Gene expression (GenEx) ontology
type: Ontology
version IRI: http://purl.org/genex/0.2
imports: caro.owl
imports: iao.owl
imports: ro.owl
imports: lscr
imports: http://purl.org/net/orth/2.0
imports: efo.owl
imports: core
abstract: Expression patterns are a major feature of gene description, and are captured in many expression related databases (e.g., Bgee, Expression Atlas, GENEVESTIGATOR, or Tissue). Yet comparison and interoperability among these heterogeneous data sources or providers is limited by a lack of agreement for describing knowledge of gene expression. Ontologies are recognized as an interesting approach to achieve a consensus for knowledge representation, and allow to leverage semantic interoperability, but are lacking for the domain of gene expression. The Relational Ontology (RO) contains preliminary efforts to define terms for describing this domain. Notably, it contains `expressed in` and `expresses` properties (i.e., relations). Nonetheless, further work was necessary to address the following issue: the representation of additional information related to gene expression, such as developmental stages, as well as absent in and highly expressed relations. Furthermore, we reuse parts of the data schemas of the ORTH and UniProt core ontologies to provide the capacity to interoperate with other biological databases from different knowledge domains which are still relevant to the gene expression domain. Moreover, different gene expression databases use distinct confidence scores to assert expressed in or absent in relations. Finally, the GenEx ontology is fully adopted by Bgee, a gene expression database, as its core data schema to structure the Bgee RDF data accessible via its SPARQL endpoint at [https://www.bgee.org/sparql/](https://www.bgee.org/sparql/).
bibliographic citation: Ana Claudia Sima, Tarcisio Mendes de Farias, Erich Zbinden, Maria Anisimova, Manuel Gil, Heinz Stockinger, Kurt Stockinger, Marc Robinson-Rechavi, Christophe Dessimoz, Enabling semantic queries across federated bioinformatics databases, Database, Volume 2019, 2019, baz106, https://doi.org/10.1093/database/baz106
contributor: Christophe Dessimoz
contributor: Julien Wollbrett
contributor: Tarcisio Mendes de Farias
contributor: Marc Robinson-Rechavi
contributor: Frederic Bastian
created: 2019-01-25
creator: Tarcisio Mendes de Farias
description: The GenEx ontology is designed to capture and structure gene expression information provided by databases such as Bgee.
issue: 2019-11-07
license: https://creativecommons.org/publicdomain/zero/1.0/
modified: 2024-04-30
publisher: SIB Swiss Institute of Bioinformatics
status: accepted
preferred namespace prefix: genex
preferred namespace uri: http://purl.org/genex#
extends: ro.owl
code repository: https://github.com/biosoda/genex
version info: 0.2
introduction: There is a general lack of a comprehensive ontology to serve as a data schema for describing knowledge in the field of gene expression. This may seem surprising, considering the ubiquity of gene expression analyses in molecular biology and the existence of multiple well-established resources for gene expression, such as Bgee, Expression Atlas (EA), GENEVESTIGATOR, RefEx (Reference Expression dataset) or the Tissue Expression database. We note here that different gene expression databases often use distinct criteria to assert expressed in or absent in relations. To the best of our knowledge, at least 3 semantic models currently exist as initial attempts to structure gene expression related data: the Relation Ontology (RO), the Expression Atlas semantic model (discontinued) and Bioschema.org / Schema.org. The Relation Ontology and Schema.org define only a few terms within the domain of gene expression and is not uniquely designed for this knowledge domain. Notably, they contain an 'expressed in' relation. The Expression Atlas defines a semantic model related to gene expression that mainly focuses on modelling the Expression Atlas data itself and not the domain of gene expression generally. In this EA model, additional data interpretations (i.e., semantics) are not explicitly represented, such as a given gene is expressed or lowly expressed in some sample relative to others. Although it would be possible to obtain this information through a more complex query on the Expression Atlas SPARQL endpoint (currently discontinued), we lack an explicit representation, which would allow us to compare gene expression data from these different databases. To provide a first step toward a general-purpose gene expression ontology, we defined a semantic model called GenEx. GenEx is aligned with the Relation Ontology and Expression Atlas models to facilitate interoperability with existing RDF stores. Furthermore, we reuse parts of the data schemas of the ORTH and UniProtKB core ontolog…

example of usage
type: AnnotationProperty

definition
type: AnnotationProperty

editor note
type: AnnotationProperty

curator note
type: AnnotationProperty

elucidation
type: AnnotationProperty

Description
range: Literal
type: DatatypeProperty
description: Description may include but is not limited to: an abstract, a table of contents, a graphical representation, or a free-text account of the resource.
comment: An account of the resource.

Description
type: AnnotationProperty
description: Description may include but is not limited to: an abstract, a table of contents, a graphical representation, or a free-text account of the resource.
comment: An account of the resource.

in database
type: AnnotationProperty
comment: A property to define the database an orthology dataset belongs to.
domain: OrthologyDataset

NCI Thesaurus definition citation
type: AnnotationProperty
definition: http://www.ebi.ac.uk/efo/NCI_Thesaurus_definition_citation is an annotation property that is drawn from NCI_Thesaurus
NCI thesaurus definition citation: http://www.ebi.ac.uk/efo/NCI_Thesaurus_definition_citation is an annotation property that is drawn from NCI_Thesaurus
sub property of: definition citation

alternative_term
type: AnnotationProperty
definition: An alternative label for a given entity such as a commonly used abbreviation or synonym.

definition citation
type: AnnotationProperty
definition: A definition citation is a document, ontology class, person or organization from which the definition of the class is derived. It is used in the same sense as a citation in literature, in that the definition may have been derived from these sources or that this definition is related to these source.

alternative label
type: AnnotationProperty
comment: The range of skos:altLabel is the class of RDF plain literals.
comment: skos:prefLabel, skos:altLabel and skos:hiddenLabel are pairwise disjoint properties.
definition: An alternative lexical label for a resource.
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).
sub property of: label

definition
type: AnnotationProperty
definition: A statement or formal explanation of the meaning of a concept.
sub property of: note

example
type: AnnotationProperty
definition: An example of the use of a concept.
sub property of: note

note
type: AnnotationProperty
definition: A general note, for any purpose.
scope note: This property may be used directly, or as a super-property for more specific note types.

scope note
type: AnnotationProperty
definition: A note that helps to clarify the meaning and/or the use of a concept.
sub property of: note

part_of
type: ObjectProperty

contained in
type: ObjectProperty

in taxon
type: ObjectProperty
example: @prefix bgee-species: <https://bgee.org/species/> . @prefix oma: <http://omabrowser.org/ontology/oma#GENE_> . @prefix up: <http://purl.uniprot.org/core/> . @prefix up-taxon: <http://purl.uniprot.org/taxonomy/> . bgee-species:10090 rdf:type orth:Organism ; obo:RO_0002162 up-taxon:10090 . up-taxon:10090 rdf:type up:Taxon ; up:scientificName "Mus musculus".
comment: Connects a biological entity to its taxon of origin.

expressed in
type: ObjectProperty
sub property of: genomically related to
inverse of: expresses
domain: continuant
range: independent continuant
example of usage: 'neural crest cell' SubClassOf expresses some 'Wnt1 gene'
definition: x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process
example: @prefix dcterms: <http://purl.org/dc/terms/> . @prefix obo: <ttp://purl.obolibrary.org/obo/> . @prefix genex: <http://purl.org/genex#> . @prefix oma: <http://omabrowser.org/ontology/oma#GENE_> . obo:UBERON_0000310 rdf:type genex:AnatomicalEntity . oma:ENSMUSG00000002396 rdf:type orth:Gene ; obo:RO_0002206 obo:UBERON_0000310 .

over-expressed in
type: ObjectProperty
sub property of: is expressed in
definition: g is over-expressed in t iff g is expressed in t, and the expression level of g is increased relative to some background.
alternative label: highly expressed in

under-expressed in
type: ObjectProperty
sub property of: is expressed in
definition: g is under-expressed in t iff g is expressed in t, and the expression level of g is decreased relative to some background.

ubiquitously expressed in
type: ObjectProperty
sub property of: is expressed in
inverse of: ubiquitously expresses
definition: x is ubiquitously expressed in y if and only if x is expressed in y, and the majority of cells in y express x
editor note: Revisit this term after coordinating with SO/SOM. The domain of this relation should be a sequence, as an instance of a DNA molecule is only expressed in the cell of which it is a part.

expresses
type: ObjectProperty
sub property of: genomically related to
definition: Inverse of 'expressed in'
example: @prefix dcterms: <http://purl.org/dc/terms/> . @prefix obo: <ttp://purl.obolibrary.org/obo/> . @prefix genex: <http://purl.org/genex#> . @prefix oma: <http://omabrowser.org/ontology/oma#GENE_> . obo:UBERON_0000310 rdf:type genex:AnatomicalEntity ; obo:RO_0002292 oma:ENSMUSG00000002396 . oma:ENSMUSG00000002396 rdf:type orth:Gene .

ubiquitously expresses
type: ObjectProperty
sub property of: expresses
definition: inverse of ubiquiotously expressed in
in subset: RO_0002259

genomically related to
type: ObjectProperty
domain: continuant
range: continuant
definition: holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts.
curator note: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving the genome of an organism

has anatomical entity
type: ObjectProperty
type: FunctionalProperty
domain: gene expression experiment condition
range: Anatomical entity
example: @prefix bgee: <http://bgee.org/#> . @prefix obo: <http://purl.obolibrary.org/obo/> . @prefix genex: <http://purl.org/genex#> . @prefix efo: <http://www.ebi.ac.uk/efo/> . bgee:EXPRESSION_CONDITION_134065 rdf:type genex:ExpressionCondition ; genex:hasAnatomicalEntity obo:UBERON_0000080 . obo:UBERON_0000080 rdf:type genex:AnatomicalEntity.

has expression or absence confidence level
type: ObjectProperty
type: FunctionalProperty
domain: Class
  union of: absence of gene expression
  union of: gene expression
range: Class
  one of: high confidence level
  one of: medium confidence level
  one of: low confidence level
example: @prefix bgee: <http://bgee.org/#> . @prefix genex: <http://purl.org/genex#> . bgee:EXPRESSION_546588859 rdf:type genex:Expression ; genex:hasConfidenceLevel obo:CIO_0000029 .

has a developmental stage
type: ObjectProperty
type: FunctionalProperty
domain: gene expression experiment condition
range: developmental stage
example: @prefix bgee: <http://bgee.org/#> . @prefix obo: <http://purl.obolibrary.org/obo/> . @prefix genex: <http://purl.org/genex#> . @prefix efo: <http://www.ebi.ac.uk/efo/> . bgee:EXPRESSION_CONDITION_134065 rdf:type genex:ExpressionCondition ; genex:hasDevelopmentalStage obo:UBERON_0000113 . obo:UBERON_0000113 rdf:type efo:EFO_0000399 .

has expression level characteristic
type: ObjectProperty
type: FunctionalProperty
domain: gene expression
range: Class
  one of: average expressed
  one of: highly expressed
  one of: high expressed
  one of: lowly expressed
  one of: low expressed
  one of: ubiquitously expressed
example: @prefix bgee: <http://bgee.org/#> . @prefix genex: <http://purl.org/genex#> . bgee:EXPRESSION_546588859 rdf:type genex:Expression ; genex:hasExpressionCharacteristic genex:AVERAGE_EXPRESSED .

has an expression condition
type: ObjectProperty
domain: Class
  union of: absence of gene expression
  union of: gene expression
range: gene expression experiment condition
example: @prefix bgee: <http://bgee.org/#> . @prefix orth: <http://purl.org/net/orth#> . @prefix genex: <http://purl.org/genex#> . bgee:EXPRESSION_546588859 rdf:type genex:Expression ; genex:hasExpressionCondition bgee:EXPRESSION_CONDITION_354899 . bgee:EXPRESSION_CONDITION_354899 rdf:type genex:ExpressionCondition .
alternative label: has an experimental condition

has sequence unit
type: ObjectProperty
domain: Class
  union of: absence of gene expression
  union of: gene expression
range: Sequence unit
example: @prefix bgee: <http://bgee.org/#> . @prefix oma: <http://omabrowser.org/ontology/oma#GENE_> . @prefix orth: <http://purl.org/net/orth#> . @prefix genex: <http://purl.org/genex#> . bgee:EXPRESSION_546588859 rdf:type genex:Expression ; genex:hasSequenceUnit oma:ENSMUSG00000022751 . oma:ENSMUSG00000022751 a orth:Gene .

has strain
type: ObjectProperty
type: FunctionalProperty
domain: gene expression experiment condition
range: strain
example: @prefix bgee: <http://bgee.org/#> . @prefix obo: <http://purl.obolibrary.org/obo/> . @prefix genex: <http://purl.org/genex#> . @prefix efo: <http://www.ebi.ac.uk/efo/> . bgee:EXPRESSION_CONDITION_134065 rdf:type genex:ExpressionCondition ; genex:hasStrain bgee:STRAIN_3d4eba69908860b0d838be983fd7f9c8 . bgee:STRAIN_3d4eba69908860b0d838be983fd7f9c8 rdf:type efo:EFO_0005135 ; rdfs:label "wild-type"

is absent in
type: ObjectProperty
sub property of: genomically related to
domain: Sequence unit
range: Class
  union of: Anatomical entity
  union of: gene expression experiment condition
  union of: developmental stage
  union of: strain
comment: A sequence unit is absent (not expressed) in some expression condition (e.g. anatomical entity and/or developmental stage). Examples how to assign this property (at a high level of abstraction): GeneA "is absent in" Brain; GeneA "is abent in" adult stage.
comment: Recommendation: prefer to instatiate 'absence of gene expression' and 'gene expression experiment condition' classes to represent Gene expression data. For example, rather than materializing this property at the data store level, it shoud be inferred by applying the logical rules: rule1- 'expressed gene'(?e),'has an expression condition'(?e, ?cond), 'has sequence unit'(?e, ?seq) -> 'is expressed in'(?seq, ?cond); rule2- 'expressed gene'(?e),'has an expression condition'(?e, ?cond), 'has a developmental stage'(?cond, ?stage), 'has sequence unit'(?e, ?seq) -> 'is expressed in'(?seq, ?stage) rule3- 'expressed gene'(?e),'has an expression condition'(?e, ?cond), 'has strain'(?cond, ?strain), 'has sequence unit'(?e, ?seq) -> 'is expressed in'(?seq, ?strain) rule4- 'expressed gene'(?e),'has an expression condition'(?e, ?cond), 'has anatomical entity'(?cond, ?anat), 'has sequence unit'(?e, ?seq) -> 'is expressed in'(?seq, ?anat) These rules are currently defined in Genex ontology as a SWRL (Semantic Web Rule Language) rule. It can be tanslated into another semantic web language such as RIF.
alternative label: is not expressed in

is expressed in
type: ObjectProperty
sub property of: expressed in
domain: Sequence unit
range: Class
  union of: Anatomical entity
  union of: gene expression experiment condition
  union of: developmental stage
  union of: strain
example: @prefix dcterms: <http://purl.org/dc/terms/> . @prefix obo: <ttp://purl.obolibrary.org/obo/> . @prefix genex: <http://purl.org/genex#> . obo:UBERON_0000310 rdf:type genex:AnatomicalEntity . oma:ENSMUSG00000002396 rdf:type orth:Gene ; genex:isExpressedIn obo:UBERON_0000310 .
comment: A sequence unit (e.g. gene) is present (expressed) in some expression condition (e.g. anatomical entity and/or developmental stage). Examples how to assign this property (at a high level of abstraction): GeneA "is expressed in" Brain; GeneA "is expressed in" adult stage.
comment: Recommendation: prefer to instatiate 'expressed gene' and 'gene expression experiment condition' classes to represent Gene expression data. For example, rather than materializing this property at the data store level, it shoud be inferred by applying the logical rules: - 'absence of gene expression'(?e),'has an expression condition'(?e, ?cond), 'has sequence unit'(?e, ?seq) -> 'is absent in'(?seq, ?cond); - 'absence of gene expression'?e),'has an expression condition'(?e, ?cond), 'has a developmental stage'(?cond, ?stage), 'has sequence unit'(?e, ?seq) -> 'is absent in'(?seq, ?stage) - 'absence of gene expression'(?e),'has an expression condition'(?e, ?cond), 'has strain'(?cond, ?strain), 'has sequence unit'(?e, ?seq) -> 'is absent in'(?seq, ?strain) - 'absence of gene expression'(?e),'has an expression condition'(?e, ?cond), 'has anatomical entity'(?cond, ?anat), 'has sequence unit'(?e, ?seq) -> 'is absent in'(?seq, ?anat) These rules are currently defined in Genex ontology as a SWRL (Semantic Web Rule Language) rule. It can be tanslated into another semantic web language such as RIF.

organism
type: ObjectProperty
domain: Sequence unit
range: Organism
example: @prefix bgee-species: <https://bgee.org/species/> . @prefix oma: <http://omabrowser.org/ontology/oma#GENE_> . oma:ENSMUSG00000002396 rdf:type orth:Gene ; orth:organism bgee-species:10090 .

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

replaces
type: ObjectProperty
domain: Taxon
range: Taxon
comment: A resource that is replaced by this resource.

encodes
type: ObjectProperty

Identifier
type: DatatypeProperty
range: Literal
description: Recommended practice is to identify the resource by means of a string conforming to an identification system. Examples include International Standard Book Number (ISBN), Digital Object Identifier (DOI), and Uniform Resource Name (URN). Persistent identifiers should be provided as HTTP URIs.
comment: An unambiguous reference to the resource within a given context.

has expression level score
type: DatatypeProperty
domain: Class
  union of: absence of gene expression
  union of: gene expression
range: double
example: @prefix bgee: <http://bgee.org/#> . @prefix genex: <http://purl.org/genex#> . bgee:EXPRESSION_546588859 rdf:type genex:Expression ; genex:hasExpressionLevel 83.9292 .
alternative label: expression score

has false discovery rate p-value
type: DatatypeProperty
domain: Class
  union of: absence of gene expression
  union of: gene expression
range: double
example: @prefix bgee: <http://bgee.org/#> . @prefix genex: <http://purl.org/genex#> . bgee:EXPRESSION_546588859 rdf:type genex:Expression ; genex:hasFDRpvalue 0.00188199 .
alternative label: has FDR p-value

hasSex
type: DatatypeProperty
type: FunctionalProperty
domain: gene expression experiment condition
range: Datatype
  one of: NA
  one of: any
  one of: female
  one of: hermaphrodite
  one of: male
  one of: mixed
  one of: not annotated
modified: 2021-06-04
example: @prefix bgee: <http://bgee.org/#> . @prefix obo: <http://purl.obolibrary.org/obo/> . @prefix genex: <http://purl.org/genex#> . bgee:EXPRESSION_CONDITION_134065 rdf:type genex:ExpressionCondition ; genex:hasSex "any" .
change note: Added the following value in the range list: any.

common name
type: DatatypeProperty
type: FunctionalProperty
range: string
example: @prefix up: <http://purl.uniprot.org/core/> . @prefix up-taxon: <http://purl.uniprot.org/taxonomy/> . up-taxon:10090 rdf:type up:Taxon ; up:commonName "mouse" .

Mnemonic
type: DatatypeProperty
range: string
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.
comment: A rememberable string that can be used to find entries, not a stable identifier!

scientific name
type: DatatypeProperty
type: FunctionalProperty
range: string
example: @prefix up: <http://purl.uniprot.org/core/> . @prefix up-taxon: <http://purl.uniprot.org/taxonomy/> . up-taxon:10090 rdf:type up:Taxon ; up:scientificName "Mus musculus".

entity
type: Class
editor note: BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81
editor note: Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf
elucidation: An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])

continuant
type: Class
subclass of: entity
editor note: BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240
editor note: Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants
elucidation: A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])

independent continuant
type: Class
subclass of: continuant
example of usage: a chair
example of usage: a heart
example of usage: a leg
example of usage: a molecule
example of usage: a spatial region
example of usage: an atom
example of usage: an orchestra.
example of usage: an organism
example of usage: the bottom right portion of a human torso
example of usage: the interior of your mouth
definition: b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])

anatomical entity
type: Class
subclass of: Anatomical entity
definition: A part of a multicellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex. Or, a substance produced by a multicellular organism with granularity above the level of a protein complex.
id: CARO:0000000
comment: Following BFO, material anatomical entities may have immaterial parts (the lumen of your stomach is part of your stomach). The granularity limit follows the limits set by the Gene Ontology on the granularity limit for GO:cellular_component. Note that substances produced by an organism (sweat, feaces, urine) do not need to be part of an organism to qualify as an anatomical structure.

biological entity
type: Class
subclass of: independent continuant
definition: Entity that is, is part of, or derived from an organism, virus, or viroid or a collection of them.
comment: Important for alignment with Darwin Core class "Organism".

Node
type: Class
comment: Basic unit of graphs and trees

Organism
type: Class
equivalent class: Organism

population
type: Class
definition: A population is a group of material entities consisting of individuals which share a particular characteristic such as inhabiting a particular region or area or ability to interbreed.

polypeptide
type: Class
equivalent class: Protein

gene
type: Class
equivalent class: Gene

absence of gene expression
type: Class
subclass of: Class
  intersection of: Restriction
    some values from: gene expression experiment condition
    on property: has an expression condition
  intersection of: Restriction
    some values from: Sequence unit
    on property: has sequence unit
subclass of: Class
  complement of: gene expression
example: @prefix bgee: <http://bgee.org/#> . @prefix oma: <http://omabrowser.org/ontology/oma#GENE_> . @prefix orth: <http://purl.org/net/orth#> . @prefix genex: <http://purl.org/genex#> . bgee:NOT_EXPRESSED_310632766 rdf:type genex:AbsenceExpression ; genex:hasExpressionLevel 6.44034 ; genex:hasConfidenceLevel obo:CIO_0000029 ; genex:hasFDRpvalue 1.0 ; genex:hasSequenceUnit oma:ENSXETG00000010593 ; genex:hasExpressionCondition bgee:EXPRESSION_CONDITION_134065 .
alternative label: Not expressed gene
alternative label: Not expressed sequence unit

Anatomical entity
type: Class
subclass of: biological entity
example: @prefix dcterms: <http://purl.org/dc/terms/> . @prefix obo: <ttp://purl.obolibrary.org/obo/> . @prefix genex: <http://purl.org/genex#> . obo:UBERON_0000310 rdf:type genex:AnatomicalEntity ; dcterms:description "The upper ventral region of the torso of an organism." ; rdfs:label "breast" .
comment: An anatomical entity can be an organism part (e.g. brain, blood, liver and so on) or a material anatomical entity such as a cell.

gene expression
type: Class
subclass of: Class
  intersection of: Restriction
    some values from: gene expression experiment condition
    on property: has an expression condition
  intersection of: Restriction
    some values from: Sequence unit
    on property: has sequence unit
subclass of: Restriction
  all values from: Class
    one of: average expressed
    one of: highly expressed
    one of: high expressed
    one of: lowly expressed
    one of: low expressed
    one of: ubiquitously expressed
  on property: has expression level characteristic
subclass of: Restriction
  all values from: double
  on property: has expression level score
example: @prefix bgee: <http://bgee.org/#> . @prefix oma: <http://omabrowser.org/ontology/oma#GENE_> . @prefix orth: <http://purl.org/net/orth#> . @prefix genex: <http://purl.org/genex#> . bgee:EXPRESSION_546588859 rdf:type genex:Expression ; genex:hasExpressionLevel 83.9292 ; genex:hasConfidenceLevel obo:CIO_0000029 ; genex:hasFDRpvalue 0.00188199 ; genex:hasSequenceUnit oma:ENSMUSG00000022751 ; genex:hasExpressionCondition bgee:EXPRESSION_CONDITION_354899 .
comment: All sequence units (e.g. Gene) that are expressed in some condition (e.g. organ and/or adult stage).
alternative label: expression
alternative label: sequence unit expression

gene expression experiment condition
type: Class
equivalent class: Class
  union of: Restriction
    some values from: Anatomical entity
    on property: has anatomical entity
  union of: Restriction
    some values from: developmental stage
    on property: has a developmental stage
  union of: Restriction
    some values from: strain
    on property: has strain
  union of: Restriction
    some values from: string
    on property: hasSex
subclass of: Restriction
  all values from: Taxon
  on property: in taxon
example: @prefix bgee: <http://bgee.org/#> . @prefix obo: <http://purl.obolibrary.org/obo/> . @prefix genex: <http://purl.org/genex#> . bgee:EXPRESSION_CONDITION_134065 rdf:type genex:ExpressionCondition ; genex:hasSex "any"; genex:hasStrain bgee:STRAIN_3d4eba69908860b0d838be983fd7f9c8 ; genex:hasAnatomicalEntity obo:UBERON_0000080 ; genex:hasDevelopmentalStage obo:UBERON_0000113 .
comment: A sequence unit (e.g. Gene) is expressed in some expression condition (e.g. anatomical entity and/or developmental stage).
alternative label: expression condition
alternative label: sequence unit expression condition

Gene
type: Class
subclass of: Sequence unit
subclass of: Restriction
  some values from: Organism
  on property: organism
subclass of: Restriction
  all values from: database
  on property: contained in
example: @prefix dcterms: <http://purl.org/dc/terms/> . @prefix obo: <ttp://purl.obolibrary.org/obo/> . @prefix oma: <http://omabrowser.org/ontology/oma#GENE_> . @prefix orth: <http://purl.org/net/orth#> . oma:ENSG00000130208 rdf:type orth:Gene ; dcterms:description "apolipoprotein C1 [Source:HGNC Symbol;Acc:HGNC:607]" ; rdfs:label "first trimester of gestation (cow)"; dcterms:identifier "ENSG00000130208" .

Gene tree node
type: Class
subclass of: Node
comment: A node of a tree whose leaf nodes are sequence units and whose internal nodes are clusters of homologs

Organism
type: Class
subclass of: Restriction
  some values from: Taxon
  on property: in taxon
comment: 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.
alternative label: Living being

Protein
type: Class
subclass of: Sequence unit
subclass of: Restriction
  some values from: Organism
  on property: organism
subclass of: Restriction
  all values from: database
  on property: contained in

Sequence unit
type: Class
subclass of: Gene tree node
comment: protein or DNA sequence as a unit of comparison

gene region
type: Class
subclass of: Sequence unit
subclass of: Restriction
  some values from: Gene
  on property: part_of
comment: A region of the sequence of the gene
label: region of a gene
label: subgene

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

Taxon
type: Class
subclass of: Restriction
  all values from: Taxon
  on property: replaces
subclass of: Restriction
  on data range: string
  max qualified cardinality: 1
  on property: Mnemonic
example: @prefix up: <http://purl.uniprot.org/core/> . @prefix up-taxon: <http://purl.uniprot.org/taxonomy/> . up-taxon:10090 rdf:type up:Taxon ; up:rank up:Species .
comment: An element of a taxonomy for classifying life forms.

database
type: Class
comment: A database is a data store such as relational, hierarchical and graph databases.

experimental factor
type: Class
disjoint with: ObsoleteClass
definition: An experimental factor in Array Express which are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This upper level class is really used to give a root class from which applications can rely on and not be tied to upper ontology classses which do change.
alternative_term: ExperimentalFactor
comment: Concept naming convention is lower case natural naming with spaces, when necessary captials should be used, for example disease factor, HIV, breast carcinoma, Ewing's sarcoma

developmental stage
type: Class
subclass of: process
definition: A developmental stage is spatiotemporal region encompassing some part of the life cycle of an organism, e.g. blastula stage
example: @prefix dcterms: <http://purl.org/dc/terms/> . @prefix obo: <ttp://purl.obolibrary.org/obo/> . @prefix efo: <http://www.ebi.ac.uk/efo/> . obo:BtauDv_0000007 rdf:type efo:EFO_0000399 ; dcterms:description "Embryo development period during the first 3 months of gestation, up to day 90 of development." ; rdfs:label "first trimester of gestation (cow)".
NCI thesaurus definition citation: NCIt:C43531
alternative_term: development stage
alternative_term: developmental_stage
alternative_term: life cycle stage
comment: This branch will be replaced by, and if necessary merged with an Uberon import in future.

organism part
type: Class
subclass of: Anatomical entity
subclass of: material entity
example of usage: tissue, organ, system, sperm, blood or body location (arm).
definition: The part of organism's anatomy or substance arising from an organism from which the biomaterial was derived, excludes cells. E.g. tissue, organ, system, sperm, blood or body location (arm).
NCI thesaurus definition citation: NCIt:C103199
alternative_term: organism_part

strain
type: Class
subclass of: population
definition: A population of organisms that is geneticaly different from others of the same species and possessing a set of defined characteristics.
NCI thesaurus definition citation: NCIt:C95501

material entity
type: Class
subclass of: experimental factor
example of usage: A heart, a human, a fly, a microarray.
definition: 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.
alternative_term: material type
source definition: An independent continuant [snap:IndependentContinuant] that is spatially extended whose identity is independent of that of other entities and can be maintained through time. Note: Material entity [snap:MaterialEntity] subsumes object [snap:Object], fiat object part [snap:FiatObjectPart], and object aggregate [snap:ObjectAggregate], which assume a three level theory of granularity, which is inadequate for some domains, such as biology.

process
type: Class
subclass of: experimental factor
definition: A process is an entity that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity during the time it occurs.
NCI thesaurus definition citation: NCIt:C29862

high confidence level
type: NamedIndividual
definition: A confidence level representing a high trust in an evidence.
id: CIO:0000029

medium confidence level
type: NamedIndividual
definition: A confidence level representing a moderate trust in an evidence.
id: CIO:0000030

low confidence level
type: NamedIndividual
definition: A confidence level representing an absence of trust in an evidence.
id: CIO:0000031

average expressed
type: NamedIndividual

highly expressed
type: NamedIndividual
comment: g is highly expressed in t iff g is expressed in t, and the expression level of g is increased relative to some background i.e all gene expressions taking into account a given gene expression condition.
alternative label: over expressed

high expressed
type: NamedIndividual

lowly expressed
type: NamedIndividual
comment: g is lowly expressed in t iff g is expressed in t, and the expression level of g is decreased relative to some background.
alternative label: under expressed

low expressed
type: NamedIndividual

ubiquitously expressed
type: NamedIndividual
comment: x is ubiquitously expressed in y if and only if x is expressed in y, and the majority of cells in y express x.

Taxonomic rank Species
type: NamedIndividual
type: Taxon rank

SIB Swiss Institute of Bioinformatics
type: NamedIndividual
type: Organization

University of Lausanne
type: NamedIndividual
type: Organization

Identifier
description: Recommended best practice is to identify the resource by means of a string conforming to a formal identification system.
comment: An unambiguous reference to the resource within a given context.

Christophe Dessimoz
member of: SIB Swiss Institute of Bioinformatics

Julien Wollbrett
member of: SIB Swiss Institute of Bioinformatics

Tarcisio Mendes de Farias
member of: SIB Swiss Institute of Bioinformatics

Marc Robinson-Rechavi
member of: University of Lausanne

Frederic Bastian
member of: SIB Swiss Institute of Bioinformatics