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ChemicalTerm

An ontology term representing a chemical or molecule

classDiagram OntologyTerm <|-- ChemicalTerm ChemicalTerm : ancestors ChemicalTerm : child_count ChemicalTerm : created_by ChemicalTerm : cross_references ChemicalTerm : curie ChemicalTerm : date_created ChemicalTerm : date_updated ChemicalTerm : db_date_created ChemicalTerm : db_date_updated ChemicalTerm : dbkey ChemicalTerm : definition ChemicalTerm : definition_urls ChemicalTerm : descendant_count ChemicalTerm : descendants ChemicalTerm : formula ChemicalTerm : inchi ChemicalTerm : inchi_key ChemicalTerm : internal ChemicalTerm : iupac ChemicalTerm : name ChemicalTerm : namespace ChemicalTerm : obsolete ChemicalTerm : secondary_identifiers ChemicalTerm : smiles ChemicalTerm : subsets ChemicalTerm : synonyms ChemicalTerm : type ChemicalTerm : updated_by

URI: alliance:ChemicalTerm

Parent Classes

Children

Slots

Name Description
ancestors The ancestors of this term in the ontology, including the term itself. This language works well for the majority of use cases, however for a relationship like "develops_from", ancestors are the terms from which this term develops (not a true parent/child or ancestor/descendant relationship).
child_count None
created_by The individual that created the entity.
cross_references Holds between an object and its CrossReferences.
curie A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI
date_created The date on which an entity was created. This can be applied to nodes or edges.
date_updated Date on which an entity was last modified.
db_date_created The date on which an entity was created in the Alliance database. This is distinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).
db_date_updated Date on which an entity was last modified in the Alliance database. This is distinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.
dbkey Typically the primary key on the table. Should be a global sequence in the database to insure uniqueness over the entire suite of tables. Alternatively, could be a serial8 identifier. Tables with a dbkey should have an alternate key to establish uniqueness based on the data in the table.
definition The definition of the ontology term. This is a reference to an object that holds the text description of the term and a collection of URLs that further define the term.
definition_urls None
descendant_count None
descendants The descendants of this term in the ontology, including the term itself. This language works well for the majority of use cases, however for a relationship like "develops_from", ancestors are the terms to which this term develops into (not a true parent/child or ancestor/descendant relationship).
formula Formula of the molecule
inchi InChi style description of the molecule
inchi_key InChi key description of the molecule
internal Classifies the entity as private (for internal use) or not (for public use).
iupac IUPAC name of the molecule
name a human-readable name for an entity
namespace the namespace of the ontology.
obsolete Entity is no longer current.
secondary_identifiers None
smiles Molecular structure in SMILES format
subsets None
synonyms A generic free-text field for objects that only have string representation of one or more synonyms and do not require meta data or attribution; if meta data or attribution are required to be captured for individual synonyms, consider the NameSlotAnnotation class
type None
updated_by The individual that last modified the entity.

Mappings

Mapping Type Mapped Value
self ['alliance:ChemicalTerm']
native ['alliance:ChemicalTerm']

LinkML Specification

Direct

name: ChemicalTerm
description: An ontology term representing a chemical or molecule
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: OntologyTerm
abstract: true
slots:
- inchi
- inchi_key
- iupac
- formula
- smiles

Induced

name: ChemicalTerm
description: An ontology term representing a chemical or molecule
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: OntologyTerm
abstract: true
attributes:
  inchi:
    name: inchi
    description: InChi style description of the molecule
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: Molecule
    alias: inchi
    owner: ChemicalTerm
    domain_of:
    - ChemicalTerm
    range: string
  inchi_key:
    name: inchi_key
    description: InChi key description of the molecule
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: Molecule
    alias: inchi_key
    owner: ChemicalTerm
    domain_of:
    - ChemicalTerm
    range: string
  iupac:
    name: iupac
    description: IUPAC name of the molecule
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: Molecule
    alias: iupac
    owner: ChemicalTerm
    domain_of:
    - ChemicalTerm
    range: string
  formula:
    name: formula
    description: Formula of the molecule
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: Molecule
    alias: formula
    owner: ChemicalTerm
    domain_of:
    - ChemicalTerm
    range: string
  smiles:
    name: smiles
    description: Molecular structure in SMILES format
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: Molecule
    alias: smiles
    owner: ChemicalTerm
    domain_of:
    - ChemicalTerm
    range: string
  curie:
    name: curie
    description: A unique identifier for a thing. Must be either a CURIE shorthand
      for a URI or a complete URI
    from_schema: https://github.com/alliance-genome/agr_curation_schema/core.yaml
    multivalued: false
    identifier: true
    alias: curie
    owner: ChemicalTerm
    domain_of:
    - CurieObject
    - Identifier
    - OntologyTerm
    - Laboratory
    - Annotation
    - ExternalDataBaseEntityDTO
    - GeneNomenclatureSet
    range: uriorcurie
    required: true
  dbkey:
    name: dbkey
    description: Typically the primary key on the table.  Should be a global sequence
      in the database to insure uniqueness over the entire suite of tables.  Alternatively,
      could be a serial8 identifier. Tables with a dbkey should have an alternate
      key to establish uniqueness based on the data in the table.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: dbkey
    owner: ChemicalTerm
    domain_of:
    - ExternalDatabaseLink
    - OntologyTerm
    range: string
  name:
    name: name
    description: a human-readable name for an entity
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: false
    alias: name
    owner: ChemicalTerm
    domain_of:
    - SequenceTargetingReagent
    - SequenceTargetingReagentDTO
    - Antibody
    - AntibodyDTO
    - Transcript
    - TranscriptDTO
    - Exon
    - ExonDTO
    - CodingSequence
    - CodingSequenceDTO
    - Chromosome
    - ChromosomeDTO
    - AssemblyComponent
    - AssemblyComponentDTO
    - Protein
    - ProteinDTO
    - AffectedGenomicModel
    - AffectedGenomicModelDTO
    - ResourceDescriptor
    - ResourceDescriptorPage
    - VocabularyTerm
    - Vocabulary
    - VocabularyTermSet
    - OntologyTerm
    - HTPExpressionDatasetAnnotation
    - HTPExpressionDatasetAnnotationDTO
    - CurationReportGroup
    - CurationReport
    - BulkLoadGroup
    - BulkLoad
    range: string
  definition:
    name: definition
    description: The definition of the ontology term. This is a reference to an object
      that holds the text description of the term and a collection of URLs that further
      define the term.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: definition
    owner: ChemicalTerm
    domain_of:
    - VocabularyTerm
    - OntologyTerm
    range: string
  definition_urls:
    name: definition_urls
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: true
    alias: definition_urls
    owner: ChemicalTerm
    domain_of:
    - OntologyTerm
    range: string
  type:
    name: type
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: type
    owner: ChemicalTerm
    domain_of:
    - OntologyTerm
    range: uriorcurie
  cross_references:
    name: cross_references
    description: Holds between an object and its CrossReferences.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    aliases:
    - xrefs
    singular_name: cross_reference
    multivalued: true
    alias: cross_references
    owner: ChemicalTerm
    domain_of:
    - Antibody
    - AuthorReference
    - GenomicEntity
    - GenomeAssembly
    - OntologyTerm
    - ExternalDataBaseEntity
    - GeneInteraction
    range: CrossReference
  synonyms:
    name: synonyms
    description: A generic free-text field for objects that only have string representation
      of one or more synonyms and do not require meta data or attribution; if meta
      data or attribution are required to be captured for individual synonyms, consider
      the NameSlotAnnotation class
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: true
    alias: synonyms
    owner: ChemicalTerm
    domain_of:
    - SequenceTargetingReagent
    - SequenceTargetingReagentDTO
    - ResourceDescriptor
    - VocabularyTerm
    - OntologyTerm
    - Resource
    - GeneNomenclatureSet
    range: string
    required: false
  namespace:
    name: namespace
    description: the namespace of the ontology.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: namespace
    owner: ChemicalTerm
    domain_of:
    - OntologyTerm
    range: string
  subsets:
    name: subsets
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: true
    alias: subsets
    owner: ChemicalTerm
    domain_of:
    - OntologyTerm
    range: string
  secondary_identifiers:
    name: secondary_identifiers
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    aliases:
    - secondary_ids
    multivalued: true
    alias: secondary_identifiers
    owner: ChemicalTerm
    domain_of:
    - SequenceTargetingReagent
    - SequenceTargetingReagentDTO
    - Reagent
    - ReagentDTO
    - OntologyTerm
    - Figure
    - Image
    - ExternalDataBaseEntity
    - ExternalDataBaseEntityDTO
    range: uriorcurie
  ancestors:
    name: ancestors
    description: The ancestors of this term in the ontology, including the term itself.
      This language works well for the majority of use cases, however for a relationship
      like "develops_from", ancestors are the terms from which this term develops
      (not a true parent/child or ancestor/descendant relationship).
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: true
    alias: ancestors
    owner: ChemicalTerm
    domain_of:
    - OntologyTerm
    range: OntologyTermClosure
  descendants:
    name: descendants
    description: The descendants of this term in the ontology, including the term
      itself. This language works well for the majority of use cases, however for
      a relationship like "develops_from", ancestors are the terms to which this term
      develops into (not a true parent/child or ancestor/descendant relationship).
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: true
    alias: descendants
    owner: ChemicalTerm
    domain_of:
    - OntologyTerm
    range: OntologyTermClosure
  child_count:
    name: child_count
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: child_count
    owner: ChemicalTerm
    domain_of:
    - OntologyTerm
    range: integer
  descendant_count:
    name: descendant_count
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: descendant_count
    owner: ChemicalTerm
    domain_of:
    - OntologyTerm
    range: integer
  created_by:
    name: created_by
    description: The individual that created the entity.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: AuditedObject
    multivalued: false
    alias: created_by
    owner: ChemicalTerm
    domain_of:
    - AuditedObject
    range: Person
  date_created:
    name: date_created
    description: The date on which an entity was created. This can be applied to nodes
      or edges.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    aliases:
    - creation_date
    exact_mappings:
    - dct:createdOn
    - WIKIDATA_PROPERTY:P577
    alias: date_created
    owner: ChemicalTerm
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: datetime
  updated_by:
    name: updated_by
    description: The individual that last modified the entity.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: AuditedObject
    multivalued: false
    alias: updated_by
    owner: ChemicalTerm
    domain_of:
    - AuditedObject
    range: Person
  date_updated:
    name: date_updated
    description: Date on which an entity was last modified.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    aliases:
    - date_last_modified
    alias: date_updated
    owner: ChemicalTerm
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: datetime
  db_date_created:
    name: db_date_created
    description: The date on which an entity was created in the Alliance database.  This
      is distinct from date_created, which represents the date when the entity was
      originally created (i.e. at the MOD for imported data).
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: db_date_created
    owner: ChemicalTerm
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: datetime
  db_date_updated:
    name: db_date_updated
    description: Date on which an entity was last modified in the Alliance database.  This
      is distinct from date_updated, which represents the date when the entity was
      last modified and may predate import into the Alliance database.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: db_date_updated
    owner: ChemicalTerm
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: datetime
  internal:
    name: internal
    description: Classifies the entity as private (for internal use) or not (for public
      use).
    notes:
    - Default value is true.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: internal
    owner: ChemicalTerm
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: boolean
    required: true
  obsolete:
    name: obsolete
    description: Entity is no longer current.
    notes:
    - Obsolete entities are preserved in the database for posterity but should not
      be publicly displayed.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: obsolete
    owner: ChemicalTerm
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: boolean