UniProt RDF schema ontology Properties and classes used for protein annotation. The UniProt RDF schema ontology contains predicates used to describe UniProt entries and associated data. UniProt RDF schema ontology 2022_03 catalytic activity The catalytic activity of an enzyme. alternativeName A synonym of the recommended name. annotation Attaches an annotation to a resource. attribution based on The sequence on which the description of a modified sequence is based. catalytic activity catalyzed physiological reaction catalyzed reaction category cellular component 1 1 1 chainSequenceMapping A mapping between a Sequence/Entry and aminoacids described in a PDB record. citation A publication from which data was extracted, or which contains additional information. classified with A concept that classifies this resource. cofactor common name common taxon proteome component A component of a protein. conflicting sequence context database disease domain A domain of a protein. encoded by The gene by which a protein is encoded. encoded in The subcellular location where a protein is encoded. enzyme The catalytic activity associated with a protein. or part of a protein. enzyme class erratum An erratum for a publication. erratum for The publication which an erratum refers to. existence host interaction isolatedFrom ligand ligand part located in 1 1 1 located on The molecule a this resource is located on. locus name mapped annotation Maps annotation to a resource. Used to link annotations/comments from external non UniProt sources via Citations to UniProt resources. mapped citation A publication from which data was by a extracted by a mapping from non UniProt origin, or which contains additional information. member One of several similar resources. member of method The experimental method that was used. modification A modification of a sequence. nucleotideSequenceMappingIssue 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. organism The organism in which a protein occurs. orientation 1 1 1 panproteome 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. part part of participant A protein that participates in a protein-protein interaction. potential sequence This is a predicate added by an automated procedure to link entries/proteins that might be isoforms of each other. published in Reserved predicate to link a citation to the Journal that it appeared in. rank The rank of a taxon. recommended name The name recommended by the UniProt consortium. redundantTo Indicates which proteome this proteome is redundant to. related location replaced by A resource that replaces this resource. replaces A resource that is replaced by this resource. representative for seed for sequence An amino acid sequence. sequence discrepancy 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. sequence for A resource that describes this sequence. signature sequence match 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. some members classified with Indicates which GO terms are somewhat consistently used to annotate UniProtKB members of this cluster. source true strain structured name submitted name A name provided by the submitter of the underlying nucleotide sequence. topology 1 1 1 transcribed from translated from translated to withdrawnFromINSDC abstract True if the class does not have any direct instances. alias An alternative name used in the flat text format. allergen name See http://www.expasy.org/cgi-bin/lists?allergen.txt atypical true author The author of a publication. authorsIncomplete true biotechName A name used in a biotechnological context. CD molecule antigen name A name from the Human Cell Differentiation Molecules (HCDM) nomenclature. certain False if there is any uncertainty about a statement. chain Maps a series of symbols representing chains of a protein to a range of amino acids. checksum 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 A cofactor required for a catalytic activity. complete true created The date a resource was created. curated If true the described database has some level of curation. date true EC as a name 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. editor The editor of a publication. true experiments proteome exclusion reason Indicates why the proteins of an Proteome where excluded from UniProtKB. fragment Indicates if a sequence is complete or consists of one or more fragments. multiple single frameshift True if a sequence modification causes a frameshift. fullName The full name. true group The group or consortium that authored a publication. height true identity The level of sequence identity in a cluster. 0.5 0.9 1.0 implicit True if existance of this resource can be inferred. institution The institution at which a thesis was written. international non proprietary name The international nonproprietary name: A generic name for a pharmaceutical substance or active pharmaceutical ingredient that is globally recognized and is a public property. length true link is explicit True if the Database is linked by an explicit action to UniProt, false if it is done using a simple hardcoded rule. locator manual predicted mass The predicted mass of a sequence in Daltons. maximum A maximum value. MD5 checksum measured activity The maximum velocity, Vmax. measured affinity The Michaelis-Menten constant, Km. measured error The magnitude of the error of a value that was measured. measured value A value that was measured. Mnemonic 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. modified date The date a resource was last modified. name negative obsolete True if this resource has been replaced or deleted. A mnemonic that is no longer in use for this entry. old mnemonic ORF name other name pages The first and last page for a chapter or article. part of lineage 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. true URL pattern A URL pattern, used to generate links by substituting an identifier. place of publication The place where a publication was published. This usually includes a country name. true precursor publisher The publisher of a book. reference proteome true representative proteome true resolution in Angstrom The resolution of an experiment, in Angstrom. reviewed Indicates whether a resource has been reviewed by a curator. scientific name scope The extent of the work carried out by the authors of a publication. shortCoden Used to link a Journal to its shortCoden short name An abbreviation of the full name or an acronym. structured name type All names of the protein, from commonly used to obsolete, to used in the literature.. submitted to The database a resource was submitted to. substitution A replacement sequence. synonym title The title of a publication. URI template An string template that can be used to figure out from the database id what uri desribes it. URL template An string template that can be used to figure out from the database id what html page talks about it. version volume The volume a publication is part of. width xeno Absorption Indicates the wavelength in nm at which photoreactive proteins such as opsins and DNA photolyases show maximal absorption. Active Site Amino acid(s) involved in the activity of an enzyme. Activity Regulation Description of an enzyme, transporter and microbial transcription regulation mechanism. Allergen Information relevant to allergenic proteins. Alternative Initiation Alternative Products 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 Splice Variant Description of sequence variants produced by alternative splicing. Alternative Splicing Annotation Description of a resource on a specific topic. Attribution Entity used to attach evidence or provenance to a rdf statement via reification. Strand Beta strand regions within the experimentally determined protein structure Binding Site Binding site for any chemical group (co-enzyme, prosthetic group, etc.). Biophysicochemical Property Biophysical and physicochemical data such as pH dependence, temperature dependence, kinetic parameters, redox potentials, and maximal absorption. Biotechnology Description of the use of a specific protein in a biotechnological process. Book Citation 1 A chapter from a book. Catalytic Activity The catalytic activity of an enzyme. Catalytic Activity Annotation Description of the reactions catalyzed by an enzyme. Caution Warning about possible errors and/or grounds for confusion. Cellular Component Chain Extent of a polypeptide chain in the mature protein. Citation Description of a publication from which data was obtained. Citation Statement The relationship between a resource and a citation. Cluster (UniRef) Cluster of proteins with similar sequences. Cofactor Description of an enzyme cofactor. Coiled-Coil Extent of a coiled-coil region. Compositionally Biased Region Extent of a compositionally biased region. Concept A concept used to classify resources. Crosslink Posttranslationally formed amino acid bonds. DNA Database (description of) Metadata for a life science database. Developmental Stage Description of the developmentally-specific expression of a protein. Disease Disease Annotation Description of the diseases associated with a deficiency of a protein. Disruption Phenotype Disulfide Bond Describes residues which are linked by an intra-chain disulfide bond. If the endpoints are identical, the disulfide bond is an interchain one. Domain Description of the domain structure of a protein. Domain Assignment Statement The relationship between a protein and a protein domain. Domain Extent 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 1 An electronic publication. Endpoint Statement Metadata for an endpoint of a range on a sequence. Enzyme 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 The use of this class has been replaced by Activity_Regulation_Annotation true Erroneous Gene Model Prediction Erroneous Initiation Erroneous Termination Erroneous Translation Excluded proteome A Proteome that has been excluded from UniProtKB for some reason, normally described by statements with the predicate up:exclusionReason Experimental Information External Sequence 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 true Frameshift Function General description of the functions of a protein. Gene 1 Genomic DNA Genomic RNA Glycosylation Site Describes the occurrence of the attachment of a glycan (mono- or polysaccharide) to a residue of a protein. Helix Helical regions within the experimentally determined protein structure Induction Description of the compounds or conditions that stimulate the synthesis of a protein. Initiator Methionine Indicates that the initiator methionine has been cleaved off and is not shown in the sequence. Interaction Description of a protein-protein interaction. INTRAMEM Extent of a region located in a membrane without crossing it Journal Journal Citation 1 An article published in a journal. Kinetics Mentions the Michaelis-Menten constant (KM) and maximal velocity (Vmax) of enzymes. Known Sequence Lipid Binding Covalent binding of a lipid moiety. mRNA Mass Measurement An experimental method for measuring the mass of a molecule. Mass 1 Indicates the mass of a sequence determined by mass spectrometry. Member Of Redudant Proteome This entry was obsoleted because its sequence belongs to a redundant protoeome Method An experimental method. Modification Describes amino acid modifications, post pre- and post-translational. Modified Residue Posttranslational modification of a residue. Modified Sequence Molecule A biological molecule. Molecule Processing Motif Short (<=20 amino acids) sequence motif of biological interest. Mutagenesis Site Site which has been experimentally altered. Sequence Variant Authors report that sequence variants exist. Natural Variation Non-consecutive Residues Indicates that two residues in a sequence are not consecutive and that there are a number of unsequenced residues between them. Non standard residue Describes the occurrence of a non standard residue in the sequence record. Non-terminal Residue The residue at an extremity of the sequence is not the terminal residue. Non self interaction Description of a non self protein-protein interaction. Not Obsolete false A class introduced to group all records that are currently in the database. Not obsolete protein (record) 1 Not obsolete taxon (record) 1 DNA Binding Extent of a DNA-binding region. Nucleotide Mapping Statement The relationship between a protein and a nucleotide sequence. Nucleotide Resource 1 A resource that descripes a nucleotide sequence. Observation Citation Citation of an unpublished result. Obsolete true The class of all obsolete records in the database (i.e. records that where once published but are now removed). Obsolete Protein Obsolete Taxon Taxa are occasionally removed from the taxonomy database (particularly internal nodes, during a taxonomic revision) – these taxids are deleted, and are not reused. Organelle Orientation Other DNA Other RNA pH Dependence Describes the optimum pH for enzyme activity and/or the variation of enzyme activity with pH variation. PTM Description of a posttranslational modification. Protein part Description of a part of a protein. Interaction participant A participant in a protein-protein interaction. Patent Citation A patent application. Pathway A hierarchical discription of a metabolic pathway. Pathway annotation Description of the metabolic pathways with which a protein is associated. Peptide Extent of a released active peptide. Pharmaceutical Description of the use of a protein as a pharmaceutical drug. Plasmid Description of a Plasmid Polymorphism Description of polymorphisms. Propeptide Extent of a propeptide. Protein Description of a protein. Protein existence evidence Proteome Description of a proteome. Proteome_Component The component of a proteome. e.g. Chromosome, Contig or Plasmid Published Citation RNA RNA Editing Description of any type of RNA editing that leads to one or more amino acid changes. true Taxon rank A rank of a taxon. Redox Potential Reports the value of the standard (midpoint) oxido-reduction potential(s) for electron transport proteins. Reference_Proteome Some proteomes have been (manually and algorithmically) selected as reference proteomes. Region Repeat Extent of an internal sequence repetition. Representative_Proteome A proteome that is believed by curators, or selected programmatically to be representative for a number of related Proteomes Resource A life science resource. Reviewed true 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) Ribosomal Frameshifting Secondary Structure Describes the secondary structure of proteins whose tertiary structure is known experimentally. Self protein interaction Description of a self protein-protein interaction. Sequence An amino acid sequence. Sequence Annotation Description of a special region or site in a protein sequence. Sequence Caution Warning about possible errors related to the protein sequence Sequence Conflict Different sources report differing sequences. Unsure Residue Used to describe region(s) of a sequence for which the authors are unsure about the sequence assignment. Signal Peptide Extent of a signal sequence (prepeptide). Similarity Description of the similarities (sequence or structural) of a protein with other proteins. Simple Sequence Site 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 Indicator for the reliability of a piece of information. Strain A strain of a species. Structure Determination An experimental method for determining the 3D structure of a protein. Structure Mapping Statement The relationship between a protein and a 3D structure. Structure Resource 1 A resource that describes the 3D structure of a protein. Structured_Name A resource that holds a set of the known names for this protein together. Subcellular Location Subcellular Location Annotation Description of the subcellular location of the mature protein. Submission Citation 1 Data that was submitted directly to a database. Subunit Description of the quaternary structure of a protein. Taxon 1 An element of a taxonomy for classifying life forms. Temperature Dependence 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 1 A Ph.D. thesis. Tissue A tissue such as lung or heart. Tissue Specificity Description of the tissue specificity of a protein. Topological Domain A topological domain. Topology Toxic Dose 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 Transcript Resource Transit Peptide Extent of a transit peptide (mitochondrion, chloroplast, thylakoid, cyanelle or microbody). Transmembrane Extent of a transmembrane region. Transposon A transposon Turn Turns within the experimentally determined protein structure. Unassigned DNA Unassigned RNA Unknown Sequence Unpublished Citation Viral cRNA Positive cRNA molecule that is made from from a single stranded genomic RNA. Zinc Finger Extent of a zinc finger region. Atmospheric Pressure Ionization Mass measurement using Atmospheric Pressure Ionization Apicoplast By Similarity Chloroplast Taxonomy rank Class Cohort Taxonomy rank cohort Cyanelle Electrospray Ionization Electron Microscopy 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 Evidence at transcript level 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. Fast Atom Bombardment Taxonomy rank Family Fiber Diffraction Taxonomy rank Forma Taxonomy rank Genus Hydrogenosome Inferred from homology Taxonomy rank Infraclass Taxonomy rank Infraorder Infrared Spectroscopy A type of spectroscopy that uses the Infrared portion of the electromagnetic spectrum. Taxonomy rank Isotype Taxonomy rank Kingdom Liquid Secondary Ionization Matrix-Assisted Laser Desorption Mitochondrion NMR Spectroscopy Neutron Diffraction Non-photosyntethic plastid Nuleomorph Taxonomy rank Order Organellar chromatophore Plasma Desorption Taxonomy rank Paratype Taxonomy rank Parvorder Taxonomy rank Phylum Plastid Potential 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 This is used for proteins without evidence at protein, transcript, or homology levels. Prediction Probable 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 Taxonomic rank Species Taxonomic rank Species Group Taxonomic rank Species Subgroup Taxonomic rank Subclass Subcohort Taxonomy rank subcohort Taxonomic rank Subfamily Taxonomic rank Subgenus Taxonomic rank Subkingdom Taxonomic rank Suborder Taxonomic rank Subphylum Taxonomic rank Subspecies Taxonomic rank Subtribe Taxonomic rank Superclass Taxonomic rank Superfamily Taxonomic rank Superkingdom Taxonomic rank Superorder Taxonomic rank Superphylum Taxonomic rank Tribe Uncertain Taxonomic rank Varietas X-Ray Crystallography 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.