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This version:
http://purl.org/stringdb/0.2
Latest version:
http://purl.org/stringdb
Revision:
STRING database Web API ontology
Authors:
http://purl.org/query/tarcisiomf
Imported Ontologies:
lscr
Download serialization:
JSON-LD RDF/XML N-Triples TTL
License:
https://creativecommons.org/publicdomain/zero/1.0/
Visualization:
Visualize with WebVowl
Cite as:
http://purl.org/query/tarcisiomf. Revision: STRING database Web API ontology. Retrieved from: http://purl.org/stringdb/0.2
Ontology Specification Draft

Abstract

This ontology was designed to represent and describe the information retrieved from the STRING database WEB API functions. The WEB API functions are fully described at https://string-db.org/help/api/.

Introduction back to ToC

This ontology is composed of graph patterns and terms from several vocabularies such as ORTH ontology, UniProt core ontology, and OBO foundry ontologies. Nevertheless, solely terms and patterns relevant to represent the information retrieved from STRING DB Web API is depicted in this document and ontology. Therefore, we do not directly import (via owl:import) the external ontologies.

Namespace declarations

Table 1: Namespaces used in the document
:<http://purl.org/stringdb#>
2020-04-23<http://purl.obolibrary.org/obo/obi/2020-04-23>
lscr<http://purl.org/lscr#>
owl<http://www.w3.org/2002/07/owl#>
wiki<https://en.wikipedia.org/wiki>
xsd<http://www.w3.org/2001/XMLSchema#>
skos<http://www.w3.org/2004/02/skos/core#>
rdfs<http://www.w3.org/2000/01/rdf-schema#>
taxonomy<http://purl.uniprot.org/taxonomy>
manual<http://www.uniprot.org/manual>
database<http://purl.uniprot.org/database>
ensembl<http://rdf.ebi.ac.uk/terms/ensembl>
pubmed<http://www.ncbi.nlm.nih.gov/pubmed>
docs<https://www.uniprot.org/docs>
dct<http://purl.org/dc/terms/>
purl-org<http://purl.org>
foaf<http://xmlns.com/foaf/0.1/>
orth<http://purl.org/net/orth#>
oboInOwl<http://www.geneontology.org/formats/oboInOwl>
sio<http://semanticscience.org/resource/>
query<http://purl.org/query#>
www-ebi-ac-uk<https://www.ebi.ac.uk>
efo<http://www.ebi.ac.uk/efo>
up<http://purl.uniprot.org/core/>
help<https://www.uniprot.org/help>
rdf<http://www.w3.org/1999/02/22-rdf-syntax-ns#>
obo<http://purl.obolibrary.org/obo/>
dc<http://purl.org/dc/elements/1.1/>
snap<http://www.ifomis.org/bfo/1.1/snap>

String database ontology: Overview back to ToC

This ontology has the following classes and properties.

Classes

Object Properties

Data Properties

Annotation Properties

Named Individuals

String database ontology: Description back to ToC

Figure 1 illustrates a data schema to represent protein information from the STRING database (DB). The information it can structure is restricted to the one available from STRING database WEB API are defined(see https://string-db.org/help/api/). In Figure 2, similarly to Figure 1, we abstractly illustrate the triple patterns to represent the core information from the STRING DB: protein to protein interactions.

Figure 1. An abstract view of how the triple-based graph is contructed to represent the protein to protein interactions from STRING database. Edges are RDF properties and nodes with the prefix xsd:, and the other nodes are IRIs (Internationalized Resource Identifier) that represents intances of a class such as orth:Protein. Prefixes (e.g. xsd:) are defined at Table 1. To simplify the illustration, in this figure, we merged two nodes into one rdfs:Literal node that has two incoming edges, rdfs:label and skos:prefLabel, but they may assign different literal values. Moreover, :functionallyInteractsWith
 and :physicallyInteractsWith properties must relate two different instances of orth:Protein. Both of them are irreflexive object properties.

Figure 2. An abstract view of how the triple-based graph is contructed to represent the protein information from STRING database. Edges are RDF properties and nodes with the prefix xsd: and the rdfs:Literal values are literals, the other nodes are IRIs (Internationalized Resource Identifier) that represents intances of a class such as orth:Protein. Prefixes are defined at Table 1. To simplify the illustration, in this figure, we merged eight nodes into one xsd:double node that has eight incoming edges (i.e. :combinedScore, :neighborhoodScore, :fusionScore, :phylogeneticScore, :coexpressionScore ?ascore, :experimentalScore, :databaseScore, and :textMiningScore) but they may assign different numerical values.
Figure 3 contains triple patterns to represent the functional annotations obtained from Retrieving functional annotation. STRING maps several databases onto its proteins, this includes: Gene Ontology, KEGG pathways, UniProt Keywords, Pfam domains, InterPro domains, and SMART domains. When it is possible instances IRIs and graph patterns are the same as defined in the UniProt RDF store. For example, we reuse the http://purl.uniprot.org/database/Reactome IRI to represent the Reactome database. Indeed, this IRI is an instance of up:Database as defined in the UniProt RDF store.

Figure 3. An abstract view of how the triple-based graph is contructed to represent the functional annotations stated in the STRING database. Edges are RDF properties and nodes with the rdfs:Literal values are literals, the other nodes are IRIs (Internationalized Resource Identifier) that represents intances of a class such as orth:Protein. Prefixes are defined at Table 1.

Cross reference for String database ontology classes, properties and dataproperties back to ToC

This section provides details for each class and property defined by String database ontology.

Classes

Cluster of homologous sequencesc back to ToC or Class ToC

IRI: http://purl.org/net/orth#HomologsCluster

Set of homologous sequences
is in range of
see also OMA group

Conceptc back to ToC or Class ToC

IRI: http://purl.uniprot.org/core/Concept

A concept used to classify resources.
Is defined by
http://purl.uniprot.org/core/
has super-classes
is in range of
classified with op

Concept Schemec back to ToC or Class ToC

IRI: http://www.w3.org/2004/02/skos/core#ConceptScheme

A set of concepts, optionally including statements about semantic relationships between those concepts.
Is defined by
http://www.w3.org/2004/02/skos/core
Example
Thesauri, classification schemes, subject heading lists, taxonomies, 'folksonomies', and other types of controlled vocabulary are all examples of concept schemes. Concept schemes are also embedded in glossaries and terminologies.
is in range of
is in scheme op
has members
Gene Ontology ni, Integrated resource of protein families, domains and functional sites ni, KEGG: Kyoto Encyclopedia of Genes and Genomes ni, Pfam protein domain database ni, PubMed publications ni, Reactome - a knowledgebase of biological pathways and processes ni, Simple Modular Architecture Research Tool; a protein domain database ni, UniProt Keywords ni

Genec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000704

Is defined by
http://purl.org/stringdb
is in range of
see also Ensembl gene

genec back to ToC or Class ToC

IRI: http://purl.org/net/orth#Gene

Is defined by
http://purl.org/stringdb

homology relationc back to ToC or Class ToC

IRI: http://purl.org/net/orth#HomologyRelation

This class represents homology relations among sequence units (e.g genes, proteins or gene regions).
has super-classes
is in domain of
bit-score dp

material entityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000040

A material entity is an entity that exists in full during the length of time of its existence, persists through this time while maintaining its identity and has no temporal parts. For example a heart, a human, a fly, a microarray.
Is defined by
http://purl.obolibrary.org/obo/bfo.owl
Example
A heart, a human, a fly, a microarray.
is equivalent to
material entity c
is in domain of
interacts with op
is in range of
interacts with op

network imagec back to ToC or Class ToC

IRI: http://purl.org/stringdb#NetworkImage

A network image of interactions among proteins, that illustrates a neighborhood surrounding one or more proteins.
has super-classes
is in domain of
format dp, network flavor dp, network type dp, resolution dp
is in range of
has network image op

Organismc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C14250

is equivalent to
Organism c

Organismc back to ToC or Class ToC

IRI: http://purl.org/net/orth#Organism

A living being, such as an animal, a plant, a bacterium, or a fungus., Any individual living (or previously living) being. Example: animal, human being. An organim can be associated to a taxon such as "Homo Sapiens", NCBI taxonomy identifier: 9606.
has super-classes
is in range of
organism op

polypeptidec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000104

is equivalent to
Protein c

Proteinc back to ToC or Class ToC

IRI: http://purl.org/net/orth#Protein

Is defined by
http://purl.org/stringdb
has super-classes
Sequence unit c
is in domain of
functionally interacts with op, has network image op, physically interacts with op
is in range of
functionally interacts with op, has protein op, physically interacts with op, see also OMA protein

proteinc back to ToC or Class ToC

IRI: http://purl.uniprot.org/core/Protein

Is defined by
http://purl.org/stringdb
is in domain of
classified with op
is in range of
see also UniProt cross-reference

proteinc back to ToC or Class ToC

IRI: http://rdf.ebi.ac.uk/terms/ensembl/protein

Is defined by
http://purl.org/stringdb
is in range of
see also Ensembl protein

protein-protein interactionc back to ToC or Class ToC

IRI: http://purl.org/stringdb#ProteinProteinInteraction

Temporary, non-covalent binding between protein molecules. Protein-protein interactions occur as a result of intermolecular physical forces and spatial complementation between domains or motifs. This interaction can be either homotypic or heterotypic and effect protein structure, conformation, and function.[source: NCIT]
has super-classes
is in domain of
has functional interaction score op, has physical interaction score op

protein-protein interaction enrichmentc back to ToC or Class ToC

IRI: http://purl.org/stringdb#PPIEnrichment

Even in the absence of annotated proteins (e.g. in novel genomes) databases such as STRING can tell if the subset of proteins is functionally related, that is, if it is enriched in interactions in comparison to the background proteome-wide interaction distribution.
is in domain of
average node degree dp, edge amount dp, edge amount dp, expected edge amount dp, p-value dp, protein amount dp

Resourcec back to ToC or Class ToC

IRI: http://purl.uniprot.org/core/Resource

A life science resource.
Is defined by
http://purl.uniprot.org/core/
is in domain of
database op

scorec back to ToC or Class ToC

IRI: http://purl.org/stringdb#Score

Class to define a set of any type of score values.
is in domain of
coexpression score dp, combined score dp, database score dp, experimental score dp, gene fusion score dp, gene neighborhood score dp, partial score dp, phylogenetic profile score dp, text mining score dp
is in range of
has functional interaction score op, has physical interaction score op

Sequence unitc back to ToC or Class ToC

IRI: http://purl.org/net/orth#SequenceUnit

protein or DNA sequence as a unit of comparison
has sub-classes
Protein c
is in domain of
has homolog op, organism op
is in range of
has homolog op

Taxonc back to ToC or Class ToC

IRI: http://purl.uniprot.org/core/Taxon

An element of a taxonomy for classifying life forms.
has super-classes
is in domain of
rank op, replaces op
is in range of
replaces op
has members
Homo sapiens ni

Transcriptc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000673

Is defined by
http://purl.org/stringdb
is in range of
see also Ensembl transcript

Object Properties

classified withop back to ToC or Object Property ToC

IRI: http://purl.uniprot.org/core/classifiedWith

A concept that classifies this resource.
Is defined by
http://purl.uniprot.org/core/
has domain
protein c
has range
Concept c

contained inop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0001018

databaseop back to ToC or Object Property ToC

IRI: http://purl.uniprot.org/core/database

Is defined by
http://purl.uniprot.org/core/

has characteristics: functional

has domain
Resource c
has range
Database (description of) c

functionally interacts withop back to ToC or Object Property ToC

IRI: http://purl.org/stringdb#functionallyInteractsWith

It states a protein that functionally interacts with another one, a pairwise relationship.

has characteristics: symmetric, irreflexive

has super-properties
interacts with op
has domain
Protein c
has range
Protein c

hasop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/CDAO_0000178

Generic 'has' property.
has sub-properties
has homolog op, has homology data op
is inverse of
part_of op

has functional interaction scoreop back to ToC or Object Property ToC

IRI: http://purl.org/stringdb#hasFunctionalInteractionScore

It states a protein-protein functional interaction score.

has characteristics: functional

has domain
protein-protein interaction c
has range
score c

has homologop back to ToC or Object Property ToC

IRI: http://purl.org/net/orth#hasHomolog

Homologous pairwise relation between sequence units (e.g.: genes, proteins or gene regions). For example, A Gene(A) hasHomolog Gene(B). This property can be materialized or inferred by applying a logical rule.

has characteristics: symmetric

has super-properties
has op
has domain
Sequence unit c
has range
Sequence unit c

has homologous memberop back to ToC or Object Property ToC

IRI: http://purl.org/net/orth#hasHomologousMember

Property that permits to define the membership of a cluster of homologs or a sequence unit to a clusters of homologs.
has super-properties
has part op
has domain
Cluster of homologous sequences c or homology relation c
has range
Cluster of homologous sequences c or Sequence unit c
is inverse of
is homologous member op

has homology dataop back to ToC or Object Property ToC

IRI: http://purl.org/net/orth#hasHomologyData

Inverse property of inDataset. It permits to retrieve the clusters or homology relations included in a particular dataset.
has super-properties
has op
has domain
orthology dataset c
has range
Cluster of homologous sequences c or homology relation c
is inverse of
in dataset op

has network imageop back to ToC or Object Property ToC

IRI: http://purl.org/stringdb#hasNetworkImage

It states a network image of interactions among proteins (e.g. from STRING database). The image is composed of a neighborhood surrounding one or more proteins.
has domain
Protein c
has range
network image c

has partop back to ToC or Object Property ToC

IRI: http://semanticscience.org/resource/SIO_000028

has part is a transitive, reflexive and antisymmetric relation between a whole and itself or a whole and its part.
Is defined by
http://purl.org/stringdb

has characteristics: transitive, reflexive

has sub-properties
has homologous member op

has physical interaction scoreop back to ToC or Object Property ToC

IRI: http://purl.org/stringdb#hasPhysicalInteractionScore

It states a protein-protein physical interaction score.

has characteristics: functional

has domain
protein-protein interaction c
has range
score c

has proteinop back to ToC or Object Property ToC

IRI: http://purl.org/stringdb#hasProtein

It states a protein that is part of or contained in the subject.
has domain
protein-protein interaction enrichment c or protein-protein interaction c
has range
Protein c

in datasetop back to ToC or Object Property ToC

IRI: http://purl.org/net/orth#inDataset

Property that provides the dataset associated with a gene tree node
has domain
Cluster of homologous sequences c or homology relation c
has range
orthology dataset c
is inverse of
has homology data op

in taxonop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002162

Connects a biological entity to its taxon of origin.

interacts withop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002434

A relationship that holds between two entities in which the processes executed by the two entities are causally connected.

has characteristics: symmetric

has sub-properties
functionally interacts with op, physically interacts with op
has domain
material entity c
has range
material entity c

is homologous memberop back to ToC or Object Property ToC

IRI: http://purl.org/net/orth#isHomologousMember

Inverse of has homologous member. This property permits to find the cluster in which a cluster or sequence unit is included.
has super-properties
member of op
is inverse of
has homologous member op

is in schemeop back to ToC or Object Property ToC

IRI: http://www.w3.org/2004/02/skos/core#inScheme

Relates a resource (for example a concept) to a concept scheme in which it is included.
Is defined by
http://www.w3.org/2004/02/skos/core
has range
Concept Scheme c

member ofop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002350

Is member of is a mereological relation between a item and a collection.
Is defined by
http://purl.org/stringdb
has sub-properties
is homologous member op

organismop back to ToC or Object Property ToC

IRI: http://purl.org/net/orth#organism

has domain
Sequence unit c
has range
Organism c

part_ofop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/CDAO_0000194

is inverse of
has op

physically interacts withop back to ToC or Object Property ToC

IRI: http://purl.org/stringdb#physicallyInteractsWith

It states a protein that physically interacts with another one, a pairwise relationship.

has characteristics: symmetric, irreflexive

has super-properties
interacts with op
has domain
Protein c
has range
Protein c

rankop back to ToC or Object Property ToC

IRI: http://purl.uniprot.org/core/rank

The rank of a taxon.

has characteristics: functional

has domain
Taxon c
has range
rank c

replacesop back to ToC or Object Property ToC

IRI: http://purl.uniprot.org/core/replaces

A resource that is replaced by this resource.
has domain
Taxon c
has range
Taxon c

Data Properties

average node degreedp back to ToC or Data Property ToC

IRI: http://purl.org/stringdb#averageNodeDegree

The mean degree of the node in the network.

has characteristics: functional

has domain
protein-protein interaction enrichment c
has range
double

bit-scoredp back to ToC or Data Property ToC

IRI: http://purl.org/stringdb#bitscore

Smith-Waterman alignment bit-score.

has characteristics: functional

has domain
homology relation c
has range
double

coexpression scoredp back to ToC or Data Property ToC

IRI: http://purl.org/stringdb#coexpressionScore

The coexpression score is derived from similar pattern of mRNA expression measured by DNA arrays and similar technologies.

has characteristics: functional

has super-properties
partial score dp
has domain
score c
has range
double

combined scoredp back to ToC or Data Property ToC

IRI: http://purl.org/stringdb#combinedScore

The combined score is computed by combining the probabilities from the different evidence channels and corrected for the probability of randomly observing an interaction. The combined score is computed from the partial scores (e.g. fusion score, experimental score).

has characteristics: functional

has domain
score c
has range
double

database scoredp back to ToC or Data Property ToC

IRI: http://purl.org/stringdb#databaseScore

The database score is derived from curated data of various databases.

has characteristics: functional

has super-properties
partial score dp
has domain
score c
has range
double

Descriptiondp back to ToC or Data Property ToC

IRI: http://purl.org/dc/elements/1.1/description

An account of the resource.
Is defined by
http://purl.org/dc/elements/1.1/
has range
literal

edge amountdp back to ToC or Data Property ToC

IRI: http://purl.org/stringdb#edgeNumber

The number of edges in the network.

has characteristics: functional

has domain
protein-protein interaction enrichment c
has range
non negative integer

edge amountdp back to ToC or Data Property ToC

IRI: http://purl.org/stringdb#localClusteringCoefficient

The average local clustering coefficient.

has characteristics: functional

has domain
protein-protein interaction enrichment c
has range
double

expected edge amountdp back to ToC or Data Property ToC

IRI: http://purl.org/stringdb#expectedEdgeNumber

The expected number of edges based on the nodes degrees.

has characteristics: functional

has domain
protein-protein interaction enrichment c
has range
non negative integer

experimental scoredp back to ToC or Data Property ToC

IRI: http://purl.org/stringdb#experimentalScore

The experimental score is derived from experimental data, such as, affinity chromatography.

has characteristics: functional

has super-properties
partial score dp
has domain
score c
has range
double

formatdp back to ToC or Data Property ToC

IRI: http://purl.org/stringdb#format

The file format (e.g. png, svg).
has domain
network image c
has range
string

gene fusion scoredp back to ToC or Data Property ToC

IRI: http://purl.org/stringdb#fusionScore

The gene fusion score is derived from fused proteins in other species.

has characteristics: functional

has super-properties
partial score dp
has domain
score c
has range
double

gene neighborhood scoredp back to ToC or Data Property ToC

IRI: http://purl.org/stringdb#neighborhoodScore

The neighborhood score is computed from the inter-gene nucleotide count.

has characteristics: functional

has super-properties
partial score dp
has domain
score c
has range
double

Mnemonicdp back to ToC or Data Property ToC

IRI: http://purl.uniprot.org/core/mnemonic

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.
has range
string

network flavordp back to ToC or Data Property ToC

IRI: http://purl.org/stringdb#networkFlavor

The style of edges in the network: evidence, confidence, actions
has domain
network image c
has range
{ "actions" , "confidence" , "evidence" }

network typedp back to ToC or Data Property ToC

IRI: http://purl.org/stringdb#networkType

The network type: functional or physical
has domain
network image c
has range
{ "functional" , "physical" }

p-valuedp back to ToC or Data Property ToC

IRI: http://purl.org/stringdb#pvalue

P-value for statistical significance. For example, in STRING DB, the significance of the network having more interactions than expected.

has characteristics: functional

has domain
protein-protein interaction enrichment c
has range
double

partial scoredp back to ToC or Data Property ToC

IRI: http://purl.org/stringdb#partialScore

The partial scores used to compute the combined scores.
has sub-properties
coexpression score dp, database score dp, experimental score dp, gene fusion score dp, gene neighborhood score dp, phylogenetic profile score dp, text mining score dp
has domain
score c
has range
double

phylogenetic profile scoredp back to ToC or Data Property ToC

IRI: http://purl.org/stringdb#phylogeneticScore

The cooccurence score of the phyletic profile that is derived from similar absence/presence patterns of genes.

has characteristics: functional

has super-properties
partial score dp
has domain
score c
has range
double

protein amountdp back to ToC or Data Property ToC

IRI: http://purl.org/stringdb#nodeNumber

The number of proteins in the network, that are representend with nodes.

has characteristics: functional

has domain
protein-protein interaction enrichment c
has range
non negative integer

resolutiondp back to ToC or Data Property ToC

IRI: http://purl.org/stringdb#resolution

The image resolution as a qualitative value (e.g. high resolution).
has domain
network image c
has range
{ "high" , "low" , "medium" , "unknown" }

scientific namedp back to ToC or Data Property ToC

IRI: http://purl.uniprot.org/core/scientificName

Is defined by
http://purl.org/stringdb

has characteristics: functional

has range
string

text mining scoredp back to ToC or Data Property ToC

IRI: http://purl.org/stringdb#textMiningScore

The textmining score is derived from the co-occurrence of gene/protein names in abstracts.

has characteristics: functional

has super-properties
partial score dp
has domain
score c
has range
double

Annotation Properties

alt labelap back to ToC or Annotation Property ToC

IRI: http://www.w3.org/2000/01/rdf-schema#altLabel

alternative labelap back to ToC or Annotation Property ToC

IRI: http://www.w3.org/2004/02/skos/core#altLabel

The range of skos:altLabel is the class of RDF plain literals.
An alternative lexical label for a resource.
Is defined by
http://www.w3.org/2004/02/skos/core
Example
Acronyms, abbreviations, spelling variants, and irregular plural/singular forms may be included among the alternative labels for a concept. Mis-spelled terms are normally included as hidden labels (see skos:hiddenLabel).
has super-properties
label

close matchap back to ToC or Annotation Property ToC

IRI: http://www.w3.org/2004/02/skos/core#closeMatch

creatorap back to ToC or Annotation Property ToC

IRI: http://purl.org/dc/elements/1.1/creator

curator noteap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000232

Is defined by
http://purl.obolibrary.org/obo/iao.owl

Date Issuedap back to ToC or Annotation Property ToC

IRI: http://purl.org/dc/terms/issued

Date of formal issuance of the resource.
Is defined by
http://purl.org/dc/terms/

definitionap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000115

definitionap back to ToC or Annotation Property ToC

IRI: http://www.w3.org/2004/02/skos/core#definition

A statement or formal explanation of the meaning of a concept.
Is defined by
http://www.w3.org/2004/02/skos/core
has super-properties
note ap

Descriptionap back to ToC or Annotation Property ToC

IRI: http://purl.org/dc/terms/description

An account of the resource.
Is defined by
http://purl.org/dc/terms/

editor noteap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000116

Is defined by
http://purl.obolibrary.org/obo/iao.owl

exampleap back to ToC or Annotation Property ToC

IRI: http://www.w3.org/2004/02/skos/core#example

example of usageap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000112

has_alternative_idap back to ToC or Annotation Property ToC

IRI: http://www.geneontology.org/formats/oboInOwl#hasAlternativeId

Is defined by
http://www.geneontology.org/formats/oboInOwl#

has_dbxrefap back to ToC or Annotation Property ToC

IRI: http://www.geneontology.org/formats/oboInOwl#hasDbXref

Is defined by
http://www.geneontology.org/formats/oboInOwl#

has_exact_synonymap back to ToC or Annotation Property ToC

IRI: http://www.geneontology.org/formats/oboInOwl#hasExactSynonym

An alias in which the alias exhibits true synonymy. Example: ornithine cycle is an exact synonym of urea cycle
Is defined by
http://www.geneontology.org/formats/oboInOwl#
has super-properties
has_synonym ap

has_related_synonymap back to ToC or Annotation Property ToC

IRI: http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym

An alias in which the alias is related the primary class name, but not necessarily broader or narrower. Example: cytochrome bc1 complex is a related synonym of ubiquinol-cytochrome-c reductase activity; virulence is a related synonym of pathogenesis
Is defined by
http://www.geneontology.org/formats/oboInOwl#
has super-properties
has_synonym ap

has_synonymap back to ToC or Annotation Property ToC

IRI: http://www.geneontology.org/formats/oboInOwl#hasSynonym

A relation between a class and an alias term.
Is defined by
http://www.geneontology.org/formats/oboInOwl#
has sub-properties
has_exact_synonym ap, has_related_synonym ap

i a o 0000111ap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000111

i a o 0000119ap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000119

Licenseap back to ToC or Annotation Property ToC

IRI: http://purl.org/dc/terms/license

A legal document giving official permission to do something with the resource.
Is defined by
http://purl.org/dc/terms/

max qualified cardinalityap back to ToC or Annotation Property ToC

IRI: http://www.w3.org/2002/07/owl#maxQualifiedCardinality

noteap back to ToC or Annotation Property ToC

IRI: http://www.w3.org/2004/02/skos/core#note

has sub-properties
definition ap

pageap back to ToC or Annotation Property ToC

IRI: http://xmlns.com/foaf/0.1/page

preferred labelap back to ToC or Annotation Property ToC

IRI: http://www.w3.org/2004/02/skos/core#prefLabel

A resource has no more than one value of skos:prefLabel per language tag, and no more than one value of skos:prefLabel without language tag.
The preferred lexical label for a resource, in a given language.
Is defined by
http://www.w3.org/2004/02/skos/core
has super-properties
label

related matchap back to ToC or Annotation Property ToC

IRI: http://www.w3.org/2004/02/skos/core#relatedMatch

scope noteap back to ToC or Annotation Property ToC

IRI: http://www.w3.org/2004/02/skos/core#scopeNote

see also EMBL sequenceap back to ToC or Annotation Property ToC

IRI: http://purl.org/lscr#xrefEMBLSequence

This cross-reference relates a given resource to any EMBL sequence database resource.
has super-properties
see also

see also Ensembl cross-referenceap back to ToC or Annotation Property ToC

IRI: http://purl.org/lscr#xrefEnsembl

This cross-reference relates a given resource to any Ensembl database resource.
has super-properties
see also
has sub-properties
see also Ensembl gene ap, see also Ensembl protein ap, see also Ensembl transcript ap

see also Ensembl geneap back to ToC or Annotation Property ToC

IRI: http://purl.org/lscr#xrefEnsemblGene

This cross-reference relates a given resource to an Ensembl gene. URI RDF instance template to assign this property: http://rdf.ebi.ac.uk/resource/ensembl/{ENSEMBL_GENE_ID}. Example: :ANY_URI lscr:xrefEnsemblGene http://rdf.ebi.ac.uk/resource/ensembl/ENSG00000139618
has super-properties
see also Ensembl cross-reference ap
has range
Gene c

see also Ensembl proteinap back to ToC or Annotation Property ToC

IRI: http://purl.org/lscr#xrefEnsemblProtein

This cross-reference relates a given resource to an Ensembl protein. URI RDF instance template to assign this property: http://rdf.ebi.ac.uk/resource/ensembl.protein/{ENSEMBL_PROTEIN_ID}. Example: :ANY_URI lscr:xrefEnsemblProtein http://rdf.ebi.ac.uk/resource/ensembl.protein/ENSP00000296370
has super-properties
see also Ensembl cross-reference ap
has range
protein c

see also Ensembl transcriptap back to ToC or Annotation Property ToC

IRI: http://purl.org/lscr#xrefEnsemblTranscript

This cross-reference relates a given resource to an Ensembl transcript. URI RDF instance template to assign this property: http://rdf.ebi.ac.uk/resource/ensembl.transcript/{ENSEMBL_TRANSCRIPT_ID}. Example: :ANY_URI lscr:xrefEnsemblTranscript http://rdf.ebi.ac.uk/resource/ensembl.transcript/ENST00000380152
has super-properties
see also Ensembl cross-reference ap
has range
Transcript c

see also MBGD cross-referenceap back to ToC or Annotation Property ToC

IRI: http://purl.org/lscr#xrefMBGD

This cross-reference relates a given resource to any MBGD database resource. MBGD: Microbial Genome Database for Comparative Analysis - mbgd.genome.ad.jp .
has super-properties
see also
has sub-properties
see also MBGD gene ap, see also MBGD gene group ap

see also MBGD geneap back to ToC or Annotation Property ToC

IRI: http://purl.org/lscr#xrefMBGDGene

This cross-reference relates a given resource to an MBGD gene. MBGD: Microbial Genome Database for Comparative Analysis - mbgd.genome.ad.jp .
has super-properties
see also MBGD cross-reference ap

see also MBGD gene groupap back to ToC or Annotation Property ToC

IRI: http://purl.org/lscr#xrefMBGDGroup

This cross-reference relates a given resource to an MBGD group of genes. MBGD: Microbial Genome Database for Comparative Analysis - mbgd.genome.ad.jp .
has super-properties
see also MBGD cross-reference ap

see also NCBI cross-referenceap back to ToC or Annotation Property ToC

IRI: http://purl.org/lscr#xrefNCBI

This cross-reference relates a given resource to any NCBI database resource. NCBI: National Center for Biotechnology Information - https://www.ncbi.nlm.nih.gov/ .
has super-properties
see also
has sub-properties
see also NCBI RefSeq ap, see also NCBI gene ap, see also NCBI protein ap

see also NCBI geneap back to ToC or Annotation Property ToC

IRI: http://purl.org/lscr#xrefNCBIGene

This cross-reference relates a given resource to an NCBI gene resource. NCBI: National Center for Biotechnology Information - https://www.ncbi.nlm.nih.gov/ .
has super-properties
see also NCBI cross-reference ap

see also NCBI proteinap back to ToC or Annotation Property ToC

IRI: http://purl.org/lscr#xrefNCBIProtein

This cross-reference relates a given resource to an NCBI protein resource. NCBI: National Center for Biotechnology Information - https://www.ncbi.nlm.nih.gov/ .
has super-properties
see also NCBI cross-reference ap

see also NCBI RefSeqap back to ToC or Annotation Property ToC

IRI: http://purl.org/lscr#xrefNCBIRefSeq

This cross-reference relates a given resource to an NCBI Reference Sequence Database (RefSeq) resource. NCBI: National Center for Biotechnology Information - https://www.ncbi.nlm.nih.gov/ .
has super-properties
see also NCBI cross-reference ap

see also OMA cross-referenceap back to ToC or Annotation Property ToC

IRI: http://purl.org/lscr#xrefOMA

This cross-reference relates a given resource to an OMA database resource.
has super-properties
see also
has sub-properties
see also OMA group ap, see also OMA protein ap

see also OMA groupap back to ToC or Annotation Property ToC

IRI: http://purl.org/lscr#xrefOMAGroup

This cross-reference relates a given resource to an OMA group of sequences (e.g.: proteins).
has super-properties
see also OMA cross-reference ap
has range
Cluster of homologous sequences c

see also OMA proteinap back to ToC or Annotation Property ToC

IRI: http://purl.org/lscr#xrefOMAProtein

This cross-reference relates a given resource to an OMA proteins. URI RDF instance template to assign this property: http://omabrowser.org/ontology/oma#PROTEIN_{OMA_ID}. Example: :ANY_URI lscr:xrefOMAProtein http://omabrowser.org/ontology/oma#PROTEIN_HUMAN22168
has super-properties
see also OMA cross-reference ap
has range
Protein c

see also UniProt cross-referenceap back to ToC or Annotation Property ToC

IRI: http://purl.org/lscr#xrefUniprot

This cross-reference relates a given resource to a UniProt protein. URI RDF instance template to assign this property: http://purl.uniprot.org/uniprot/{UNIPROT_ID}. Example: :ANY_URI lscr:xrefUniprot http://purl.uniprot.org/uniprot/P68871
has super-properties
see also
has range
protein c

source definitionap back to ToC or Annotation Property ToC

IRI: http://www.ebi.ac.uk/efo/source_definition

term editorap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000117

Named Individuals

Gene Ontologyni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/go.owl

belongs to
Concept Scheme c

Homo sapiensni back to ToC or Named Individual ToC

IRI: http://purl.uniprot.org/taxonomy/9606

belongs to
Taxon c

Integrated resource of protein families, domains and functional sitesni back to ToC or Named Individual ToC

IRI: http://purl.uniprot.org/database/InterPro

belongs to
Database (description of) c
database c

KEGG: Kyoto Encyclopedia of Genes and Genomesni back to ToC or Named Individual ToC

IRI: http://purl.uniprot.org/database/KEGG

belongs to
Database (description of) c
database c

p-valueni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000175

has facts
is in scheme op obi.owl
is also defined as
class

Pfam protein domain databaseni back to ToC or Named Individual ToC

IRI: http://purl.uniprot.org/database/Pfam

belongs to
Database (description of) c
database c

PubMed publicationsni back to ToC or Named Individual ToC

IRI: https://pubmed.ncbi.nlm.nih.gov

belongs to
database c

Reactome - a knowledgebase of biological pathways and processesni back to ToC or Named Individual ToC

IRI: http://purl.uniprot.org/database/Reactome

belongs to
Database (description of) c
database c

Simple Modular Architecture Research Tool; a protein domain databaseni back to ToC or Named Individual ToC

IRI: http://purl.uniprot.org/database/SMART

belongs to
Database (description of) c
database c

STRING databaseni back to ToC or Named Individual ToC

IRI: https://string-db.org

STRING is a database of known and predicted protein-protein interactions. The interactions include direct (physical) and indirect (functional) associations; they stem from computational prediction, from knowledge transfer between organisms, and from interactions aggregated from other (primary) databases.
belongs to
database c

UniProt Keywordsni back to ToC or Named Individual ToC

IRI: https://www.uniprot.org/docs/keywlist.txt

belongs to
Concept Scheme c

Legend back to ToC

c: Classes
op: Object Properties
dp: Data Properties
ni: Named Individuals

References back to ToC

Add your references here. It is recommended to have them as a list.

Acknowledgements back to ToC

The authors would like to thank Silvio Peroni for developing LODE, a Live OWL Documentation Environment, which is used for representing the Cross Referencing Section of this document and Daniel Garijo for developing Widoco, the program used to create the template used in this documentation.