UniProt RDF schema ontology
type: Ontology
comment: Properties and classes used for protein annotation.
imports: core
imports: http://xmlns.com/foaf/0.1/
imports: faldo
imports: 22-rdf-syntax-ns
imports: rdf-schema
description: The UniProt RDF schema ontology contains predicates used to describe UniProt entries and associated data.
license: http://creativecommons.org/licenses/by/4.0/
version info: 2022_04

catalytic activity
type: ObjectProperty
comment: The catalytic activity of an enzyme.
domain: Enzyme
range: Catalytic Activity

alternativeName
type: ObjectProperty
comment: A synonym of the recommended name.
range: Structured_Name
sub property of: structured name
domain: Class
  union of: Protein part
  union of: Protein

annotation
type: ObjectProperty
comment: Attaches an annotation to a resource.
range: Annotation
domain: Protein

attribution
type: ObjectProperty
range: Attribution
domain: Class
  union of: Protein
  union of: Statement

based on
type: ObjectProperty
type: FunctionalProperty
comment: The sequence on which the description of a modified sequence is based.
domain: Modified Sequence
range: Simple Sequence

catalytic activity
type: ObjectProperty
domain: Catalytic Activity Annotation
range: Catalytic Activity

catalyzed physiological reaction
type: ObjectProperty
domain: Catalytic Activity Annotation

catalyzed reaction
type: ObjectProperty
type: FunctionalProperty
domain: Catalytic Activity

category
type: ObjectProperty
domain: Database (description of)

cellular component
type: ObjectProperty
range: Cellular Component
domain: Class
  intersection of: Restriction
    on property: cellular component
    on class: Cellular Component
    qualified cardinality: 1
  intersection of: Restriction
    on property: orientation
    on class: Orientation
    max qualified cardinality: 1
  intersection of: Restriction
    on property: topology
    on class: Topology
    max qualified cardinality: 1

chainSequenceMapping
type: ObjectProperty
comment: A mapping between a Sequence/Entry and aminoacids described in a PDB record.
domain: Protein

citation
type: ObjectProperty
comment: A publication from which data was extracted, or which contains additional information.
range: Citation
domain: Class
  union of: Cellular Component
  union of: Database (description of)
  union of: External Sequence
  union of: Nucleotide Resource
  union of: Orientation
  union of: Protein
  union of: Topology

classified with
type: ObjectProperty
comment: A concept that classifies this resource.
range: Concept
domain: Protein

cofactor
type: ObjectProperty
domain: Cofactor

common name
type: ObjectProperty
type: FunctionalProperty
domain: Taxon
sub property of: name

common taxon
type: ObjectProperty
type: FunctionalProperty
domain: Cluster (UniRef)
range: Taxon

proteome component
type: ObjectProperty
comment: A component of a protein.
range: Protein part
domain: Protein
sub property of: part

conflicting sequence
type: ObjectProperty
range: External Sequence
domain: Class
  union of: Protein
  union of: Sequence Caution
  union of: Sequence Conflict

context
type: ObjectProperty
domain: Citation Statement

database
type: ObjectProperty
type: FunctionalProperty
range: Database (description of)
domain: Resource

disease
type: ObjectProperty
range: Disease
domain: Disease Annotation

domain
type: ObjectProperty
comment: A domain of a protein.
range: Protein part
domain: Protein
sub property of: part

encoded by
type: ObjectProperty
comment: The gene by which a protein is encoded.
range: Gene
domain: Protein

encoded in
type: ObjectProperty
comment: The subcellular location where a protein is encoded.
domain: Protein
range: Subcellular Location

enzyme
type: ObjectProperty
comment: The catalytic activity associated with a protein. or part of a protein.
range: Enzyme
domain: Class
  union of: Protein part
  union of: Protein

enzyme class
type: ObjectProperty
domain: Catalytic Activity
range: Enzyme

erratum
type: ObjectProperty
comment: An erratum for a publication.
range: Published Citation
domain: Published Citation
inverse of: erratum for

erratum for
type: ObjectProperty
comment: The publication which an erratum refers to.
range: Published Citation
domain: Published Citation

existence
type: ObjectProperty
domain: Protein

host
type: ObjectProperty
domain: Taxon
range: Taxon

interaction
type: ObjectProperty
range: Interaction
domain: Protein

isolatedFrom
type: ObjectProperty
domain: Protein
range: Tissue

ligand
type: ObjectProperty
domain: Binding Site

ligand part
type: ObjectProperty
domain: Binding Site

located in
type: ObjectProperty
domain: Subcellular Location Annotation
range: Class
  intersection of: Restriction
    on property: cellular component
    on class: Cellular Component
    qualified cardinality: 1
  intersection of: Restriction
    on property: orientation
    on class: Orientation
    max qualified cardinality: 1
  intersection of: Restriction
    on property: topology
    on class: Topology
    max qualified cardinality: 1

located on
type: ObjectProperty
comment: The molecule a this resource is located on.
range: Molecule
domain: Nucleotide Resource

locus name
type: ObjectProperty
domain: Gene
sub property of: name

mapped annotation
type: ObjectProperty
comment: Maps annotation to a resource. Used to link annotations/comments from external non UniProt sources via Citations to UniProt resources.
range: Annotation
domain: Class
  union of: Citation Statement
  union of: Protein

mapped citation
type: ObjectProperty
comment: A publication from which data was by a extracted by a mapping from non UniProt origin, or which contains additional information.
range: Citation
domain: Protein

member
type: ObjectProperty
comment: One of several similar resources.
domain: Cluster (UniRef)
range: Sequence
inverse of: member of

member of
type: ObjectProperty
range: Cluster (UniRef)
domain: Sequence

method
type: ObjectProperty
comment: The experimental method that was used.
range: Method
domain: Class
  union of: Mass
  union of: Structure Resource

modification
type: ObjectProperty
comment: A modification of a sequence.
range: Splice Variant
domain: Modified Sequence

nucleotideSequenceMappingIssue
type: ObjectProperty
comment: When a CDS differs substantially from a reviewed UniProtKB/Swiss-Prot sequence, the UniProt curators indicate the nature of the difference in the corresponding cross-reference.
range: Nucleotide Resource
domain: Reviewed protein (records)

organism
type: ObjectProperty
comment: The organism in which a protein occurs.
range: Taxon
domain: Class
  union of: Protein
  union of: Sequence

orientation
type: ObjectProperty
range: Orientation
domain: Class
  intersection of: Restriction
    on property: cellular component
    on class: Cellular Component
    qualified cardinality: 1
  intersection of: Restriction
    on property: orientation
    on class: Orientation
    max qualified cardinality: 1
  intersection of: Restriction
    on property: topology
    on class: Topology
    max qualified cardinality: 1

panproteome
type: ObjectProperty
comment: The current pan proteome sequences are derived from the reference proteome clusters (75% proteome similarity for Fungus and 55% proteome similarity for Archaea and Bacteria). A reference proteome cluster is also known as a representative proteome group (RPG) (Chen et al., 2011). A RPG contains similar proteomes calculated based on their co-membership in UniRef50 clusters. For each non-singleton reference proteome cluster, a pan proteome is a set of sequences consisting of all the sequences in the reference proteome, plus the addition of unique protein sequences that are found in other species or strains of the cluster but not in the reference proteome. These additional sequences are identified using UniRef50 membership.
range: Proteome
domain: Proteome

part
type: ObjectProperty
range: Protein part

part of
type: ObjectProperty

participant
type: ObjectProperty
comment: A protein that participates in a protein-protein interaction.
domain: Interaction
range: Interaction participant

potential sequence
type: ObjectProperty
comment: This is a predicate added by an automated procedure to link entries/proteins that might be isoforms of each other.
domain: Protein
range: Sequence

published in
type: ObjectProperty
comment: Reserved predicate to link a citation to the Journal that it appeared in.
domain: Citation
range: Journal

rank
type: ObjectProperty
type: FunctionalProperty
comment: The rank of a taxon.
range: Taxon rank
domain: Taxon

recommended name
type: ObjectProperty
comment: The name recommended by the UniProt consortium.
range: Structured_Name
sub property of: structured name
domain: Class
  union of: Protein part
  union of: Protein

redundantTo
type: ObjectProperty
comment: Indicates which proteome this proteome is redundant to.
range: Proteome
domain: Resource

related location
type: ObjectProperty
domain: Subcellular Location
range: Subcellular Location

replaced by
type: ObjectProperty
comment: A resource that replaces this resource.
inverse of: replaces
range: Class
  union of: Enzyme
  union of: Protein
  union of: Taxon
domain: Class
  union of: Enzyme
  union of: Protein
  union of: Taxon

replaces
type: ObjectProperty
comment: A resource that is replaced by this resource.
range: Class
  intersection of: Obsolete
  intersection of: Class
    union of: Enzyme
    union of: Protein
    union of: Taxon
    union of: Proteome
domain: Class
  union of: Enzyme
  union of: Protein
  union of: Taxon
  union of: Proteome

representative for
type: ObjectProperty
type: FunctionalProperty
type: InverseFunctionalProperty
range: Cluster (UniRef)
domain: Class
  union of: Protein
  union of: Sequence

seed for
type: ObjectProperty
range: Cluster (UniRef)
domain: Sequence

sequence
type: ObjectProperty
comment: An amino acid sequence.
range: Sequence
inverse of: sequence for
domain: Class
  union of: Annotation
  union of: Protein
  union of: Resource

sequence discrepancy
type: ObjectProperty
comment: Used when a CoDing Sequences (CDS) from the INSDC differs substantially from a reviewed UniProtKB/Swiss-Prot sequence, the UniProt curators indicate the nature of the difference as a rdfs:comment linked via this predicate.
domain: Nucleotide Resource

sequence for
type: ObjectProperty
comment: A resource that describes this sequence.
domain: Sequence
range: Class
  union of: Annotation
  union of: Protein
  union of: Resource

signature sequence match
type: ObjectProperty
comment: Indicates that the signature described by the subject resource matches mathematically and that that match is described by the object of a triple using this property as predicate.
domain: Resource

some members classified with
type: ObjectProperty
comment: Indicates which GO terms are somewhat consistently used to annotate UniProtKB members of this cluster.
domain: Cluster (UniRef)
range: Class
  union of: GO_0003674
  union of: GO_0005575
  union of: GO_0008150

source
type: ObjectProperty
domain: Attribution

status
type: ObjectProperty
deprecated: true

strain
type: ObjectProperty
range: Strain
domain: Taxon

structured name
type: ObjectProperty
range: Structured_Name
domain: Class
  union of: Protein part
  union of: Protein

submitted name
type: ObjectProperty
comment: A name provided by the submitter of the underlying nucleotide sequence.
range: Structured_Name
sub property of: structured name
domain: Class
  union of: Protein part
  union of: Protein

topology
type: ObjectProperty
range: Topology
domain: Class
  intersection of: Restriction
    on property: cellular component
    on class: Cellular Component
    qualified cardinality: 1
  intersection of: Restriction
    on property: orientation
    on class: Orientation
    max qualified cardinality: 1
  intersection of: Restriction
    on property: topology
    on class: Topology
    max qualified cardinality: 1

transcribed from
type: ObjectProperty
domain: Transcript Resource

translated from
type: ObjectProperty
domain: External Sequence
range: Nucleotide Resource

translated to
type: ObjectProperty
domain: Transcript Resource

withdrawnFromINSDC
type: ObjectProperty

abstract
type: DatatypeProperty
type: FunctionalProperty
comment: True if the class does not have any direct instances.
domain: Database (description of)
range: boolean

alias
type: DatatypeProperty
comment: An alternative name used in the flat text format.
range: string

allergen name
type: DatatypeProperty
comment: See http://www.expasy.org/cgi-bin/lists?allergen.txt
sub property of: structured name type

atypical
type: DatatypeProperty
deprecated: true

author
type: DatatypeProperty
comment: The author of a publication.
domain: Citation
range: string

authorsIncomplete
type: DatatypeProperty
domain: Citation
range: boolean

begin
type: DatatypeProperty
deprecated: true

biotechName
type: DatatypeProperty
comment: A name used in a biotechnological context.
sub property of: structured name type

CD molecule antigen name
type: DatatypeProperty
comment: A name from the Human Cell Differentiation Molecules (HCDM) nomenclature.
sub property of: structured name type

certain
type: DatatypeProperty
type: FunctionalProperty
comment: False if there is any uncertainty about a statement.
range: boolean
domain: Absorption

chain
type: DatatypeProperty
comment: Maps a series of symbols representing chains of a protein to a range of amino acids.
domain: Structure Mapping Statement
range: string

checksum
type: DatatypeProperty
comment: An caclulated value that is used to detect if there are errors in the sequence as shown due to among others IO errors. Both the crc64 and md5sum have collisions in UniProt data and cannot be used as unique keys.

cofactorLabel
type: DatatypeProperty
comment: A cofactor required for a catalytic activity.
domain: Enzyme
range: string

complete
type: DatatypeProperty
domain: Taxon
range: boolean

crc64Checksum
type: DatatypeProperty
deprecated: true

created
type: DatatypeProperty
type: FunctionalProperty
comment: The date a resource was created.
range: date
domain: Class
  union of: Protein
  union of: Resource
  union of: Sequence

curated
type: DatatypeProperty
comment: If true the described database has some level of curation.
domain: Database (description of)
range: boolean

date
type: DatatypeProperty
type: FunctionalProperty
domain: Class
  union of: Attribution
  union of: Citation

domains
type: DatatypeProperty
deprecated: true

EC as a name
type: DatatypeProperty
comment: The ecName is the enzyme classification associated with a structured name of the protein. Proteins are often named after their enzymatic activity but can have more than one activity leading to multiple names.
sub property of: structured name type

editor
type: DatatypeProperty
comment: The editor of a publication.
domain: Book Citation
range: string

end
type: DatatypeProperty
deprecated: true

experiments
type: DatatypeProperty
type: FunctionalProperty
domain: Interaction
range: int

proteome exclusion reason
type: DatatypeProperty
comment: Indicates why the proteins of an Proteome where excluded from UniProtKB.
domain: Proteome
range: string

fragment
type: DatatypeProperty
comment: Indicates if a sequence is complete or consists of one or more fragments.
domain: Simple Sequence
range: Datatype
  one of: multiple
  one of: single

frameshift
type: DatatypeProperty
comment: True if a sequence modification causes a frameshift.
domain: RNA Editing
range: boolean

fullName
type: DatatypeProperty
comment: The full name.
sub property of: structured name type

fused
type: DatatypeProperty
deprecated: true

group
type: DatatypeProperty
comment: The group or consortium that authored a publication.
domain: Citation
sub property of: author
range: string

height
type: DatatypeProperty
type: FunctionalProperty
range: int
domain: Image

hits
type: DatatypeProperty
deprecated: true

identity
type: DatatypeProperty
type: FunctionalProperty
comment: The level of sequence identity in a cluster.
domain: Cluster (UniRef)
range: Datatype
  one of: 0.5
  one of: 0.9
  one of: 1.0

implicit
type: DatatypeProperty
type: FunctionalProperty
comment: True if existance of this resource can be inferred.
domain: Database (description of)
range: boolean

institution
type: DatatypeProperty
comment: The institution at which a thesis was written.
domain: Thesis Citation
range: string

international non proprietary name
type: DatatypeProperty
comment: The international nonproprietary name: A generic name for a pharmaceutical substance or active pharmaceutical ingredient that is globally recognized and is a public property.
sub property of: structured name type

length
type: DatatypeProperty
type: FunctionalProperty
domain: Sequence
range: int

limit
type: DatatypeProperty
deprecated: true

link is explicit
type: DatatypeProperty
comment: True if the Database is linked by an explicit action to UniProt, false if it is done using a simple hardcoded rule.
domain: Database (description of)
range: boolean

locator
type: DatatypeProperty
domain: Citation
range: string

manual
type: DatatypeProperty
type: FunctionalProperty
domain: Attribution
range: boolean

predicted mass
type: DatatypeProperty
type: FunctionalProperty
comment: The predicted mass of a sequence in Daltons.
domain: Sequence
range: int

maximum
type: DatatypeProperty
type: FunctionalProperty
comment: A maximum value.
domain: Absorption
range: float

MD5 checksum
type: DatatypeProperty
type: FunctionalProperty
domain: Sequence
sub property of: checksum
range: string

measured activity
type: DatatypeProperty
comment: The maximum velocity, Vmax.
domain: Kinetics
range: string

measured affinity
type: DatatypeProperty
comment: The Michaelis-Menten constant, Km.
domain: Kinetics
range: string

measured error
type: DatatypeProperty
type: FunctionalProperty
comment: The magnitude of the error of a value that was measured.
domain: Mass
range: float

measured value
type: DatatypeProperty
type: FunctionalProperty
comment: A value that was measured.
domain: Mass
range: float

Mnemonic
type: DatatypeProperty
comment: A rememberable string that can be used to find entries, not a stable identifier!
comment: A easy to remember identifier for a UniProtKB entry, but it is not a stable identifier and should not be used by programs to identify entries.
range: string
sub property of: name
domain: Class
  union of: Cluster (UniRef)
  union of: Protein
  union of: Sequence

modified date
type: DatatypeProperty
type: FunctionalProperty
comment: The date a resource was last modified.
range: date
domain: Class
  union of: Cluster (UniRef)
  union of: Protein
  union of: Sequence

name
type: DatatypeProperty
range: string

negative
type: DatatypeProperty
type: FunctionalProperty
domain: Interaction
range: boolean

obsolete
type: DatatypeProperty
type: FunctionalProperty
comment: True if this resource has been replaced or deleted.
range: boolean
domain: Class
  union of: Protein
  union of: Taxon

old mnemonic
type: DatatypeProperty
comment: A mnemonic that is no longer in use for this entry.
domain: Protein
sub property of: name
range: string

ORF name
type: DatatypeProperty
domain: Gene
range: string

other name
type: DatatypeProperty
range: string
domain: Taxon
sub property of: name

pages
type: DatatypeProperty
type: FunctionalProperty
comment: The first and last page for a chapter or article.
range: string
domain: Class
  union of: Book Citation
  union of: Journal Citation

part of lineage
type: DatatypeProperty
type: FunctionalProperty
comment: True for taxa that can appear as part of an organism's non abbreviated lineage. In the flatfile and XML views of an UniProt entry (as well as at INSDC) only these taxonomic nodes are shown.
domain: Taxon
range: boolean

partial
type: DatatypeProperty
deprecated: true

URL pattern
type: DatatypeProperty
type: FunctionalProperty
comment: A URL pattern, used to generate links by substituting an identifier.
domain: Database (description of)
range: string

place of publication
type: DatatypeProperty
type: FunctionalProperty
comment: The place where a publication was published. This usually includes a country name.
range: string
domain: Class
  union of: Book Citation
  union of: Thesis Citation

position
type: DatatypeProperty
deprecated: true

precursor
type: DatatypeProperty
domain: Simple Sequence
range: boolean

publisher
type: DatatypeProperty
comment: The publisher of a book.
domain: Book Citation
range: string

reference proteome
type: DatatypeProperty
deprecated: true

representative proteome
type: DatatypeProperty
deprecated: true

resolution in Angstrom
type: DatatypeProperty
type: FunctionalProperty
comment: The resolution of an experiment, in Angstrom.
domain: Structure Resource
range: float

reviewed
type: DatatypeProperty
type: FunctionalProperty
comment: Indicates whether a resource has been reviewed by a curator.
range: boolean
domain: Class
  union of: Protein
  union of: Taxon

scientific name
type: DatatypeProperty
type: FunctionalProperty
range: string
domain: Taxon
sub property of: name

scope
type: DatatypeProperty
comment: The extent of the work carried out by the authors of a publication.
domain: Citation Statement
range: string

shortCoden
type: DatatypeProperty
comment: Used to link a Journal to its shortCoden
domain: Journal
range: string

short name
type: DatatypeProperty
comment: An abbreviation of the full name or an acronym.
sub property of: structured name type

structured name type
type: DatatypeProperty
comment: All names of the protein, from commonly used to obsolete, to used in the literature..
domain: Structured_Name
range: string

submitted to
type: DatatypeProperty
comment: The database a resource was submitted to.
domain: Submission Citation

substitution
type: DatatypeProperty
comment: A replacement sequence.
range: string
domain: Class
  union of: Mutagenesis Site
  union of: Sequence Variant
  union of: Sequence Conflict

synonym
type: DatatypeProperty
type: FunctionalProperty
range: string
domain: Taxon
sub property of: name

title
type: DatatypeProperty
type: FunctionalProperty
comment: The title of a publication.
domain: Citation
range: string

URI template
type: DatatypeProperty
comment: An string template that can be used to figure out from the database id what uri desribes it.
domain: Database (description of)
range: string

URL template
type: DatatypeProperty
comment: An string template that can be used to figure out from the database id what html page talks about it.
domain: Database (description of)
range: string

version
type: DatatypeProperty
type: FunctionalProperty
range: int
domain: Class
  union of: Protein
  union of: Sequence

volume
type: DatatypeProperty
type: FunctionalProperty
comment: The volume a publication is part of.
domain: Class
  union of: Book Citation
  union of: Journal Citation

width
type: DatatypeProperty
type: FunctionalProperty
range: int
domain: Image

xeno
type: DatatypeProperty
type: FunctionalProperty
domain: Interaction
range: boolean

Absorption
type: Class
subclass of: Biophysicochemical Property
comment: Indicates the wavelength in nm at which photoreactive proteins such as opsins and DNA photolyases show maximal absorption.

Active Site
type: Class
subclass of: Site
comment: Amino acid(s) involved in the activity of an enzyme.

Activity Regulation
type: Class
subclass of: Annotation
comment: Description of an enzyme, transporter and microbial transcription regulation mechanism.

Allergen
type: Class
subclass of: Annotation
comment: Information relevant to allergenic proteins.

Alternative Initiation
type: Class
subclass of: Alternative Products

Alternative Products
type: Class
subclass of: Annotation
comment: Description of the existence of related protein sequences produced by alternative splicing of the same gene or by the use of alternative initiation codons.

Alternative Promoter Usage
type: Class
subclass of: Alternative Products

Splice Variant
type: Class
subclass of: Natural Variation
comment: Description of sequence variants produced by alternative splicing.

Alternative Splicing
type: Class
subclass of: Alternative Products

Annotation
type: Class
comment: Description of a resource on a specific topic.

Attribution
type: Class
comment: Entity used to attach evidence or provenance to a rdf statement via reification.

Strand
type: Class
subclass of: Secondary Structure
comment: Beta strand regions within the experimentally determined protein structure

Binding Site
type: Class
subclass of: Site
comment: Binding site for any chemical group (co-enzyme, prosthetic group, etc.).

Biophysicochemical Property
type: Class
subclass of: Annotation
comment: Biophysical and physicochemical data such as pH dependence, temperature dependence, kinetic parameters, redox potentials, and maximal absorption.

Biotechnology
type: Class
subclass of: Annotation
comment: Description of the use of a specific protein in a biotechnological process.

Book Citation
type: Class
subclass of: Published Citation
subclass of: Restriction
  on property: name
  cardinality: 1
comment: A chapter from a book.

Catalytic Activity
type: Class
comment: The catalytic activity of an enzyme.

Catalytic Activity Annotation
type: Class
subclass of: Annotation
comment: Description of the reactions catalyzed by an enzyme.

Caution
type: Class
subclass of: Annotation
comment: Warning about possible errors and/or grounds for confusion.

Cellular Component
type: Class
subclass of: Subcellular Location

Chain
type: Class
subclass of: Molecule Processing
comment: Extent of a polypeptide chain in the mature protein.

Citation
type: Class
subclass of: Class
  union of: Restriction
    on property: date
    some values from: date
  union of: Restriction
    on property: date
    some values from: gYear
  union of: Restriction
    on property: date
    some values from: gYearMonth
disjoint with: Protein
disjoint with: Sequence
comment: Description of a publication from which data was obtained.

Citation Statement
type: Class
subclass of: Statement
subclass of: Restriction
  on property: context
  all values from: Class
    union of: Strain
    union of: Tissue
    union of: Transposon
comment: The relationship between a resource and a citation.

Cluster (UniRef)
type: Class
subclass of: Thing
subclass of: Restriction
  on property: member
  all values from: Sequence
disjoint with: Protein
disjoint with: Sequence
comment: Cluster of proteins with similar sequences.

Cofactor
type: Class
subclass of: Annotation
comment: Description of an enzyme cofactor.

Coiled-Coil
type: Class
subclass of: Region
comment: Extent of a coiled-coil region.

Compositionally Biased Region
type: Class
subclass of: Region
comment: Extent of a compositionally biased region.

Concept
type: Class
subclass of: Class
subclass of: Restriction
  on property: replaces
  all values from: Concept
comment: A concept used to classify resources.

Crosslink
type: Class
subclass of: Modification
comment: Posttranslationally formed amino acid bonds.

DNA
type: Class
subclass of: Molecule

Database (description of)
type: Class
subclass of: Class
comment: Metadata for a life science database.

Developmental Stage
type: Class
subclass of: Annotation
comment: Description of the developmentally-specific expression of a protein.

Disease
type: Class

Disease Annotation
type: Class
subclass of: Annotation
comment: Description of the diseases associated with a deficiency of a protein.

Disruption Phenotype
type: Class
subclass of: Annotation

Disulfide Bond
type: Class
subclass of: Modification
comment: Describes residues which are linked by an intra-chain disulfide bond. If the endpoints are identical, the disulfide bond is an interchain one.

Domain
type: Class
subclass of: Annotation
comment: Description of the domain structure of a protein.

Domain Assignment Statement
type: Class
subclass of: Statement
comment: The relationship between a protein and a protein domain.

Domain Extent
type: Class
subclass of: Region
comment: Extent of a domain, which is defined as a specific combination of secondary structures organized into a characteristic three-dimensional structure or fold.

Electronic Citation
type: Class
subclass of: Published Citation
subclass of: Restriction
  on property: name
  cardinality: 1
comment: An electronic publication.

Endpoint Statement
type: Class
subclass of: Statement
comment: Metadata for an endpoint of a range on a sequence.

Enzyme
type: Class
subclass of: Restriction
  on property: replaced by
  all values from: Enzyme
subclass of: Restriction
  on property: replaces
  all values from: Enzyme
comment: A specific catalytic activity, defined by the Enzyme Commission of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (IUBMB).

Enzyme Regulation
type: Class
comment: The use of this class has been replaced by Activity_Regulation_Annotation
deprecated: true

Erroneous Gene Model Prediction
type: Class
subclass of: Sequence Caution

Erroneous Initiation
type: Class
subclass of: Sequence Caution

Erroneous Termination
type: Class
subclass of: Sequence Caution

Erroneous Translation
type: Class
subclass of: Sequence Caution

Excluded proteome
type: Class
comment: A Proteome that has been excluded from UniProtKB for some reason, normally described by statements with the predicate up:exclusionReason

Experimental Information
type: Class
subclass of: Sequence Annotation

External Sequence
type: Class
subclass of: Known Sequence
comment: The protein described in the linked record is an alternative splice form of the same gene product as described in this record. The function between the two isoforms is highly divergent.

Family Membership Statement
type: Class
deprecated: true

Frameshift
type: Class
subclass of: Sequence Caution

Function
type: Class
subclass of: Annotation
comment: General description of the functions of a protein.

Gene
type: Class
subclass of: Thing
subclass of: Concept
subclass of: Restriction
  on property: prefLabel
  on class: Gene
  qualified cardinality: 1

Genomic DNA
type: Class
subclass of: DNA

Genomic RNA
type: Class
subclass of: RNA

Glycosylation Site
type: Class
subclass of: Modification
comment: Describes the occurrence of the attachment of a glycan (mono- or polysaccharide) to a residue of a protein.

Helix
type: Class
subclass of: Secondary Structure
comment: Helical regions within the experimentally determined protein structure

Induction
type: Class
subclass of: Annotation
comment: Description of the compounds or conditions that stimulate the synthesis of a protein.

Initiator Methionine
type: Class
subclass of: Molecule Processing
comment: Indicates that the initiator methionine has been cleaved off and is not shown in the sequence.

Interaction
type: Class
comment: Description of a protein-protein interaction.

INTRAMEM
type: Class
subclass of: Region
comment: Extent of a region located in a membrane without crossing it

Journal
type: Class
subclass of: Thing

Journal Citation
type: Class
subclass of: Published Citation
subclass of: Restriction
  on property: name
  cardinality: 1
comment: An article published in a journal.

Kinetics
type: Class
subclass of: Biophysicochemical Property
comment: Mentions the Michaelis-Menten constant (KM) and maximal velocity (Vmax) of enzymes.

Known Sequence
type: Class
subclass of: Sequence

Lipid Binding
type: Class
subclass of: Modification
comment: Covalent binding of a lipid moiety.

mRNA
type: Class
subclass of: RNA

Mass Measurement
type: Class
subclass of: Method
comment: An experimental method for measuring the mass of a molecule.

Mass
type: Class
subclass of: Experimental Information
subclass of: Restriction
  on property: method
  max cardinality: 1
subclass of: Restriction
  on property: method
  all values from: Mass Measurement
comment: Indicates the mass of a sequence determined by mass spectrometry.

Member Of Redudant Proteome
type: Class
subclass of: Obsolete Protein
comment: This entry was obsoleted because its sequence belongs to a redundant protoeome

Method
type: Class
comment: An experimental method.

Modification
type: Class
subclass of: Sequence Annotation
comment: Describes amino acid modifications, post pre- and post-translational.

Modified Residue
type: Class
subclass of: Modification
comment: Posttranslational modification of a residue.

Modified Sequence
type: Class
subclass of: Known Sequence
subclass of: Restriction
  on property: based on
  all values from: Simple Sequence
subclass of: Restriction
  on property: modification
  all values from: Splice Variant

Molecule
type: Class
comment: A biological molecule.

Molecule Processing
type: Class
subclass of: Sequence Annotation

Motif
type: Class
subclass of: Region
comment: Short (<=20 amino acids) sequence motif of biological interest.

Mutagenesis Site
type: Class
subclass of: Experimental Information
comment: Site which has been experimentally altered.

Sequence Variant
type: Class
subclass of: Natural Variation
comment: Authors report that sequence variants exist.

Natural Variation
type: Class
subclass of: Sequence Annotation

Non-consecutive Residues
type: Class
subclass of: Experimental Information
comment: Indicates that two residues in a sequence are not consecutive and that there are a number of unsequenced residues between them.

Non standard residue
type: Class
subclass of: Modification
comment: Describes the occurrence of a non standard residue in the sequence record.

Non-terminal Residue
type: Class
subclass of: Experimental Information
comment: The residue at an extremity of the sequence is not the terminal residue.

Non self interaction
type: Class
subclass of: Interaction
comment: Description of a non self protein-protein interaction.

Not Obsolete
type: Class
equivalent class: Restriction
  on property: obsolete
  has value: false
disjoint with: Obsolete
comment: A class introduced to group all records that are currently in the database.

Not obsolete protein (record)
type: Class
subclass of: Not Obsolete
subclass of: Protein
subclass of: Restriction
  on property: sequence
  some values from: Simple Sequence
subclass of: Restriction
  on property: organism
  cardinality: 1
subclass of: Restriction
  on property: existence
  some values from: Protein existence evidence

Not obsolete taxon (record)
type: Class
subclass of: Not Obsolete
subclass of: Taxon
subclass of: Restriction
  on property: scientific name
  cardinality: 1

DNA Binding
type: Class
subclass of: Region
comment: Extent of a DNA-binding region.

Nucleotide Mapping Statement
type: Class
subclass of: Statement
comment: The relationship between a protein and a nucleotide sequence.

Nucleotide Resource
type: Class
equivalent class: Restriction
  on property: located on
  min cardinality: 1
subclass of: Resource
comment: A resource that descripes a nucleotide sequence.

Observation Citation
type: Class
subclass of: Unpublished Citation
comment: Citation of an unpublished result.

Obsolete
type: Class
equivalent class: Restriction
  on property: obsolete
  has value: true
comment: The class of all obsolete records in the database (i.e. records that where once published but are now removed).

Obsolete Protein
type: Class
subclass of: Obsolete
subclass of: Protein

Obsolete Taxon
type: Class
subclass of: Obsolete
subclass of: Taxon
comment: Taxa are occasionally removed from the taxonomy database (particularly internal nodes, during a taxonomic revision) – these taxids are deleted, and are not reused.

Organelle
type: Class

Orientation
type: Class
subclass of: Subcellular Location

Other DNA
type: Class
subclass of: DNA

Other RNA
type: Class
subclass of: RNA

pH Dependence
type: Class
subclass of: Biophysicochemical Property
comment: Describes the optimum pH for enzyme activity and/or the variation of enzyme activity with pH variation.

PTM
type: Class
subclass of: Annotation
comment: Description of a posttranslational modification.

Protein part
type: Class
subclass of: Thing
comment: Description of a part of a protein.

Interaction participant
type: Class
comment: A participant in a protein-protein interaction.

Patent Citation
type: Class
subclass of: Published Citation
comment: A patent application.

Pathway
type: Class
comment: A hierarchical discription of a metabolic pathway.

Pathway annotation
type: Class
subclass of: Annotation
comment: Description of the metabolic pathways with which a protein is associated.

Peptide
type: Class
subclass of: Molecule Processing
comment: Extent of a released active peptide.

Pharmaceutical
type: Class
subclass of: Annotation
comment: Description of the use of a protein as a pharmaceutical drug.

Plasmid
type: Class
comment: Description of a Plasmid

Polymorphism
type: Class
subclass of: Annotation
comment: Description of polymorphisms.

Propeptide
type: Class
subclass of: Molecule Processing
comment: Extent of a propeptide.

Protein
type: Class
subclass of: Thing
subclass of: Restriction
  on property: replaced by
  all values from: Protein
subclass of: Restriction
  on property: replaces
  all values from: Protein
disjoint with: Sequence
comment: Description of a protein.

Protein existence evidence
type: Class
equivalent class: Class
  one of: Predicted
  one of: Evidence at transcript level
  one of: Uncertain
  one of: Inferred from homology
  one of: Evidence at protein level

Proteome
type: Class
comment: Description of a proteome.

Proteome_Component
type: Class
subclass of: Thing
comment: The component of a proteome. e.g. Chromosome, Contig or Plasmid

Published Citation
type: Class
subclass of: Citation
disjoint with: Unpublished Citation

RNA
type: Class
subclass of: Molecule

RNA Editing
type: Class
subclass of: Annotation
comment: Description of any type of RNA editing that leads to one or more amino acid changes.

range
type: DatatypeProperty
deprecated: true

Taxon rank
type: Class
comment: A rank of a taxon.

Redox Potential
type: Class
subclass of: Biophysicochemical Property
comment: Reports the value of the standard (midpoint) oxido-reduction potential(s) for electron transport proteins.

Reference_Proteome
type: Class
subclass of: Proteome
comment: Some proteomes have been (manually and algorithmically) selected as reference proteomes.

Region
type: Class
subclass of: Sequence Annotation

Repeat
type: Class
subclass of: Region
comment: Extent of an internal sequence repetition.

Representative_Proteome
type: Class
subclass of: Proteome
comment: A proteome that is believed by curators, or selected programmatically to be representative for a number of related Proteomes

Resource
type: Class
equivalent class: Restriction
  on property: database
  some values from: Thing
comment: A life science resource.

Reviewed
type: Class
equivalent class: Restriction
  on property: reviewed
  has value: true
comment: The class of all reviewed records in the database (i.e. records that where looked at by a curator for integration into the database).

Reviewed protein (records)
type: Class
subclass of: Protein
subclass of: Reviewed

Ribosomal Frameshifting
type: Class
subclass of: Alternative Products

Secondary Structure
type: Class
subclass of: Sequence Annotation
comment: Describes the secondary structure of proteins whose tertiary structure is known experimentally.

Self protein interaction
type: Class
subclass of: Interaction
comment: Description of a self protein-protein interaction.

Sequence
type: Class
comment: An amino acid sequence.

Sequence Annotation
type: Class
subclass of: Annotation
comment: Description of a special region or site in a protein sequence.

Sequence Caution
type: Class
subclass of: Annotation
comment: Warning about possible errors related to the protein sequence

Sequence Conflict
type: Class
subclass of: Experimental Information
comment: Different sources report differing sequences.

Unsure Residue
type: Class
subclass of: Experimental Information
comment: Used to describe region(s) of a sequence for which the authors are unsure about the sequence assignment.

Signal Peptide
type: Class
subclass of: Molecule Processing
comment: Extent of a signal sequence (prepeptide).

Similarity
type: Class
subclass of: Annotation
comment: Description of the similarities (sequence or structural) of a protein with other proteins.

Simple Sequence
type: Class
subclass of: Known Sequence

Site
type: Class
subclass of: Sequence Annotation
comment: Any interesting single amino-acid site on the sequence, that is not defined by another feature key. It can also apply to an amino acid bond which is represented by the positions of the two flanking amino acids.

Status
type: Class
comment: Indicator for the reliability of a piece of information.

Strain
type: Class
comment: A strain of a species.

Structure Determination
type: Class
subclass of: Method
comment: An experimental method for determining the 3D structure of a protein.

Structure Mapping Statement
type: Class
subclass of: Statement
comment: The relationship between a protein and a 3D structure.

Structure Resource
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: method
    all values from: Structure Determination
  intersection of: Restriction
    on property: method
    cardinality: 1
subclass of: Resource
comment: A resource that describes the 3D structure of a protein.

Structured_Name
type: Class
comment: A resource that holds a set of the known names for this protein together.

Subcellular Location
type: Class

Subcellular Location Annotation
type: Class
subclass of: Annotation
comment: Description of the subcellular location of the mature protein.

Submission Citation
type: Class
subclass of: Published Citation
subclass of: Restriction
  on property: submitted to
  cardinality: 1
comment: Data that was submitted directly to a database.

Subunit
type: Class
subclass of: Annotation
comment: Description of the quaternary structure of a protein.

Taxon
type: Class
subclass of: Restriction
  on property: Mnemonic
  max cardinality: 1
subclass of: Restriction
  on property: replaces
  all values from: Taxon
comment: An element of a taxonomy for classifying life forms.

Temperature Dependence
type: Class
subclass of: Biophysicochemical Property
comment: Indicates the optimum temperature for enzyme activity and/or the variation of enzyme activity with temperature variation; the thermostability/thermolability of the enzyme is also mentioned when it is known.

Thesis Citation
type: Class
subclass of: Published Citation
subclass of: Restriction
  on property: institution
  cardinality: 1
comment: A Ph.D. thesis.

Tissue
type: Class
comment: A tissue such as lung or heart.

Tissue Specificity
type: Class
subclass of: Annotation
comment: Description of the tissue specificity of a protein.

Topological Domain
type: Class
subclass of: Region
comment: A topological domain.

Topology
type: Class
subclass of: Subcellular Location

Toxic Dose
type: Class
subclass of: Annotation
comment: Information on the LD(50). LD stands for "Lethal Dose". LD(50) is the amount of a toxin, given all at once, which causes the death of 50% (one half) of a group of test animals.

Transcribed RNA
type: Class
subclass of: RNA

Transcript Resource
type: Class
subclass of: Resource

Transit Peptide
type: Class
subclass of: Molecule Processing
comment: Extent of a transit peptide (mitochondrion, chloroplast, thylakoid, cyanelle or microbody).

Transmembrane
type: Class
subclass of: Region
comment: Extent of a transmembrane region.

Transposon
type: Class
comment: A transposon

Turn
type: Class
subclass of: Secondary Structure
comment: Turns within the experimentally determined protein structure.

Unassigned DNA
type: Class
subclass of: DNA

Unassigned RNA
type: Class
subclass of: RNA

Unknown Sequence
type: Class
subclass of: Sequence

Unpublished Citation
type: Class
subclass of: Citation

Viral cRNA
type: Class
subclass of: RNA
comment: Positive cRNA molecule that is made from from a single stranded genomic RNA.

Zinc Finger
type: Class
subclass of: Region
comment: Extent of a zinc finger region.

Atmospheric Pressure Ionization
type: Thing
type: Mass Measurement
type: NamedIndividual
comment: Mass measurement using Atmospheric Pressure Ionization

Apicoplast
type: Thing
type: Organelle
type: NamedIndividual

By Similarity
type: Thing
type: Status
type: NamedIndividual

Chloroplast
type: Thing
type: Organelle
type: NamedIndividual

Taxonomy rank Class
type: Thing
type: Taxon rank
type: NamedIndividual

Cohort
type: Thing
type: Taxon rank
type: NamedIndividual
comment: Taxonomy rank cohort

Cyanelle
type: Thing
type: Organelle
type: NamedIndividual

Electrospray Ionization
type: Thing
type: Mass Measurement
type: NamedIndividual

Electron Microscopy
type: Thing
type: Structure Determination
type: NamedIndividual
comment: The electron microscope is a microscope that can magnify very small details with high resolving power due to the use of electrons rather than light to scatter off material, magnifying at levels up to 500,000 times.

Evidence at protein level
type: Thing
type: Protein existence evidence
type: NamedIndividual

Evidence at transcript level
type: Thing
type: Protein existence evidence
type: NamedIndividual
comment: Indicates that the existence of a protein has not been strictly proven but that expression data (such as existence of cDNA(s), RT-PCR or Northern blots) indicate the existence of a transcript.

Indicates that there is some experimental evidence that the given annotation could apply.
type: Thing
type: Status
type: NamedIndividual

Fast Atom Bombardment
type: Thing
type: Mass Measurement
type: NamedIndividual

Taxonomy rank Family
type: Thing
type: Taxon rank
type: NamedIndividual

Fiber Diffraction
type: Thing
type: Structure Determination
type: NamedIndividual

Taxonomy rank Forma
type: Thing
type: Taxon rank
type: NamedIndividual

Taxonomy rank Genus
type: Thing
type: Taxon rank
type: NamedIndividual

Hydrogenosome
type: Thing
type: Organelle
type: NamedIndividual

Inferred from homology
type: Thing
type: Protein existence evidence
type: NamedIndividual

Taxonomy rank Infraclass
type: Thing
type: Taxon rank
type: NamedIndividual

Taxonomy rank Infraorder
type: Thing
type: Taxon rank
type: NamedIndividual

Infrared Spectroscopy
type: Thing
type: Structure Determination
type: NamedIndividual
comment: A type of spectroscopy that uses the Infrared portion of the electromagnetic spectrum.

Taxonomy rank Isotype
type: Thing
type: Taxon rank
type: NamedIndividual

Taxonomy rank Kingdom
type: Thing
type: Taxon rank
type: NamedIndividual

Liquid Secondary Ionization
type: Thing
type: Mass Measurement
type: NamedIndividual

Matrix-Assisted Laser Desorption
type: Thing
type: Mass Measurement
type: NamedIndividual

Mitochondrion
type: Thing
type: Organelle
type: NamedIndividual

NMR Spectroscopy
type: Thing
type: Structure Determination
type: NamedIndividual

Neutron Diffraction
type: Thing
type: Structure Determination
type: NamedIndividual

Non-photosyntethic plastid
type: Thing
type: Organelle
type: NamedIndividual

Nuleomorph
type: Thing
type: Organelle
type: NamedIndividual

Taxonomy rank Order
type: Thing
type: Taxon rank
type: NamedIndividual

Organellar chromatophore
type: Thing
type: Organelle
type: NamedIndividual

Plasma Desorption
type: Thing
type: Mass Measurement
type: NamedIndividual

Taxonomy rank Paratype
type: Thing
type: Taxon rank
type: NamedIndividual

Taxonomy rank Parvorder
type: Thing
type: Taxon rank
type: NamedIndividual

Taxonomy rank Phylum
type: Thing
type: Taxon rank
type: NamedIndividual

Plastid
type: Thing
type: Organelle
type: NamedIndividual

Potential
type: Thing
type: Status
type: NamedIndividual
comment: indicates that there is some logical or conclusive evidence that the given annotation could apply. This non-experimental qualifier is often used to present results from protein sequence analysis software tools, which are only annotated if the result makes sense in the biological context of a given protein. A typical example is the annotation of N-glycosylation sites in secreted proteins

Predicted
type: Thing
type: Protein existence evidence
type: NamedIndividual
comment: This is used for proteins without evidence at protein, transcript, or homology levels.

Prediction
type: Thing
type: Structure Determination
type: NamedIndividual

Probable
type: Thing
type: Status
type: NamedIndividual
comment: The status ‘Probable’ indicates stronger evidence than the qualifier ‘Potential’. This qualifier implies that there must be at least some experimental evidence, which indicates, that the information is expected to be found in the natural environment of a protein.

Surface Enhanced Laser Desorption Ionization
type: Thing
type: Mass Measurement
type: NamedIndividual

Taxonomic rank Species
type: Thing
type: Taxon rank
type: NamedIndividual

Taxonomic rank Species Group
type: Thing
type: Taxon rank
type: NamedIndividual

Taxonomic rank Species Subgroup
type: Thing
type: Taxon rank
type: NamedIndividual

Taxonomic rank Subclass
type: Thing
type: Taxon rank
type: NamedIndividual

Subcohort
type: Thing
type: Taxon rank
type: NamedIndividual
comment: Taxonomy rank subcohort

Taxonomic rank Subfamily
type: Thing
type: Taxon rank
type: NamedIndividual

Taxonomic rank Subgenus
type: Thing
type: Taxon rank
type: NamedIndividual

Taxonomic rank Subkingdom
type: Thing
type: Taxon rank
type: NamedIndividual

Taxonomic rank Suborder
type: Thing
type: Taxon rank
type: NamedIndividual

Taxonomic rank Subphylum
type: Thing
type: Taxon rank
type: NamedIndividual

Taxonomic rank Subspecies
type: Thing
type: Taxon rank
type: NamedIndividual

Taxonomic rank Subtribe
type: Thing
type: Taxon rank
type: NamedIndividual

Taxonomic rank Superclass
type: Thing
type: Taxon rank
type: NamedIndividual

Taxonomic rank Superfamily
type: Thing
type: Taxon rank
type: NamedIndividual

Taxonomic rank Superkingdom
type: Thing
type: Taxon rank
type: NamedIndividual

Taxonomic rank Superorder
type: Thing
type: Taxon rank
type: NamedIndividual

Taxonomic rank Superphylum
type: Thing
type: Taxon rank
type: NamedIndividual

Taxonomic rank Tribe
type: Thing
type: Taxon rank
type: NamedIndividual

Uncertain
type: Thing
type: Protein existence evidence
type: NamedIndividual

Taxonomic rank Varietas
type: Thing
type: Taxon rank
type: NamedIndividual

X-Ray Crystallography
type: Thing
type: Structure Determination
type: NamedIndividual
comment: A technique in crystallography in which the pattern produced by the diffraction of x-rays through the closely spaced lattice of atoms in a crystal is recorded and then analyzed to reveal the nature of that lattice.