Properties and classes used for protein annotation.
The UniProt RDF schema ontology contains predicates used to describe UniProt entries and associated data.
The UniProt RDF schema ontology is used to describe concepts that are central to the UniProt datasets. Especially those for which there is on consensus concept available in the wider Bioinformatics community.
UniProt as a large knowledge graph has a need to introduce the concepts it uses in it's RDF depiction. The UniProt consortium tries to reuse as much as possible existing ontologies and concepts widely used by authorative resources. When this is not possible UniProt has introduced it's own concepts described in this ontology file.
The sequence on which the description of a modified sequence is based.
A publication from which data was extracted, or which contains additional information.
A concept that classifies this resource.
The subcellular location where a protein is encoded.
The catalytic activity associated with a protein. or part of a protein.
The publication which an erratum refers to.
The molecule a this resource is located on.
Maps annotation to a resource. Used to link annotations/comments from external non UniProt sources via Citations to UniProt resources.
A publication from which data was by a extracted by a mapping from non UniProt origin, or which contains additional information.
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.
A protein that participates in a protein-protein interaction.
This is a predicate added by an automated procedure to link entries/proteins that might be isoforms of each other.
Reserved predicate to link a citation to the Journal that it appeared in.
The name recommended by the UniProt consortium.
Indicates which proteome this proteome is redundant to.
A resource that is replaced by this resource.
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.
A resource that describes this sequence.
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.
Indicates which GO terms are somewhat consistently used to annotate UniProtKB members of this cluster.
A name provided by the submitter of the underlying nucleotide sequence.
True if the class does not have any direct instances.
An alternative name used in the flat text format.
See http://www.expasy.org/cgi-bin/lists?allergen.txt
A name used in a biotechnological context.
A name from the Human Cell Differentiation Molecules (HCDM) nomenclature.
False if there is any uncertainty about a statement.
Maps a series of symbols representing chains of a protein to a range of amino acids.
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.
A cofactor required for a catalytic activity.
If true the described database has some level of curation.
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.
Indicates why the proteins of an Proteome where excluded from UniProtKB.
Indicates if a sequence is complete or consists of one or more fragments.
True if a sequence modification causes a frameshift.
The group or consortium that authored a publication.
The level of sequence identity in a cluster.
True if existance of this resource can be inferred.
The institution at which a thesis was written.
The international nonproprietary name: A generic name for a pharmaceutical substance or active pharmaceutical ingredient that is globally recognized and is a public property.
True if the Database is linked by an explicit action to UniProt, false if it is done using a simple hardcoded rule.
The predicted mass of a sequence in Daltons.
The magnitude of the error of a value that was measured.
A rememberable string that can be used to find entries, not a stable identifier!
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.
True if this resource has been replaced or deleted.
A mnemonic that is no longer in use for this entry.
The first and last page for a chapter or article.
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.
A URL pattern, used to generate links by substituting an identifier.
The place where a publication was published. This usually includes a country name.
The resolution of an experiment, in Angstrom.
Indicates whether a resource has been reviewed by a curator.
The extent of the work carried out by the authors of a publication.
Used to link a Journal to its shortCoden
An abbreviation of the full name or an acronym.
All names of the protein, from commonly used to obsolete, to used in the literature..
The database a resource was submitted to.
An string template that can be used to figure out from the database id what uri desribes it.
An string template that can be used to figure out from the database id what html page talks about it.
Indicates the wavelength in nm at which photoreactive proteins such as opsins and DNA photolyases show maximal absorption.
Amino acid(s) involved in the activity of an enzyme.
Description of an enzyme, transporter and microbial transcription regulation mechanism.
Information relevant to allergenic proteins.
Description of the existence of related protein sequences produced by alternative splicing of the same gene or by the use of alternative initiation codons.
Description of sequence variants produced by alternative splicing.
Description of a resource on a specific topic.
Entity used to attach evidence or provenance to a rdf statement via reification.
Beta strand regions within the experimentally determined protein structure
Binding site for any chemical group (co-enzyme, prosthetic group, etc.).
Biophysical and physicochemical data such as pH dependence, temperature dependence, kinetic parameters, redox potentials, and maximal absorption.
Description of the use of a specific protein in a biotechnological process.
Description of the reactions catalyzed by an enzyme.
Warning about possible errors and/or grounds for confusion.
Extent of a polypeptide chain in the mature protein.
Description of a publication from which data was obtained.
The relationship between a resource and a citation.
Cluster of proteins with similar sequences.
Extent of a compositionally biased region.
Posttranslationally formed amino acid bonds.
Description of the developmentally-specific expression of a protein.
Description of the diseases associated with a deficiency of a protein.
Describes residues which are linked by an intra-chain disulfide bond. If the endpoints are identical, the disulfide bond is an interchain one.
Description of the domain structure of a protein.
The relationship between a protein and a protein domain.
Extent of a domain, which is defined as a specific combination of secondary structures organized into a characteristic three-dimensional structure or fold.
Metadata for an endpoint of a range on a sequence.
A specific catalytic activity, defined by the Enzyme Commission of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (IUBMB).
The use of this class has been replaced by Activity_Regulation_Annotation
A Proteome that has been excluded from UniProtKB for some reason, normally described by statements with the predicate up:exclusionReason
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.
General description of the functions of a protein.
Describes the occurrence of the attachment of a glycan (mono- or polysaccharide) to a residue of a protein.
Helical regions within the experimentally determined protein structure
Description of the compounds or conditions that stimulate the synthesis of a protein.
Indicates that the initiator methionine has been cleaved off and is not shown in the sequence.
Description of a protein-protein interaction.
Extent of a region located in a membrane without crossing it
Mentions the Michaelis-Menten constant (KM) and maximal velocity (Vmax) of enzymes.
An experimental method for measuring the mass of a molecule.
Indicates the mass of a sequence determined by mass spectrometry.
This entry was obsoleted because its sequence belongs to a redundant protoeome
Describes amino acid modifications, post pre- and post-translational.
Posttranslational modification of a residue.
Short (<=20 amino acids) sequence motif of biological interest.
Site which has been experimentally altered.
Authors report that sequence variants exist.
Indicates that two residues in a sequence are not consecutive and that there are a number of unsequenced residues between them.
Describes the occurrence of a non standard residue in the sequence record.
The residue at an extremity of the sequence is not the terminal residue.
Description of a non self protein-protein interaction.
A class introduced to group all records that are currently in the database.
The relationship between a protein and a nucleotide sequence.
A resource that descripes a nucleotide sequence.
The class of all obsolete records in the database (i.e. records that where once published but are now removed).
Taxa are occasionally removed from the taxonomy database (particularly internal nodes, during a taxonomic revision) – these taxids are deleted, and are not reused.
Describes the optimum pH for enzyme activity and/or the variation of enzyme activity with pH variation.
Description of a posttranslational modification.
A participant in a protein-protein interaction.
A hierarchical discription of a metabolic pathway.
Description of the metabolic pathways with which a protein is associated.
Description of the use of a protein as a pharmaceutical drug.
The component of a proteome. e.g. Chromosome, Contig or Plasmid
Description of any type of RNA editing that leads to one or more amino acid changes.
A specialization of faldo:location where all objects are faldo:Regions
Reports the value of the standard (midpoint) oxido-reduction potential(s) for electron transport proteins.
Some proteomes have been (manually and algorithmically) selected as reference proteomes.
Extent of an internal sequence repetition.
A proteome that is believed by curators, or selected programmatically to be representative for a number of related Proteomes
The class of all reviewed records in the database (i.e. records that where looked at by a curator for integration into the database).
Describes the secondary structure of proteins whose tertiary structure is known experimentally.
Description of a self protein-protein interaction.
Description of a special region or site in a protein sequence.
Warning about possible errors related to the protein sequence
Different sources report differing sequences.
Used to describe region(s) of a sequence for which the authors are unsure about the sequence assignment.
Extent of a signal sequence (prepeptide).
Description of the similarities (sequence or structural) of a protein with other proteins.
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.
Indicator for the reliability of a piece of information.
An experimental method for determining the 3D structure of a protein.
The relationship between a protein and a 3D structure.
A resource that describes the 3D structure of a protein.
A resource that holds a set of the known names for this protein together.
Description of the subcellular location of the mature protein.
Data that was submitted directly to a database.
Description of the quaternary structure of a protein.
An element of a taxonomy for classifying life forms.
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.
Description of the tissue specificity of a protein.
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.
Extent of a transit peptide (mitochondrion, chloroplast, thylakoid, cyanelle or microbody).
Turns within the experimentally determined protein structure.
Positive cRNA molecule that is made from from a single stranded genomic RNA.
Mass measurement using Atmospheric Pressure Ionization
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.
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.
A type of spectroscopy that uses the Infrared portion of the electromagnetic spectrum.
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
This is used for proteins without evidence at protein, transcript, or homology levels.
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
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.