/
    exact_mappings:
    - mmCIF:_chem_comp.name
    rank: 1000
    domain_of:
    - SmallMolecule
    recommended: true
  chebi_id:
    name: chebi_id
    description: ChEBI identifier as a CURIE (CHEBI:30616). Normally identical to
      id.
    from_schema: http://w3id.org/lambda/
    rank: 1000
    domain_of:
    - SmallMolecule
    range: uriorcurie
    pattern: ^CHEBI:[0-9]+$
  pdb_ligand_id:
    name: pdb_ligand_id
    description: wwPDB Chemical Component Dictionary code as a CURIE (pdb.ligand:ATP,
      pdb.ligand:HEM, pdb.ligand:ZN). Every ligand in a deposited structure has one,
      so it is the join key between a sample's components and the ligands of the structure
      it produced.
    from_schema: http://w3id.org/lambda/
    exact_mappings:
    - mmCIF:_chem_comp.id
    rank: 1000
    domain_of:
    - SmallMolecule
    range: uriorcurie
    pattern: ^pdb\.ligand:[A-Z0-9]{1,5}$
  chemical_class:
    name: chemical_class
    description: 'Broad chemical kind: ion, lipid, detergent, carbohydrate, nucleotide,
      ...'
    from_schema: http://w3id.org/lambda/
    rank: 1000
    domain_of:
    - SmallMolecule
    range: ChemicalClassEnum
  molecular_formula:
    name: molecular_formula
    description: Molecular formula (e.g., C10H16N5O13P3 for ATP)
    from_schema: http://w3id.org/lambda/
    exact_mappings:
    - mmCIF:_chem_comp.formula
    rank: 1000
    domain_of:
    - SmallMolecule
  smiles:
    name: smiles
    description: SMILES string for the structure
    from_schema: http://w3id.org/lambda/
    rank: 1000
    domain_of:
    - SmallMolecule
    range: smiles_string
  inchi:
    name: inchi
    description: IUPAC InChI string for the structure
    from_schema: http://w3id.org/lambda/
    rank: 1000
    domain_of:
    - SmallMolecule
    pattern: ^InChI=1S?/
  inchikey:
    name: inchikey
    description: InChIKey hash of the InChI, the 27-character form used for exact-structure
      lookup
    from_schema: http://w3id.org/lambda/
    rank: 1000
    domain_of:
    - SmallMolecule
    pattern: ^[A-Z]{14}-[A-Z]{10}-[A-Z]$
  molecular_weight_theoretical:
    name: molecular_weight_theoretical
    description: Mass computed from the formula, typically in daltons
    from_schema: http://w3id.org/lambda/
    exact_mappings:
    - mmCIF:_chem_comp.formula_weight
    domain_of:
    - Protein
    - NucleicAcid
    - SmallMolecule
    range: QuantityValue
    inlined: true
  cross_references:
    name: cross_references
    description: Cross-references to databases other than those named by chebi_id
      and pdb_ligand_id (ChEMBL, PubChem, DrugBank, KEGG, ...).
    from_schema: http://w3id.org/lambda/
    domain_of:
    - Protein
    - NucleicAcid
    - SmallMolecule
    - AggregatedProteinView
    range: DatabaseCrossReference
    multivalued: true
    inlined: true
    inlined_as_list: true

Induced

name: SmallMolecule
id_prefixes:
- CHEBI
- chembl.compound
- pubchem.compound
- drugbank
- pdb.ligand
- lambda
description: 'A small molecule as a chemical entity: a ligand, drug, substrate, cofactor,
  metal ion, lipid, detergent, sugar or crystallization additive, with its structure
  and identifiers. The counterpart of Protein and NucleicAcid for everything in a
  sample that is not a biopolymer. One SmallMolecule record is shared by every Sample
  that contains it, through SampleComponent. Facts about a particular preparation
  - how much was added, what it was added for, what it is bound to - stay on SampleComponent
  and SampleComponentInteraction.'
comments:
- Use the ChEBI CURIE for the id wherever one exists (CHEBI:30616 for ATP, CHEBI:29105
  for zinc(2+)). Where ChEBI has no entry use ChEMBL, PubChem or DrugBank, or the
  wwPDB Chemical Component Dictionary code (pdb.ligand:ATP), which every ligand in
  a deposited structure has. Reserve lambda-prefixed ids for compounds with no entry
  anywhere, such as a hit from an in-house screening library.
- A peptide is a Protein, however short. A modified nucleotide that is part of a strand
  is described on the NucleicAcid. A free nucleotide such as ATP, or a free amino
  acid, is a SmallMolecule.
from_schema: http://w3id.org/lambda/
related_mappings:
- mmCIF:_chem_comp
- mmCIF:_pdbx_entity_nonpoly
is_a: NamedThing
attributes:
  small_molecule_name:
    name: small_molecule_name
    description: Name as ChEBI, the depositor or the supplier gives it (e.g., 'ATP',
      'heme b', 'n-dodecyl beta-D-maltoside'). Recommended, not required, so that
      a record seeded from an identifier alone can be enriched later.
    from_schema: http://w3id.org/lambda/
    exact_mappings:
    - mmCIF:_chem_comp.name
    rank: 1000
    alias: small_molecule_name
    owner: SmallMolecule
    domain_of:
    - SmallMolecule
    range: string
    recommended: true
  chebi_id:
    name: chebi_id
    description: ChEBI identifier as a CURIE (CHEBI:30616). Normally identical to
      id.
    from_schema: http://w3id.org/lambda/
    rank: 1000
    alias: chebi_id
    owner: SmallMolecule
    domain_of:
    - SmallMolecule
    range: uriorcurie
    pattern: ^CHEBI:[0-9]+$
  pdb_ligand_id:
    name: pdb_ligand_id
    description: wwPDB Chemical Component Dictionary code as a CURIE (pdb.ligand:ATP,
      pdb.ligand:HEM, pdb.ligand:ZN). Every ligand in a deposited structure has one,
      so it is the join key between a sample's components and the ligands of the structure
      it produced.
    from_schema: http://w3id.org/lambda/
    exact_mappings:
    - mmCIF:_chem_comp.id
    rank: 1000
    alias: pdb_ligand_id
    owner: SmallMolecule
    domain_of:
    - SmallMolecule
    range: uriorcurie
    pattern: ^pdb\.ligand:[A-Z0-9]{1,5}$
  chemical_class:
    name: chemical_class
    description: 'Broad chemical kind: ion, lipid, detergent, carbohydrate, nucleotide,
      ...'
    from_schema: http://w3id.org/lambda/
    rank: 1000
    alias: chemical_class
    owner: SmallMolecule
    domain_of:
    - SmallMolecule
    range: ChemicalClassEnum
  molecular_formula:
    name: molecular_formula
    description: Molecular formula (e.g., C10H16N5O13P3 for ATP)
    from_schema: http://w3id.org/lambda/
    exact_mappings:
    - mmCIF:_chem_comp.formula
    rank: 1000
    alias: molecular_formula
    owner: SmallMolecule
    domain_of:
    - SmallMolecule
    range: string
  smiles:
    name: smiles
    description: SMILES string for the structure
    from_schema: http://w3id.org/lambda/
    rank: 1000
    alias: smiles
    owner: SmallMolecule
    domain_of:
    - SmallMolecule
    range: smiles_string
  inchi:
    name: inchi
    description: IUPAC InChI string for the structure
    from_schema: http://w3id.org/lambda/
    rank: 1000
    alias: inchi
    owner: SmallMolecule
    domain_of:
    - SmallMolecule
    range: string
    pattern: ^InChI=1S?/
  inchikey:
    name: inchikey
    description: InChIKey hash of the InChI, the 27-character form used for exact-structure
      lookup
    from_schema: http://w3id.org/lambda/
    rank: 1000
    alias: inchikey
    owner: SmallMolecule
    domain_of:
    - SmallMolecule
    range: string
    pattern: ^[A-Z]{14}-[A-Z]{10}-[A-Z]$
  molecular_weight_theoretical:
    name: molecular_weight_theoretical
    description: Mass computed from the formula, typically in daltons
    from_schema: http://w3id.org/lambda/
    exact_mappings:
    - mmCIF:_chem_comp.formula_weight
    alias: molecular_weight_theoretical
    owner: SmallMolecule
    domain_of:
    - Protein
    - NucleicAcid
    - SmallMolecule
    range: QuantityValue
    inlined: true
  cross_references:
    name: cross_references
    description: Cross-references to databases other than those named by chebi_id
      and pdb_ligand_id (ChEMBL, PubChem, DrugBank, KEGG, ...).
    from_schema: http://w3id.org/lambda/
    alias: cross_references
    owner: SmallMolecule
    domain_of:
    - Protein
    - NucleicAcid
    - SmallMolecule
    - AggregatedProteinView
    range: DatabaseCrossReference
    multivalued: true
    inlined: true
    inlined_as_list: true
  id:
    name: id
    description: Globally unique identifier as an IRI or CURIE for machine processing
      and external references. Used for linking data across systems and semantic web
      integration.
    from_schema: http://w3id.org/lambda/
    rank: 1000
    identifier: true
    alias: id
    owner: SmallMolecule
    domain_of:
    - NamedThing
    - Attribute
    range: uriorcurie
    required: true
  title:
    name: title
    description: A human-readable name or title for this entity
    from_schema: http://w3id.org/lambda/
    rank: 1000
    slot_uri: dcterms:title
    alias: title
    owner: SmallMolecule
    domain_of:
    - NamedThing
    range: string
  description:
    name: description
    description: A detailed textual description of this entity
    from_schema: http://w3id.org/lambda/
    rank: 1000
    alias: description
    owner: SmallMolecule
    domain_of:
    - NamedThing
    - AttributeGroup
    - SampleComponentInteraction
    range: string