cbio
type: Ontology
version IRI: http://purl.org/cbio/0.3
imports: http://purl.org/lscr/0.1
imports: faldo
version info: Cancer biomarker ontology (CBIO).
creator: Tarcisio Mendes de Farias

example of usage
type: AnnotationProperty

definition
type: AnnotationProperty

editor note
type: AnnotationProperty

curator note
type: AnnotationProperty

elucidation
type: AnnotationProperty

Description
type: Property
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.

id
type: AnnotationProperty
equivalent property: Identifier

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
inverse of: has part

contained in
type: ObjectProperty

in taxon
type: ObjectProperty
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

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'

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

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

has a developmental stage
type: ObjectProperty
type: FunctionalProperty
domain: gene expression experiment condition
range: developmental stage

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

has an expression condition
type: ObjectProperty
domain: Class
  union of: absence of gene expression
  union of: gene expression
range: gene expression experiment condition
alternative label: has an experimental condition

has sequence unit
type: ObjectProperty
domain: Class
  union of: absence of gene expression
  union of: gene expression
  union of: biomarker
  union of: cancer differential expression
  union of: disease mutation
range: Sequence unit

has strain
type: ObjectProperty
type: FunctionalProperty
domain: gene expression experiment condition
range: strain

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
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.

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
inverse of: is encoded by
description: A relation between two objects, in which the first object contains information that is used to produce the second object.

Description
type: Property
range: Literal
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.

has expression level score
type: DatatypeProperty
domain: gene expression
range: double
alternative label: expression score

hasSex
type: DatatypeProperty
type: FunctionalProperty
domain: gene expression experiment condition
range: Datatype
  one of: NA
  one of: female
  one of: hermaphrodite
  one of: male
  one of: mixed
  one of: not annotated

common name
type: DatatypeProperty
type: FunctionalProperty
range: string

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

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
equivalent class: 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
    on property: has an expression condition
    some values from: gene expression experiment condition
  intersection of: Restriction
    on property: has sequence unit
    some values from: Sequence unit
subclass of: Class
  complement of: gene expression
alternative label: Not expressed gene
alternative label: Not expressed sequence unit

Anatomical entity
type: Class
subclass of: biological entity
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
    on property: has an expression condition
    some values from: gene expression experiment condition
  intersection of: Restriction
    on property: has sequence unit
    some values from: Sequence unit
subclass of: Restriction
  on property: has expression level characteristic
  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
subclass of: Restriction
  on property: has expression level score
  all values from: double
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
    on property: has anatomical entity
    some values from: Anatomical entity
  union of: Restriction
    on property: has a developmental stage
    some values from: developmental stage
  union of: Restriction
    on property: has strain
    some values from: strain
  union of: Restriction
    on property: hasSex
    some values from: string
subclass of: Restriction
  on property: in taxon
  all values from: Taxon
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
  on property: organism
  some values from: Organism
subclass of: Restriction
  on property: contained in
  all values from: database

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
  on property: in taxon
  some values from: 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
  on property: organism
  some values from: Organism
subclass of: Restriction
  on property: contained in
  all values from: database

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
  on property: part_of
  some values from: Gene
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
  on property: replaces
  all values from: Taxon
subclass of: Restriction
  on property: Mnemonic
  max qualified cardinality: 1
  on data range: string
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
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
has related match: SIO_000004
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
alternative label: medium expressed

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, e.g. 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

Creator
description: Examples of a Creator include a person, an organization, or a service. Typically, the name of a Creator should be used to indicate the entity.
issued: 1999-07-02
type: Property
comment: An entity primarily responsible for making the resource.
note: A [second property](/specifications/dublin-core/dcmi-terms/#http://purl.org/dc/terms/creator) with the same name as this property has been declared in the [dcterms: namespace](http://purl.org/dc/terms/). See the Introduction to the document [DCMI Metadata Terms](/specifications/dublin-core/dcmi-terms/) for an explanation.

Identifier
description: Recommended practice is to identify the resource by means of a string conforming to an identification system.
issued: 1999-07-02
type: Property
comment: An unambiguous reference to the resource within a given context.
note: A [second property](/specifications/dublin-core/dcmi-terms/#http://purl.org/dc/terms/identifier) with the same name as this property has been declared in the [dcterms: namespace](http://purl.org/dc/terms/). See the Introduction to the document [DCMI Metadata Terms](/specifications/dublin-core/dcmi-terms/) for an explanation.

Source
type: Property
type: DatatypeProperty
description: This property is intended to be used with non-literal values. The described resource may be derived from the related resource in whole or in part. Best practice is to identify the related resource by means of a URI or a string conforming to a formal identification system.
issued: 2008-01-14
comment: A related resource from which the described resource is derived.
range: Literal

References
description: This property is intended to be used with non-literal values. This property is an inverse property of Is Referenced By.
issued: 2000-07-11
type: Property
comment: A related resource that is referenced, cited, or otherwise pointed to by the described resource.

Is Referenced By
description: This property is intended to be used with non-literal values. This property is an inverse property of References.
inverse of: References
issued: 2000-07-11
type: Property
comment: A related resource that references, cites, or otherwise points to the described resource.

License
description: Recommended practice is to identify the license document with a URI. If this is not possible or feasible, a literal value that identifies the license may be provided.
type: Property
comment: A legal document giving official permission to do something with the resource.

Date Modified
description: Recommended practice is to describe the date, date/time, or period of time as recommended for the property Date, of which this is a subproperty.
issued: 2000-07-11
type: Property
comment: Date on which the resource was changed.

Provenance
range: Provenance Statement
description: The statement may include a description of any changes successive custodians made to the resource.
issued: 2004-09-20
type: AnnotationProperty
comment: A statement of any changes in ownership and custody of the resource since its creation that are significant for its authenticity, integrity, and interpretation.

Provenance Statement
issued: 2008-01-14
type: Class
comment: Any changes in ownership and custody of a resource since its creation that are significant for its authenticity, integrity, and interpretation.

Date Issued
description: Recommended practice is to describe the date, date/time, or period of time as recommended for the property Date, of which this is a subproperty.
issued: 2000-07-11
type: Property
comment: Date of formal issuance of the resource.

Date Created
description: Recommended practice is to describe the date, date/time, or period of time as recommended for the property Date, of which this is a subproperty.
issued: 2000-07-11
type: Property
comment: Date of creation of the resource.

Creator
range: Agent
description: Recommended practice is to identify the creator with a URI. If this is not possible or feasible, a literal value that identifies the creator may be provided.
issued: 2008-01-14
type: Property
comment: An entity responsible for making the resource.
equivalent property: maker

MODIFIED EFO TERM RESTRICTIONS
type: Provenance Statement
Date Created: 2020-08-03
description: The term from <http://www.ebi.ac.uk/efo/releases/v3.20.0/efo.owl> was adapted for the cancer biomarker data context. This provenance statement is asserted only for the case of modifications that include either deletion or replacement of class restrictions (e.g. quantifiers) and disjunction statements or property domain and ranges. Disjunction assertions are often removed for the sake of simplicity. This is because many of the dinjunctions and domain specificities are out of scope when actually structuring cancer biomarker data.
creator: Tarcisio Mendes de Farias

Tarcisio Mendes de Farias
type: Person

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

Title
issued: 2008-01-14
type: Property
comment: A name given to the resource.
range: Literal

has member
type: ObjectProperty
sub property of: has part
type: IrreflexiveProperty
definition: has member is a mereological relation between a collection and an item.
License: https://creativecommons.org/publicdomain/zero/1.0/

has part
type: ObjectProperty
type: TransitiveProperty
example of usage: my body has part my brain (continuant parthood, two material entities)
example of usage: my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)
example of usage: this year has part this day (occurrent parthood)
definition: a core relation that holds between a whole and its part
editor note: Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part.
editor note: Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
editor note: Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'.
License: https://creativecommons.org/publicdomain/zero/1.0/

located_in
type: ObjectProperty
has_dbxref: RO:0001025
alternative label: located in
License: LICENSE-2.0

material property
type: Class
subclass of: experimental factor
definition: An experimental factor which is a property or characteristic of some other entity. For example, the mouse has the colour white.
source definition: A continuant [snap:Continuant] that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same.
License: LICENSE-2.0

role
type: Class
subclass of: material property
example of usage: For example, the role of a person as a surgeon, the role of an artificial heart in pumping blood, the role of a chemical compound in an experiment, the role of a drug in the treatment of a disease.
definition: A role is an entity which is borne in a material entity in some kinds of natural, social or institutional contexts, but which is not essential to the fundamental definition of that material entity (i.e. the material entity exists with or without the role). For example, the role of a person as a surgeon, the role of an artificial heart in pumping blood, the role of a chemical compound in an experiment, the role of a drug in the treatment of a disease.
source definition: A realizable entity [snap:RealizableEntity] the manifestation of which brings about some result or end that is not essential to a continuant [snap:Continuant] in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant [snap:Continuant] in some kinds of natural, social or institutional contexts.
License: LICENSE-2.0

biological role
type: Class
subclass of: role
definition: A role played by the molecular entity or part thereof within a biological context.
License: LICENSE-2.0

biomarker
type: Class
subclass of: biological role
definition: A substance used as an indicator of a biological state.
has_exact_synonym: biological marker
License: LICENSE-2.0

disease
type: Class
subclass of: disposition
definition: A disease is a disposition that describes states of disease associated with a particular sample and/or organism.
definition: A disease is a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism.
IAO_0000117: James Malone
has_dbxref: DOID:4
has_dbxref: ICD10:N18
has_dbxref: ICD10:R69
has_dbxref: ICD9:799.9
has_dbxref: MESH:D004194
has_dbxref: MONDO:0000001
has_dbxref: MSH:D004194
has_dbxref: NCIT:C2991
has_dbxref: OGMS:0000031
has_dbxref: Orphanet:377788
has_dbxref: SCTID:64572001
has_dbxref: SNOMEDCT:64572001
has_dbxref: UMLS:C0012634
has_exact_synonym: Homo sapiens disease
has_exact_synonym: condition
has_exact_synonym: disease
has_exact_synonym: disease or disorder
has_exact_synonym: disease or disorder, non-neoplastic
has_exact_synonym: diseases
has_exact_synonym: diseases and disorders
has_exact_synonym: disorder
has_exact_synonym: disorders
has_exact_synonym: human disease
has_exact_synonym: medical condition
has_exact_synonym: other disease
id: EFO:0000408
Date Modified: 2020-08-03
contributor: tarcisiotmf
Provenance: MODIFIED EFO TERM RESTRICTIONS
License: LICENSE-2.0

disposition
type: Class
subclass of: material property
example of usage: For example, the disposition of vegetables to decay when not refrigerated, the disposition of blood to coagulate, the disposition of a patient with a weakened immune system to contract disease.
definition: A disposition is an entity that causes a specific process or transformation in an entity in which it inheres, under specific circumstances and in conjunction with the laws of nature. For example, the disposition of vegetables to decay when not refrigerated, the disposition of blood to coagulate, the disposition of a patient with a weakened immune system to contract disease.
IAO_0000117: James Malone modified from original
array express label: disease property
EFO URI: http://www.ebi.ac.uk/efo/EFO_0001438
source definition: A realizable entity [snap:RealizableEntity] that essentially causes a specific process or transformation in the object [snap:Object] in which it inheres, under specific circumstances and in conjunction with the laws of nature. A general formula for dispositions is: X (object [snap:Object] has the disposition D to (transform, initiate a process) R under conditions C.
has_alternative_id: http://www.ifomis.org/bfo/1.1/snap#Disposition
has_dbxref: NCIt:C41205
License: LICENSE-2.0

cell proliferation disorder
type: Class
equivalent class: Class
  union of: precancerous condition
  union of: neoplastic disease or syndrome
  union of: cancer-related condition
  union of: hyperplasia
subclass of: disease
definition: Any disorder that features disrupted cell proliferation. Includes hyperplasia, neoplastic syndrome and isolated neoplasm diseases as well as precancerous conditions.
id: MONDO:0045024
License: LICENSE-2.0

precancerous condition
type: Class
subclass of: cell proliferation disorder
definition: A pathological process with signs indicating it may become cancerous. Representative examples include leukoplakia, dysplastic nevus, actinic keratosis, xeroderma pigmentosum, and intraepithelial neoplasia.
has_dbxref: MESH:D011230
has_dbxref: NCIT:C3341
has_exact_synonym: precancerous condition
has_exact_synonym: precancerous state
has_exact_synonym: premalignant condition
has_exact_synonym: premalignant state
id: MONDO:0021074
comment: Editor note: check classification. Also consider changing def, NCIT defines as disease. Also consider a grouping for this and paraneoplastic syndrome
License: LICENSE-2.0

neoplastic disease or syndrome
type: Class
equivalent class: Class
  union of: neoplastic syndrome
  union of: neoplasm
subclass of: cell proliferation disorder
definition: Either an isolated neoplasm or a syndrome with neoplasm as a major feature.
has_related_synonym: neoplastic disease
has_related_synonym: neoplastic disorder
id: MONDO:0023370
License: LICENSE-2.0

cancer-related condition
type: Class
subclass of: cell proliferation disorder
definition: A disorder either associated with an increased risk for malignant transformation (e.g., intraepithelial neoplasia, leukoplakia, dysplastic nevus, myelodysplastic syndrome) or that develops as a result of the presence of an existing malignant neoplasm (e.g., paraneoplastic syndrome).
has_dbxref: NCIT:C8278
has_dbxref: UMLS:C0280950
has_exact_synonym: cancer related problem/condition
has_exact_synonym: cancer-related condition
has_exact_synonym: cancer-related problem or condition
has_exact_synonym: oncologic complications
has_exact_synonym: problem/condition, cancer related
has_exact_synonym: problem/condition, cancer-related
id: MONDO:0045054
License: LICENSE-2.0

hyperplasia
type: Class
subclass of: cell proliferation disorder
definition: An abnormal increase in the number of (otherwise normal) cells in an organ or a tissue with consequent enlargement.
definition: An abnormal increase in the number of cells in an organ or a tissue with consequent enlargement.
has_dbxref: MESH:D006965
has_dbxref: MONDO:0005043
has_dbxref: MSH:D006965
has_dbxref: NCIT:C3113
has_dbxref: NCIt:C3113
has_dbxref: SNOMEDCT:76197007
has_exact_synonym: Hyperplastic
has_exact_synonym: hyperplasia
has_exact_synonym: hyperplastic
id: EFO:0000536
License: LICENSE-2.0

neoplastic syndrome
type: Class
equivalent class: Class
  intersection of: syndromic disease
  intersection of: Restriction
    on property: disease has major feature
    some values from: neoplasm
subclass of: syndromic disease
subclass of: neoplastic disease or syndrome
subclass of: Restriction
  on property: has modifier
  some values from: rare
subclass of: Restriction
  on property: disease has major feature
  some values from: neoplasm
definition: A broad classification for disorders in which the development of neoplasms typically occur in association with a characteristic set of signs or symptoms. These disorders may be inherited or acquired.
has_dbxref: NCIT:C54705
has_exact_synonym: cancer-related syndrome
has_exact_synonym: neoplastic syndrome
has_exact_synonym: tumor syndrome
id: MONDO:0021058
License: LICENSE-2.0

syndromic disease
type: Class
equivalent class: Class
  intersection of: disease
  intersection of: Restriction
    on property: has modifier
    some values from: has a syndromic presentation
subclass of: disease
subclass of: Restriction
  on property: has modifier
  some values from: has a syndromic presentation
definition: A group of signs, symptoms, and clinicopathological characteristics that may or may not have a genetic basis and collectively define an abnormal condition.
has_dbxref: DOID:225
has_dbxref: MESH:D013577
has_dbxref: NCIT:C28193
has_dbxref: OGMS:0000086
has_dbxref: UMLS:C0039082
has_exact_synonym: cluster, symptom
has_exact_synonym: clusters, symptom
has_exact_synonym: symptom cluster
has_exact_synonym: symptom clusters
has_exact_synonym: syndrome
has_exact_synonym: syndrome associated with disease or disorder
has_exact_synonym: syndromes
has_exact_synonym: syndromic disease
has_exact_synonym: syndromic disease or disorder
has_related_synonym: syndrome associated with disease or disorder
id: MONDO:0002254
License: LICENSE-2.0

has a syndromic presentation
type: Class
subclass of: syndromic or isolated
definition: An characteristic of a disease in which the disease is not manifested as an isolated feature but has multiple distinct features.
id: MONDO:0021127
License: LICENSE-2.0

syndromic or isolated
type: Class
subclass of: disease characteristic
definition: An characteristic of a disease that varies depending on whether the disease appears as an isolated feature or whether the disease is a syndrome consisting of multiple features.
id: MONDO:0021126
License: LICENSE-2.0

disease has major feature
type: ObjectProperty
sub property of: disease has feature
id: disease_has_major_feature
License: LICENSE-2.0

disease has feature
type: ObjectProperty
definition: A relationship between a disease and some feature of that disease, where the feature is either a phenotype or an isolated disease.
has_dbxref: RO:0004029
id: disease_has_feature
shorthand: disease_has_feature
License: LICENSE-2.0

has modifier
type: ObjectProperty
has_dbxref: RO:0002573
id: has_modifier
shorthand: has_modifier
License: LICENSE-2.0

rare
type: Class
subclass of: rare or common
definition: A disease or disorder is defined as rare in Europe when it affects fewer than 1 in 2000. A disease or disorder is defined as rare in the USA when it affects fewer than 200,000 Americans at any given time. Here we take the European definition to be consistent with Orphanet.
has_exact_synonym: rare (European definition)
id: MONDO:0021136
License: LICENSE-2.0

rare or common
type: Class
subclass of: disease characteristic
id: MONDO:0021135
in subset: obsoletion candidate
License: LICENSE-2.0

disease characteristic
type: Class
subclass of: quality
definition: An attribute of a disease.
has_dbxref: MONDO:0021125
has_dbxref: NCIT:C41009
has_exact_synonym: disease characteristic
has_exact_synonym: disease qualifier
has_exact_synonym: modifier
has_exact_synonym: qualifier
id: EFO:0009813
License: LICENSE-2.0

quality
type: Class
subclass of: material property
definition: A quality is an entity that describes some aspect which is intrinsic to that particular object and is dependent on or more material entities in which it inheres in or is borne by. Example the color of a tomato, the ambient temperature of air, the circumference of a waist, the shape of a nose, the mass of a piece of gold, the weight of a chimpanzee
IAO_0000117: James Malone
EFO URI: http://www.ebi.ac.uk/efo/EFO_0001436
organizational class: true
source definition: A specifically dependent continuant [snap:SpecificallyDependentContinuant] that is exhibited if it inheres in an entity or entities at all (a categorical property).
has_alternative_id: http://www.ifomis.org/bfo/1.1/snap#Quality
has_dbxref: NCIt:C25283
has_dbxref: SNOMEDCT:263496004
License: LICENSE-2.0

neoplasm
type: Class
subclass of: neoplastic disease or syndrome
definition: A benign or malignant tissue growth resulting from uncontrolled cell proliferation. Benign neoplastic cells resemble normal cells without exhibiting significant cytologic atypia, while malignant cells exhibit overt signs such as dysplastic features, atypical mitotic figures, necrosis, nuclear pleomorphism, and anaplasia. Representative examples of benign neoplasms include papillomas, cystadenomas, and lipomas; malignant neoplasms include carcinomas, sarcomas, lymphomas, and leukemias.
IAO_0000117: James Malone
IAO_0000117: Tomasz Adamusiak
has broad synonym: cell process disease
has_dbxref: COHD:438112
has_dbxref: DOID:14566
has_dbxref: HP:0002664
has_dbxref: ICD10:C00.D48
has_dbxref: ICD10:D48
has_dbxref: ICD10:Z85
has_dbxref: ICD9:140-239.99
has_dbxref: ICD9:239.8
has_dbxref: ICD9:239.9
has_dbxref: MESH:D009369
has_dbxref: MONDO:0005070
has_dbxref: MSH:D009369
has_dbxref: NCIT:C3262
has_dbxref: NCIt:C3262
has_dbxref: ONCOTREE:OTHER
has_dbxref: SCTID:55342001
has_dbxref: SNOMEDCT:108369006
has_dbxref: UMLS:CN236628
has_exact_synonym: NEOPL
has_exact_synonym: NEOPLASMS BENIGN, MALIGNANT AND UNSPECIFIED (INCL CYSTS AND POLYPS)
has_exact_synonym: Neoplasia
has_exact_synonym: Neoplasms
has_exact_synonym: Neoplastic Growth
has_exact_synonym: Tumor
has_exact_synonym: Tumors
has_exact_synonym: disease of cellular proliferation
has_exact_synonym: neoplasia
has_exact_synonym: neoplasm
has_exact_synonym: neoplasm (disease)
has_exact_synonym: neoplastic disease
has_exact_synonym: neoplastic growth
has_exact_synonym: tumor
has_exact_synonym: tumor disease
has_exact_synonym: tumour
has_exact_synonym: tumours
has narrow synonym: other neoplasm
id: EFO:0000616
Date Modified: 2020-08-03
contributor: tarcisiotmf
Provenance: MODIFIED EFO TERM RESTRICTIONS
License: LICENSE-2.0

cancer
type: Class
subclass of: neoplasm
disjoint with: benign neoplasm
example of usage: ductal carcinoma in situ
definition: A malignant neoplasm in which new abnormal tissue grow by excessive cellular division and proliferation more rapidly than normal and continues to grow after the stimuli that initiated the new growth cease.
definition: A tumor composed of atypical neoplastic, often pleomorphic cells that invade other tissues. Malignant neoplasms often metastasize to distant anatomic sites and may recur after excision. The most common malignant neoplasms are carcinomas (adenocarcinomas or squamous cell carcinomas), Hodgkin and non-Hodgkin lymphomas, leukemias, melanomas, and sarcomas.
IAO_0000117: James Malone
IAO_0000117: Tomasz Adamusiak
has_dbxref: COHD:443392
has_dbxref: DOID:0050686
has_dbxref: DOID:0050687
has_dbxref: DOID:162
has_dbxref: GARD:0011960
has_dbxref: ICD10:C80
has_dbxref: ICD10:C80.1
has_dbxref: ICD9:195.8
has_dbxref: ICD9:199
has_dbxref: ICD9:199.1
has_dbxref: ICDO:8000/3
has_dbxref: MONDO:0004992
has_dbxref: NCIT:C9305
has_dbxref: NCIt:C9305
has_dbxref: NIFSTD:birnlex_406
has_dbxref: ONCOTREE:MT
has_dbxref: SCTID:363346000
has_dbxref: UMLS:C0006826
has_exact_synonym: CA
has_exact_synonym: Malignant Neoplasm
has_exact_synonym: cancer
has_exact_synonym: cell type cancer
has_exact_synonym: malignancy
has_exact_synonym: malignant Growth
has_exact_synonym: malignant neoplasia
has_exact_synonym: malignant neoplasm
has_exact_synonym: malignant neoplasm (disease)
has_exact_synonym: malignant neoplastic disease
has_exact_synonym: malignant tumor
has_exact_synonym: malignant tumour
has_exact_synonym: neoplasm (disease), malignant
has_exact_synonym: neoplasm, malignant
has_exact_synonym: organ system cancer
has_exact_synonym: primary cancer
has_related_synonym: MT
id: EFO:0000311
License: LICENSE-2.0

benign neoplasm
type: Class
subclass of: neoplasm
definition: A neoplasm which is characterized by the absence of morphologic features associated with malignancy (severe cytologic atypia, tumor cell necrosis, and high mitotic rate). Benign neoplasms remain confined to the original site of growth and do not metastasize to other anatomic sites.
IAO_0000117: James Malone
IAO_0000117: Sirarat Sarntivijai
IAO_0000117: Tomasz Adamusiak
has_dbxref: DOID:0060072
has_dbxref: DOID:0060084
has_dbxref: DOID:0060085
has_dbxref: ICD10:D10.D36
has_dbxref: ICD10:D36
has_dbxref: ICD9:210-229.99
has_dbxref: ICD9:229.8
has_dbxref: ICD9:229.9
has_dbxref: ICDO:8000/0
has_dbxref: MONDO:0005165
has_dbxref: NCIT:C3677
has_dbxref: NCIt:C3677
has_dbxref: SCTID:20376005
has_dbxref: SNOMEDCT:3898006
has_exact_synonym: BENIGN NEOPL
has_exact_synonym: Benign Neoplasm
has_exact_synonym: Benign Neoplasms
has_exact_synonym: NEOPL BENIGN
has_exact_synonym: Neoplasm, Benign
has_exact_synonym: Neoplasms, Benign
has_exact_synonym: benign neoplasm
has_exact_synonym: benign neoplasm (disease)
has_exact_synonym: benign tumor
has_exact_synonym: neoplasm (disease), benign
has_related_synonym: benign tumor
has_related_synonym: benign unclassifiable tumor
has_related_synonym: cell type benign neoplasm
has_related_synonym: neoplasm, benign
has_related_synonym: organ system benign neoplasm
id: EFO:0002422
comment: Editor note: see https://github.com/NCI-Thesaurus/thesaurus-obo-edition/issues/14
License: LICENSE-2.0

instrument
type: Class
subclass of: material entity
definition: An instrument is a device which provides a mechanical or electronic function.
IAO_0000117: James Malone
IAO_0000117: Jie Zheng
IAO_0000117: Tomasz Adamusiak
definition citation: OBI_0400003
has_dbxref: MO:113
has_dbxref: MO:134
has_dbxref: SNOMEDCT:57134006
has_exact_synonym: HardwareType
has_exact_synonym: hardware
License: LICENSE-2.0

material entity
type: Class
subclass of: independent continuant
has related match: SIO_000004
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.
IAO_0000117: James Malone
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.
equivalent class: material entity
has_exact_synonym: material type
License: http://creativecommons.org/licenses/by/4.0/

process
type: Class
subclass of: occurrent
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.
IAO_0000117: James Malone
source definition: An occurrent [span:Occurrent] that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity.
equivalent class: process
has_dbxref: NCIt:C29862
has_dbxref: SNOMEDCT:415178003
License: http://creativecommons.org/licenses/by/4.0/

occurrent
type: Class
subclass of: entity
definition: An entity that has temporal parts and that happens, unfolds or develops through time.
editor note: BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region
editor note: BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players.
editor note: Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process.
editor note: Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame.
elucidation: An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])

investigation
type: Class
subclass of: planned process
example of usage: Lung cancer investigation using expression profiling, a stem cell transplant investigation, biobanking is not an investigation, though it may be part of an investigation
definition: a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s).
License: LICENSE-2.0

planned process
type: Class
subclass of: process
definition: A processual entity that realizes a plan which is the concretization of a plan specification.
definition citation: OBI_0000011
License: LICENSE-2.0

clinical trial
type: Class
subclass of: human subject study
definition: a clinical trial is a medical interventional study where participants are assigned prospectively to an intervention or interventions according to a protocol to evaluate the safety and efficacy of the intervention(s) on biomedical or other health related outcomes. The Interventions include but are not restricted to drugs, cells and other biological products, surgical procedures, radiologic procedures, devices, behavioral treatments, process-of-care changes, preventive care, etc.
IAO_0000117: Oliver He, Asiyah Yu Lin, Qingliang Li
alternative label: interventional trial

human subject study
type: Class
subclass of: investigation
definition: A systematic, scientific investigation that can be either interventional or observational and involves human beings as research subjects. Human subject research can be either medical (clinical) research or non-medical (e.g., social science) research.
IAO_0000117: Oliver He
alternative label: human investigation
alternative label: human study

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

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

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

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

Metal Ion Binding Site
type: Class
subclass of: Site
comment: Binding site for a metal ion.

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

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

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

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

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

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

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

Initiator Methionine
type: Class
subclass of: Molecule Processing
comment: Indicates that the initiator methionine has been cleaved off and is not shown in the sequence.
description: Cleavage of the initiator methionine is one of the most common protein modifications and occurs co-translationally.

Molecule Processing
type: Class
subclass of: Sequence Annotation

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

Natural Variation
type: Class
subclass of: Sequence Annotation

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

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

PTM
type: Class
subclass of: Annotation
comment: Although proteins can be modified pre-translationally (on the amino acid component of AMINO ACYL TRNA), co-translationally (during the process of GENETIC TRANSLATION), or after translation is completed (POST-TRANSLATIONAL PROTEIN PROCESSING), all protein modifications are generally referred to as PTMs, because a majority of them are made post-translationally, after the protein is folded. As a result, PTM here means a pre-, co- or post-translationally protein modification.
has narrower match: PTM Annotation
alternative label: post-translational modification

has probability
type: DatatypeProperty
range: double
domain: functional impact prediction
comment: A probability is quantity of how likely it is that some event will occur.
has related match: probability measure

functional impact prediction
type: Class
comment: Predictions for functional affect of variation on the protein reported by a tool such as PolyPhen-2 (e.g. benign, possibly damaging, or probably damaging) and NetNGlyc2.0, and the prediction probability to occur, if applicable.
alt label: site prediction

predict
type: DatatypeProperty
comment: It states the funtional impact prediction due to the fact of a variation in the protein sequence (e.g. caused by a mutation) reported by a tool such as PolyPhen-2 (e.g. benign, possibly damaging, or probably damaging) and NetNGlyc2.0 (e.g. gain, loss, no change).
domain: functional impact prediction
range: string
alt label: has predicted result

has functional impact prediction
type: ObjectProperty
comment: It states a funtional impact prediction (i.e. a predicted effect of the protein variant, for example, due to mutation).
domain: disease mutation
range: functional impact prediction
alt label: has functional prediction

biomarker test
type: Class
subclass of: instrument
subclass of: Restriction
  on property: has the target disease
  some values from: disease
comment: A biochemical or other measurement device developed to quantitate a biomarker. These tests can evaluate biomarkers for the detection and treatment of asymptomatic individuals (screening), establishing the presence and precise description of disease (diagnosis), estimating the risk or time to clinical outcomes (prognosis), identifying patient likelihood to benefit from certain therapies (predictive) or to experience therapy-related risks (pharmacogenomics), or treatment and post-treatment monitoring purposes (e.g., early detection and treatment of advancing disease or complications).

is used in
type: ObjectProperty
range: biomarker test
domain: biomarker
comment: A relationship between a biomarker and a test by which the biomarker is used.

has the target disease
type: ObjectProperty
range: disease
domain: Class
  union of: biomarker test
  union of: cancer differential expression
  union of: disease mutation
comment: It states the disease target of a biomarker test or a differential gene expression analysis. The disease is defined by the controlled vocabulary: the Disease Ontology (DO). DO classes is therefore considered instances of efo:EFO_0000408 (EFO Disease class) by applying OWL 2 punning (see https://www.w3.org/TR/owl2-new-features/#F12:_Punning).

is manufactured by
type: DatatypeProperty
domain: instrument
range: string
comment: It relates an instrument to its manufacturer name.
has broader match: isManufacturedBy

has FDA submission identifier
type: DatatypeProperty
sub property of: identifier
domain: biomarker test
range: string
comment: It relates a biomarker test to its FDA (US Food and Drug Administration) submission identifier.

has clinical trial
type: ObjectProperty
domain: biomarker test
range: clinical trial
comment: It assings clinical trials for a biomarker test device. If it is a FDA biomarker clinical, trials are represented with the following URI scheme https://clinicaltrials.gov/ct2/show/{trial id}.

has approved indication
type: ObjectProperty
domain: biomarker test
range: Class
  one of: Prediction
  one of: Diagnosis
  one of: Risk Assessment
  one of: Early Detection
  one of: Prognosis
  one of: Companion Diagnosis
comment: The approved indication of a biomarker test.

has actual use
type: ObjectProperty
domain: biomarker test
range: Class
  one of: Prediction
  one of: Diagnosis
  one of: Risk Assessment
  one of: Susceptibility
comment: The actual use of a biomarker test.

biomarker origin
type: DatatypeProperty
type: FunctionalProperty
domain: biomarker
range: Datatype
  one of: amplification
  one of: multigene prediction
  one of: somatic mutation
comment: It relates a biomarker to its origin: multigene prediction, somatic mutation, or amplification.

has histological type
type: DatatypeProperty
domain: cancer
range: string
comment: It classifies a cancer by the type of tissue in which the cancer originates (histological type).
note: In the future this property might be replaced by an object property that assings, if exist, NCIT controlled vocabulary terms as instance values such as http://purl.obolibrary.org/obo/NCIT_C3224 (melanoma).

specimen
type: DatatypeProperty
domain: biomarker test
range: Datatype
  one of: blood
  one of: fresh tissue
  one of: human stool
  one of: paraffin block
  one of: parrafin block
  one of: saliva
  one of: urine
comment: The specimen type for the biomarker test.

platform method
type: DatatypeProperty
domain: biomarker test
range: string
comment: The platform method used by the biomarker test.

gene amount
type: DatatypeProperty
type: FunctionalProperty
domain: biomarker panel
range: nonNegativeInteger
comment: The number of genes that are members of a biomarker panel.

has test adoption evidence
type: DatatypeProperty
type: FunctionalProperty
domain: biomarker test
range: Datatype
  one of: clinical use
  one of: experimental use
comment: It denotes the adoption evidence of a biomarker test.

has approval status
type: DatatypeProperty
type: FunctionalProperty
domain: biomarker test
range: string
comment: It denotes the state of a biomarker test approval.
has broader match: hasApprovalStatus

has test study design
type: DatatypeProperty
type: FunctionalProperty
domain: biomarker test
range: string
comment: It states a specific study design for a biomarker test. A study design is a plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution.

has clinical significance
type: DatatypeProperty
type: FunctionalProperty
domain: biomarker test
range: string
comment: A finding that has treatment or management implications for a patient's condition.

cancer biomarker
type: Class
subclass of: biomarker
subclass of: Restriction
  on property: is a measurable indicator of
  some values from: cancer
comment: A cancer biomarker refers to a substance or process that is indicative of the presence of cancer in the body. A biomarker may be a molecule secreted by a tumor or a specific response of the body to the presence of cancer.

genetic biomarker
type: Class
subclass of: genomic biomarker
comment: A segment of DNA with an identifiable physical location on a chromosome and whose inheritance can be followed. It is indeed an alteration in DNA that may indicate an increased risk of developing a specific disease or disorder.

genomic biomarker
type: Class
subclass of: biomarker
comment: A measurable DNA or RNA characteristic that is an indicator of normal biologic processes, pathogenic processes, and/or response to therapeutic or other intervention. The definition for a genomic biomarker is not limited to human samples. A genomic biomarker could, for example, reflect: the expression of a gene; the function of a gene; the regulation of a gene. A genomic biomarker can consist of one or more deoxyribonucleic acid (DNA) or ribonucleic acid (RNA) characteristics. The definition for a genomic biomarker does not include the measurement and characterisation of proteins or low molecular weight metabolites. DNA characteristics include, but are not limited to: single nucleotide polymorphisms (SNPs); variability of short sequence repeats; DNA modification, e.g., methylation; insertions; deletions; copy number variation; cytogenetic rearrangements, e.g., translocations, duplications, deletions or inversions. RNA characteristics include, but are not limited to: RNA sequence; RNA expression levels; RNA processing, e.g., splicing and editing; microRNA levels (ICH Draft Consensus Guideline E15).
disjoint with: Class
  union of: proteomic biomarker
  union of: metabolomic biomarker
  union of: epigenetic biomarker

proteomic biomarker
type: Class
subclass of: biomarker
has related match: NCIT C97139
comment: it provides key information about the dynamic nature of proteins, including functionality, post‐translational modifications, interaction with other biological molecules, and response to environmental factors. Proteomic biomarkers are often referred to those biomarkers discovered using technologies capable of analyzing many proteins simultaneously, such as protein microarray and mass spectrometry (MS).
disjoint with: Class
  union of: metabolomic biomarker
  union of: epigenetic biomarker

metabolomic biomarker
type: Class
subclass of: biomarker
has narrower match: NCIT C18520
comment: Metabolomic biomarker refers to the systematic identification and quantification of the small molecule metabolic products (the metabolome) of a biological system (cell, tissue, organ, biological fluid, or organism) at a specific point in time that acts as a biomarker. Mass spectrometry and NMR spectroscopy are the techniques most often used for metabolome profiling. It can also enable diagnostic and prognostic prediction.
disjoint with: epigenetic biomarker

metabolic biomarker
type: Class
subclass of: metabolomic biomarker
comment: NCI defines a metabolic marker as follows: specific metabolic changes that characterize an organism's state of health or disease, or response to a particular therapeutic intervention, and helps make diagnosis more accurate or enable physicians to make diagnosis before symptoms appear and to track disease progression.

epigenetic biomarker
type: Class
subclass of: biomarker

gene biomarker
type: Class
subclass of: genomic biomarker
has narrower match: NCIT C48182
comment: A form of gene expression that is indicative of a biological behavior such as a tumor or cancer.

protein biomarker
type: Class
subclass of: proteomic biomarker
has related match: NCIT C97139
comment: it is a biomarker discovered from a simplified, semiquantitative, unbiased binary comparison between diseased and normal using biological samples for maximal detection of significant protein expression differences.

is a measurable indicator of
type: ObjectProperty
range: disease
domain: biomarker
comment: It relates a biomarker to the severity or presence of some disease state. The disease is defined with the controlled vocabulary: the Disease Ontology (DO). DO classes is therefore considered instances of efo:EFO_0000408 (EFO Disease class) by applying OWL 2 punning (see https://www.w3.org/TR/owl2-new-features/#F12:_Punning).

biomarker panel
type: Class
subclass of: biomarker
subclass of: Restriction
  on property: consist of
  min qualified cardinality: 2
  on class: single biomarker
subclass of: Restriction
  on property: gene amount
  all values from: nonNegativeInteger
disjoint with: single biomarker
comment: A biomarker composed of 2 or more single biomarkers

single biomarker
type: Class
subclass of: biomarker
example of usage: ALDH1A2 gene by itself is a specific biomarker for prostate cancer.
comment: A biomarker that is composed of solely one marker (e.g. a unique gene).

consist of
type: ObjectProperty
sub property of: has member
range: biomarker
domain: biomarker panel
has related match: AFX_0000940
comment: It states which biomarkers composes a biomarker panel.

cancer biomarker panel
type: Class
equivalent class: Class
  intersection of: biomarker panel
  intersection of: cancer biomarker
comment: A biomarker panel that indicates some cancer disease.

cancer single biomarker
type: Class
equivalent class: Class
  intersection of: cancer biomarker
  intersection of: single biomarker
comment: A single biomarker that indicates some cancer disease.

has biomarker status
type: ObjectProperty
comment: It denotes whether biomarker has been accepted, curated or is under review.
range: Biomarker quality assessment state
domain: biomarker

Biomarker quality assessment state
equivalent class: Class
  one of: Curated
  one of: Accepted
  one of: Under review
type: Class
subclass of: Concept
commnet: The :BiomarkerState class provides a categorisation of the possible states a biomarker may have as a result of a quality evaluation process. For example, whether it has been Curated', 'Accepted' or 'Under review'. This categorisation is implemented as a SKOS vocabulary.
has related match: ReviewState

Under review
type: Biomarker quality assessment state
alternative label: under review
commnet: A state to assign the biomarker status under review (i.e. being evaluated). After the reviewing process, the status can change into curated or accepted, for example.

Curated
type: Biomarker quality assessment state
alternative label: curated
has narrower match: curated information
commnet: It indicates that a curation process was performed by a curator for accuracy checks and compliance with a set of requirements to confirm the veracity of an assertion, i.e. statement. The statement which has been assessed for accuracy by domain experts.

Five-phase approach
type: Class
equivalent class: Class
  one of: phase one
  one of: phase two
  one of: phase three
  one of: phase four
  one of: phase five
subclass of: Concept
comment: The Early Detection Research Network (EDRN) implemented a nationally recognized research schema designed to bring forward into clinical practice verifiably effective cancer biomarkers. The network established a roadmap and standards for research that minimizes chance, bias and over-fitting, based on a protocol driven, five-phase approach.

phase one
type: Five-phase approach
comment: Preclinical Exploratory – Exploratory studies to identify potentially useful biomarkers
alternative label: preclinical exploratory

phase two
type: Five-phase approach
comment: Clinical Assay and Validation – Studies to determine the capacity of biomarkers to distinguish between people with cancer and those without.
alternative label: clinical assay and validation

phase three
type: Five-phase approach
comment: Retrospective Longitudinal – Determine how well biomarkers detect preclinical disease by testing the markers against specimens collected longitudinally from research cohorts.
alternative label: retrospective longitudinal

phase four
type: Five-phase approach
comment: Prospective Screening – Identify the extent and characteristics of disease detected by the test and determine the false referral rate.
alternative label: prospective screening

phase five
type: Five-phase approach
comment: Cancer Control – Evaluate both the role of the biomarkers for detection of cancer and the overall impact of screening on the population through large-scale population studies.
alternative label: cancer control

hasEDRNPhase
type: ObjectProperty
sub property of: at phase
domain: cancer biomarker
comment: It states one of the 5 phases of a biomarker research as defined by Early Detection Research Network (EDRN).
range: Five-phase approach

at phase
type: ObjectProperty
type: FunctionalProperty
comment: It states the phase of a research or a trial such as a biomarker research phase.
alternative label: has phase
has narrower match: ERO_0001518

cancer differential expression
type: Class
has broader match: operation 3223
comment: Cancer differential gene expression analysis to identify which genes are up-regulated (increased expression) or down-regulated (decreased expression) between normal (i.e. healthy) and cancer cells. Identify from molecular sequence analysis (typically from analysis of microarray or RNA-seq data) genes whose expression levels are significantly different or not between two sample groups.
subclass of: Restriction
  on property: has the target disease
  some values from: cancer
subclass of: Restriction
  on property: has sequence unit
  some values from: Gene
subclass of: Restriction
  on property: is statistically significant
  some values from: boolean

fold change log2
type: DatatypeProperty
type: FunctionalProperty
has related match: fold change
comment: The logarithm (to base 2) of the fold change from normal expression to tumor expression. Fold change is equivalent to the expression level of a gene in cancer divided by the expression level of a gene in the same kind of tissue but a healthy one.
range: double
domain: cancer differential expression

p-value
type: DatatypeProperty
type: FunctionalProperty
has related match: p-value
comment: P-value for statistical significance of the reported change, computed directly by DESeq2. DESeq2 is a tool to verify the change of expression of genes between two samples.
range: double
domain: cancer differential expression

FDR adjusted p-value
type: DatatypeProperty
type: FunctionalProperty
has related match: q-value
comment: P-value adjusted for multiple testing with the Benjamini-Hochberg procedure, which controls false discovery rate (FDR).
range: double
domain: cancer differential expression

is statistically significant
type: DatatypeProperty
type: FunctionalProperty
has related match: Statistical Significance
comment: Trends are considered significant when FDR adjusted p-value < 0.05
range: boolean
domain: cancer differential expression

has expression change
type: ObjectProperty
type: FunctionalProperty
range: Class
  one of: increased
  one of: decreased
  one of: normal
domain: cancer differential expression
comment: Gene expression trend. Possible values are normal (no change), increased (up) and decreased (down).

has subjects up number
type: DatatypeProperty
type: FunctionalProperty
comment: The amount of patients with increased gene expression.
range: nonNegativeInteger
domain: cancer differential expression

has subjects down number
type: DatatypeProperty
type: FunctionalProperty
comment: The amount of patients with decreased gene expression.
range: nonNegativeInteger
domain: cancer differential expression

has normal subjects number
type: DatatypeProperty
type: FunctionalProperty
comment: The amount of patients with no change in terms of gene expression.
range: nonNegativeInteger
domain: cancer differential expression

has no coverage subjects number
type: DatatypeProperty
type: FunctionalProperty
comment: The amount of patients with no coverage.
range: nonNegativeInteger
domain: cancer differential expression

has subject total number
type: DatatypeProperty
type: FunctionalProperty
comment: The total number of patients with data for the study.
range: nonNegativeInteger
domain: cancer differential expression

is a sequence unit related to
type: ObjectProperty
comment: This property relates a sequence unit such as a gene to a biological concept explicilty defined in its range.
inverse of: has sequence unit
range: Class
  union of: absence of gene expression
  union of: gene expression
  union of: biomarker
  union of: cancer differential expression
domain: Sequence unit

disease mutation
type: Class
subclass of: Restriction
  some values from: disease
  on property: has the target disease
subclass of: Restriction
  some values from: sequence_alteration
  on property: has sequence alteration
comment: A gene alteration due to mutation that causes or predisposes an individual to a specific disease. It depicts mutation positions and functional annotations.

has mutation frequency
type: DatatypeProperty
type: FunctionalProperty
comment: The mutation frequency.
range: nonNegativeInteger
domain: disease mutation

has sequence alteration
type: ObjectProperty
alternative label: has sequence modification
comment: A sequence variation that deviates from a canonical or reference sequence.
range: sequence_alteration
domain: disease mutation

altered from
type: ObjectProperty
type: FunctionalProperty
domain: sequence_alteration
range: Class
  union of: nucleotide
  union of: amino acid
alternative label: modified from
comment: The nucleotide or amino acid in a sequence before modification.

altered to
type: ObjectProperty
type: FunctionalProperty
domain: sequence_alteration
range: Class
  union of: nucleotide
  union of: amino acid
alternative label: modified to
comment: The nucleotide or amino acid in a sequence after modification.

human chromosome
type: Class
subclass of: chromosome
subclass of: Restriction
  has value: Homo sapiens
  on property: in taxon
has broader match: chromosome
comment: A structure found in the nucleus of human cells that is comprised of a strand of linearized double-stranded DNA plus proteins that package the DNA in a condensed coil form and regulate chromosomal function. [def-source: NCI]

Homo sapiens
type: Taxon

chromosome
type: Class
has narrower match: Human Chromosome
comment: One of the bodies in the cell nucleus that is the bearer of genes, has the form of a delicate chromatin filament during interphase, contracts to form a compact cylinder segmented into two arms by the centromere during metaphase and anaphase stages of cell division, and is capable of reproducing its physical and chemical structure through successive cell divisions. [def-source: NCI]

nucleotide
type: Class
equivalent class: Class
  one of: thymine
  one of: cytosine
  one of: guanine
  one of: CHEBI_16335
  one of: uracil
comment: Nucleotides are organic molecules consisting of a nucleoside and a phosphate. Nucleobases are used to represent intances of nucleotides. Nucleobases, also known as nitrogenous bases or often simply bases, are nitrogen-containing biological compounds that form nucleosides, which in turn are components of nucleotides. A set of five nitrogenous bases is used in the construction of nucleotides, which in turn build up nucleic acids like DNA and RNA. These nitrogenous bases are adenine (A), uracil (U), guanine (G), thymine (T), and cytosine (C).

amino acid
type: Class
equivalent class: Class
  one of: alanine
  one of: cysteine
  one of: aspartic acid
  one of: glutamic acid
  one of: phenylalanine
  one of: glycine
  one of: L-histidine
  one of: L-isoleucine
  one of: lysine
  one of: leucine
  one of: methionine
  one of: asparagine
  one of: L-proline
  one of: L-glutamine
  one of: L-arginine
  one of: L-serine
  one of: L-threonine
  one of: L-valine
  one of: tryptophan
  one of: tyrosine
  one of: stop codon
  one of: any codon
comment: A carboxylic acid containing one or more amino groups.

any codon
type: amino acid
alternative label: X
comment: It indicates the presence of an undertermined amino acid
has_related_synonym: X
has_related_synonym: NNN
has_related_synonym: Xaa

sequence_alteration
type: Class
definition: A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence.
alternative term: partially characterised change in DNA sequence
alternative term: partially_characterised_change_in_DNA_sequence
alternative term: sequence alteration
IAO_0000412: so.owl

alanine
type: amino acid
definition: An alpha-amino acid that consists of propionic acid bearing an amino substituent at position 2.
charge: 0
formula: C3H7NO2
inchi: InChI=1S/C3H7NO2/c1-2(4)3(5)6/h2H,4H2,1H3,(H,5,6)
inchikey: QNAYBMKLOCPYGJ-UHFFFAOYSA-N
mass: 89.09322
monoisotopicmass: 89.04768
smiles: CC(N)C(O)=O
has_alternative_id: CHEBI:13748
has_alternative_id: CHEBI:22277
has_alternative_id: CHEBI:2539
has_dbxref: Beilstein:635807
has_dbxref: CAS:302-72-7
has_dbxref: Drug_Central:4306
has_dbxref: Gmelin:2449
has_dbxref: KEGG:C01401
has_dbxref: PMID:17439666
has_dbxref: PMID:22264337
has_dbxref: Reaxys:635807
has_dbxref: Wikipedia:Alanine
has_exact_synonym: 2-aminopropanoic acid
has_exact_synonym: Alanine
has_exact_synonym: alanine
has_related_synonym: 2-Aminopropanoic acid
has_related_synonym: 2-Aminopropionic acid
has_related_synonym: A
has_related_synonym: ALA
has_related_synonym: Alanin
has_related_synonym: alanina
id: CHEBI:16449

cysteine
type: amino acid
definition: A sulfur-containing amino acid that is propanoic acid with an amino group at position 2 and a sulfanyl group at position 3.
charge: 0
formula: C3H7NO2S
inchi: InChI=1S/C3H7NO2S/c4-2(1-7)3(5)6/h2,7H,1,4H2,(H,5,6)
inchikey: XUJNEKJLAYXESH-UHFFFAOYSA-N
mass: 121.15922
monoisotopicmass: 121.01975
smiles: NC(CS)C(O)=O
has_alternative_id: CHEBI:14061
has_alternative_id: CHEBI:23508
has_alternative_id: CHEBI:4050
has_dbxref: Beilstein:1721406
has_dbxref: CAS:3374-22-9
has_dbxref: Gmelin:2933
has_dbxref: KEGG:C00736
has_dbxref: KNApSAcK:C00001351
has_dbxref: KNApSAcK:C00007323
has_dbxref: PMID:17439666
has_dbxref: PMID:25181601
has_dbxref: Reaxys:1721406
has_dbxref: Wikipedia:Cysteine
has_exact_synonym: Cysteine
has_exact_synonym: cysteine
has_related_synonym: 2-Amino-3-mercaptopropionic acid
has_related_synonym: 2-amino-3-mercaptopropanoic acid
has_related_synonym: 2-amino-3-sulfanylpropanoic acid
has_related_synonym: C
has_related_synonym: Cys
has_related_synonym: Cystein
has_related_synonym: Hcys
has_related_synonym: Zystein
has_related_synonym: cisteina
id: CHEBI:15356

aspartic acid
type: amino acid
definition: An alpha-amino acid that consists of succinic acid bearing a single alpha-amino substituent
charge: 0
formula: C4H7NO4
inchi: InChI=1S/C4H7NO4/c5-2(4(8)9)1-3(6)7/h2H,1,5H2,(H,6,7)(H,8,9)
inchikey: CKLJMWTZIZZHCS-UHFFFAOYSA-N
mass: 133.10272
monoisotopicmass: 133.03751
smiles: NC(CC(O)=O)C(O)=O
has_dbxref: Beilstein:774618
has_dbxref: CAS:617-45-8
has_dbxref: Gmelin:185140
has_dbxref: KEGG:C16433
has_dbxref: PMID:22264337
has_dbxref: Reaxys:774618
has_dbxref: Wikipedia:Aspartic_acid
has_exact_synonym: Aspartic acid
has_exact_synonym: aspartic acid
has_related_synonym: (+-)-Aspartic acid
has_related_synonym: (R,S)-Aspartic acid
has_related_synonym: 2-aminobutanedioic acid
has_related_synonym: Asp
has_related_synonym: D
has_related_synonym: DL-Aminosuccinic acid
has_related_synonym: DL-Asparagic acid
id: CHEBI:22660

glutamic acid
type: amino acid
definition: An alpha-amino acid that is glutaric acid bearing a single amino substituent at position 2.
charge: 0
formula: C5H9NO4
inchi: InChI=1S/C5H9NO4/c6-3(5(9)10)1-2-4(7)8/h3H,1-2,6H2,(H,7,8)(H,9,10)
inchikey: WHUUTDBJXJRKMK-UHFFFAOYSA-N
mass: 147.12930
monoisotopicmass: 147.05316
smiles: NC(CCC(O)=O)C(O)=O
has_alternative_id: CHEBI:24314
has_alternative_id: CHEBI:5431
has_dbxref: Beilstein:1723799
has_dbxref: CAS:617-65-2
has_dbxref: Gmelin:101971
has_dbxref: KEGG:C00302
has_dbxref: KEGG:D04341
has_dbxref: KNApSAcK:C00001358
has_dbxref: KNApSAcK:C00019577
has_dbxref: PMID:15739367
has_dbxref: PMID:17190852
has_dbxref: PMID:24616376
has_dbxref: PMID:24984001
has_dbxref: Reaxys:1723799
has_dbxref: Wikipedia:Glutamic_acid
has_exact_synonym: 2-aminopentanedioic acid
has_exact_synonym: Glutamic acid
has_exact_synonym: glutamic acid
has_related_synonym: 2-Aminoglutaric acid
has_related_synonym: DL-Glutamic acid
has_related_synonym: DL-Glutaminic acid
has_related_synonym: E
has_related_synonym: Glu
has_related_synonym: Glutamate
has_related_synonym: Glutaminic acid
has_related_synonym: Glutaminsaeure
id: CHEBI:18237

phenylalanine
type: amino acid
definition: An aromatic amino acid that is alanine in which one of the methyl hydrogens is substituted by a phenyl group.
charge: 0
formula: C9H11NO2
inchi: InChI=1S/C9H11NO2/c10-8(9(11)12)6-7-4-2-1-3-5-7/h1-5,8H,6,10H2,(H,11,12)
inchikey: COLNVLDHVKWLRT-UHFFFAOYSA-N
mass: 165.18918
monoisotopicmass: 165.07898
smiles: NC(Cc1ccccc1)C(O)=O
has_alternative_id: CHEBI:25984
has_alternative_id: CHEBI:8089
has_dbxref: Beilstein:1910407
has_dbxref: CAS:150-30-1
has_dbxref: Gmelin:50836
has_dbxref: KEGG:C02057
has_dbxref: PMID:17439666
has_dbxref: PMID:22264337
has_dbxref: Reaxys:1910407
has_dbxref: Wikipedia:Phenylalanine
has_exact_synonym: 2-amino-3-phenylpropanoic acid
has_exact_synonym: Phenylalanine
has_exact_synonym: phenylalanine
has_related_synonym: DL-Phenylalanine
has_related_synonym: F
has_related_synonym: PHE
has_related_synonym: Phenylalanin
has_related_synonym: alpha-Amino-beta-phenylpropionic acid
has_related_synonym: fenilalanina
id: CHEBI:28044

glycine
type: amino acid
definition: The simplest (and the only achiral) proteinogenic amino acid, with a hydrogen atom as its side chain.
charge: 0
formula: C2H5NO2
inchi: InChI=1S/C2H5NO2/c3-1-2(4)5/h1,3H2,(H,4,5)
inchikey: DHMQDGOQFOQNFH-UHFFFAOYSA-N
mass: 75.06664
monoisotopicmass: 75.03203
smiles: NCC(O)=O
has_alternative_id: CHEBI:10792
has_alternative_id: CHEBI:14344
has_alternative_id: CHEBI:24368
has_alternative_id: CHEBI:42964
has_alternative_id: CHEBI:5460
has_dbxref: Beilstein:635782
has_dbxref: CAS:56-40-6
has_dbxref: DrugBank:DB00145
has_dbxref: Drug_Central:1319
has_dbxref: ECMDB:ECMDB00123
has_dbxref: Gmelin:1808
has_dbxref: HMDB:HMDB0000123
has_dbxref: KEGG:C00037
has_dbxref: KEGG:D00011
has_dbxref: KNApSAcK:C00001361
has_dbxref: MetaCyc:GLY
has_dbxref: PDBeChem:GLY
has_dbxref: PMID:10930630
has_dbxref: PMID:11019925
has_dbxref: PMID:11174716
has_dbxref: PMID:11542461
has_dbxref: PMID:11806864
has_dbxref: PMID:12631515
has_dbxref: PMID:12754315
has_dbxref: PMID:12770151
has_dbxref: PMID:12921899
has_dbxref: PMID:15331688
has_dbxref: PMID:15388434
has_dbxref: PMID:15710237
has_dbxref: PMID:16105183
has_dbxref: PMID:16151895
has_dbxref: PMID:16214212
has_dbxref: PMID:16417482
has_dbxref: PMID:16444815
has_dbxref: PMID:16664855
has_dbxref: PMID:16901953
has_dbxref: PMID:16918424
has_dbxref: PMID:16986325
has_dbxref: PMID:16998855
has_dbxref: PMID:17154252
has_dbxref: PMID:17383967
has_dbxref: PMID:17582620
has_dbxref: PMID:17970719
has_dbxref: PMID:18079355
has_dbxref: PMID:18396796
has_dbxref: PMID:18440992
has_dbxref: PMID:18593588
has_dbxref: PMID:18816054
has_dbxref: PMID:18840508
has_dbxref: PMID:19028609
has_dbxref: PMID:19120667
has_dbxref: PMID:19449910
has_dbxref: PMID:19526731
has_dbxref: PMID:19544666
has_dbxref: PMID:19738917
has_dbxref: PMID:19916621
has_dbxref: PMID:19924257
has_dbxref: PMID:21751272
has_dbxref: PMID:22044190
has_dbxref: PMID:22079563
has_dbxref: PMID:22234938
has_dbxref: PMID:22264337
has_dbxref: PMID:22293292
has_dbxref: PMID:22401276
has_dbxref: PMID:22434786
has_dbxref: Reaxys:635782
has_dbxref: Wikipedia:Glycine
has_dbxref: YMDB:YMDB00016
has_exact_synonym: GLYCINE
has_exact_synonym: Glycine
has_exact_synonym: aminoacetic acid

L-histidine
type: amino acid
definition: The L-enantiomer of the amino acid histidine.
charge: 0
formula: C6H9N3O2
inchi: InChI=1S/C6H9N3O2/c7-5(6(10)11)1-4-2-8-3-9-4/h2-3,5H,1,7H2,(H,8,9)(H,10,11)/t5-/m0/s1
inchikey: HNDVDQJCIGZPNO-YFKPBYRVSA-N
mass: 155.15468
monoisotopicmass: 155.06948
smiles: N[C@@H](Cc1c[nH]cn1)C(O)=O
has_alternative_id: CHEBI:13117
has_alternative_id: CHEBI:21324
has_alternative_id: CHEBI:43048
has_alternative_id: CHEBI:43114
has_alternative_id: CHEBI:43190
has_alternative_id: CHEBI:43239
has_alternative_id: CHEBI:6240
has_dbxref: Beilstein:84088
has_dbxref: CAS:71-00-1
has_dbxref: DrugBank:DB00117
has_dbxref: ECMDB:ECMDB00177
has_dbxref: Gmelin:83042
has_dbxref: HMDB:HMDB0000177
has_dbxref: KEGG:C00135
has_dbxref: KEGG:D00032
has_dbxref: KNApSAcK:C00001363
has_dbxref: MetaCyc:HIS
has_dbxref: PDBeChem:HIS
has_dbxref: PMID:15206581
has_dbxref: PMID:21608102
has_dbxref: PMID:21719207
has_dbxref: PMID:22324399
has_dbxref: PMID:22415677
has_dbxref: PMID:22517640
has_dbxref: Reaxys:84088
has_dbxref: Wikipedia:L-histidine
has_dbxref: YMDB:YMDB00369
has_exact_synonym: (2S)-2-amino-3-(1H-imidazol-4-yl)propanoic acid
has_exact_synonym: L-Histidine
has_exact_synonym: L-histidine
has OBO namespace: chebi_ontology
has_related_synonym: (S)-4-(2-Amino-2-carboxyethyl)imidazole
has_related_synonym: (S)-alpha-Amino-1H-imidazole-4-propionic acid
has_related_synonym: (S)-alpha-amino-1H-Imidazole-4-propanoic acid
has_related_synonym: H
has_related_synonym: HISTIDINE
has_related_synonym: His
has_related_synonym: L-(-)-histidine
has_related_synonym: L-Histidin
id: CHEBI:15971

L-isoleucine
type: amino acid
definition: The L-enantiomer of isoleucine.
charge: 0
formula: C6H13NO2
inchi: InChI=1S/C6H13NO2/c1-3-4(2)5(7)6(8)9/h4-5H,3,7H2,1-2H3,(H,8,9)/t4-,5-/m0/s1
inchikey: AGPKZVBTJJNPAG-WHFBIAKZSA-N
mass: 131.175
monoisotopicmass: 131.09463
smiles: OC([C@H]([C@H](CC)C)N)=O
has_alternative_id: CHEBI:13127
has_alternative_id: CHEBI:21344
has_alternative_id: CHEBI:43290
has_alternative_id: CHEBI:43342
has_alternative_id: CHEBI:43366
has_alternative_id: CHEBI:6255
has_dbxref: Beilstein:1721792
has_dbxref: CAS:73-32-5
has_dbxref: DrugBank:DB00167
has_dbxref: Drug_Central:4129
has_dbxref: ECMDB:ECMDB00172
has_dbxref: Gmelin:486381
has_dbxref: HMDB:HMDB0000172
has_dbxref: KEGG:C00407
has_dbxref: KEGG:D00065
has_dbxref: KNApSAcK:C00001374
has_dbxref: MetaCyc:ILE
has_dbxref: PDBeChem:ILE
has_dbxref: PMID:14651987
has_dbxref: PMID:16140883
has_dbxref: PMID:17299083
has_dbxref: PMID:17409434
has_dbxref: PMID:22298573
has_dbxref: PMID:24284437
has_dbxref: PMID:24406630
has_dbxref: PMID:24738868
has_dbxref: PMID:24831709
has_dbxref: Reaxys:1721792
has_dbxref: Wikipedia:Isoleucine
has_dbxref: YMDB:YMDB00038
has_exact_synonym: L-Isoleucine
has_exact_synonym: L-isoleucine
has OBO namespace: chebi_ontology
has_related_synonym: (2S,3S)-2-amino-3-methylpentanoic acid
has_related_synonym: 2-Amino-3-methylvaleric acid
has_related_synonym: I
has_related_synonym: ISOLEUCINE
has_related_synonym: Ile
has_related_synonym: alpha-amino-beta-methylvaleric acid
id: CHEBI:17191

lysine
type: amino acid
definition: A diamino acid that is caproic (hexanoic) acid bearing two amino substituents at positions 2 and 6.
charge: 0
formula: C6H14N2O2
inchi: InChI=1S/C6H14N2O2/c7-4-2-1-3-5(8)6(9)10/h5H,1-4,7-8H2,(H,9,10)
inchikey: KDXKERNSBIXSRK-UHFFFAOYSA-N
mass: 146.18764
monoisotopicmass: 146.10553
smiles: NCCCCC(N)C(O)=O
has_dbxref: Beilstein:1616991
has_dbxref: CAS:70-54-2
has_dbxref: Gmelin:279284
has_dbxref: KEGG:C16440
has_dbxref: PMID:17439666
has_dbxref: PMID:22264337
has_dbxref: Reaxys:1616991
has_dbxref: Wikipedia:Lysine
has_exact_synonym: 2,6-diaminohexanoic acid
has_exact_synonym: lysine
has_related_synonym: K
has_related_synonym: LYS
has_related_synonym: Lysin
has_related_synonym: alpha,epsilon-diaminocaproic acid
id: CHEBI:25094

leucine
type: amino acid
definition: A branched-chain amino acid that consists of glycine in which one of the hydrogens attached to the alpha-carbon is substituted by an isobutyl group.
charge: 0
formula: C6H13NO2
inchi: InChI=1S/C6H13NO2/c1-4(2)3-5(7)6(8)9/h4-5H,3,7H2,1-2H3,(H,8,9)
inchikey: ROHFNLRQFUQHCH-UHFFFAOYSA-N
mass: 131.17296
monoisotopicmass: 131.09463
smiles: CC(C)CC(N)C(O)=O
has_dbxref: Beilstein:636005
has_dbxref: CAS:328-39-2
has_dbxref: Gmelin:50203
has_dbxref: KEGG:C16439
has_dbxref: LIPID_MAPS_instance:LMFA01100048
has_dbxref: PMID:17439666
has_dbxref: Reaxys:636005
has_dbxref: Wikipedia:Leucine
has_exact_synonym: leucine
has_related_synonym: (+-)-Leucine
has_related_synonym: (RS)-Leucine
has_related_synonym: 2-amino-4-methylpentanoic acid
has_related_synonym: DL-Leucine
has_related_synonym: Hleu
has_related_synonym: L
has_related_synonym: Leu
has_related_synonym: Leucin
has_related_synonym: Leuzin
id: CHEBI:25017

methionine
type: amino acid
definition: A sulfur-containing amino acid that is butyric acid bearing an amino substituent at position 2 and a methylthio substituent at position 4.
charge: 0
formula: C5H11NO2S
inchi: InChI=1S/C5H11NO2S/c1-9-3-2-4(6)5(7)8/h4H,2-3,6H2,1H3,(H,7,8)
inchikey: FFEARJCKVFRZRR-UHFFFAOYSA-N
mass: 149.21238
monoisotopicmass: 149.05105
smiles: CSCCC(N)C(O)=O
has_alternative_id: CHEBI:14590
has_alternative_id: CHEBI:25229
has_alternative_id: CHEBI:6829
has_dbxref: Beilstein:636185
has_dbxref: CAS:59-51-8
has_dbxref: Gmelin:3117
has_dbxref: KEGG:C01733
has_dbxref: KEGG:D04983
has_dbxref: PMID:16702333
has_dbxref: PMID:22264337
has_dbxref: PMID:2543976
has_dbxref: Reaxys:636185
has_dbxref: UM-BBD_compID:c0094
has_dbxref: Wikipedia:Methionine
has_exact_synonym: Methionine
has_exact_synonym: methionine
has_related_synonym: 2-Amino-4-(methylthio)butyric acid
has_related_synonym: 2-amino-4-(methylsulfanyl)butanoic acid
has_related_synonym: 2-amino-4-(methylthio)butanoic acid
has_related_synonym: DL-Methionine
has_related_synonym: Hmet
has_related_synonym: M
has_related_synonym: Met
has_related_synonym: Methionin
has_related_synonym: Racemethionine
has_related_synonym: alpha-amino-gamma-methylmercaptobutyric acid
has_related_synonym: metionina
id: CHEBI:16811

asparagine
type: amino acid
definition: An alpha-amino acid in which one of the hydrogens attached to the alpha-carbon of glycine is substituted by a 2-amino-2-oxoethyl group.
charge: 0
formula: C4H8N2O3
inchi: InChI=1S/C4H8N2O3/c5-2(4(8)9)1-3(6)7/h2H,1,5H2,(H2,6,7)(H,8,9)
inchikey: DCXYFEDJOCDNAF-UHFFFAOYSA-N
mass: 132.11800
monoisotopicmass: 132.05349
smiles: NC(CC(N)=O)C(O)=O
has_dbxref: Beilstein:1723525
has_dbxref: CAS:3130-87-8
has_dbxref: Gmelin:279043
has_dbxref: KEGG:C16438
has_dbxref: PMID:22264337
has_dbxref: PMID:22770225
has_dbxref: Reaxys:1723525
has_dbxref: Wikipedia:Asparagine
has_exact_synonym: asparagine
has_related_synonym: 2,4-diamino-4-oxobutanoic acid
has_related_synonym: 2-amino-3-carbamoylpropanoic acid
has_related_synonym: ASN
has_related_synonym: Asn
has_related_synonym: Asparagin
has_related_synonym: DL-Asparagine
has_related_synonym: Hasp
has_related_synonym: N
has_related_synonym: asparagina
id: CHEBI:22653

L-proline
type: amino acid
definition: Pyrrolidine in which the pro-S hydrogen at position 2 is substituted by a carboxylic acid group. L-Proline is the only one of the twenty DNA-encoded amino acids which has a secondary amino group alpha to the carboxyl group. It is an essential component of collagen and is important for proper functioning of joints and tendons. It also helps maintain and strengthen heart muscles.
charge: 0
formula: C5H9NO2
inchi: InChI=1S/C5H9NO2/c7-5(8)4-2-1-3-6-4/h4,6H,1-3H2,(H,7,8)/t4-/m0/s1
inchikey: ONIBWKKTOPOVIA-BYPYZUCNSA-N
mass: 115.13050
monoisotopicmass: 115.06333
smiles: OC(=O)[C@@H]1CCCN1
has_alternative_id: CHEBI:13154
has_alternative_id: CHEBI:184637
has_alternative_id: CHEBI:21373
has_alternative_id: CHEBI:42067
has_alternative_id: CHEBI:45040
has_alternative_id: CHEBI:45100
has_alternative_id: CHEBI:45159
has_alternative_id: CHEBI:6286
has_dbxref: Beilstein:80810
has_dbxref: CAS:147-85-3
has_dbxref: DrugBank:DB00172
has_dbxref: Drug_Central:4125
has_dbxref: Gmelin:50152
has_dbxref: HMDB:HMDB0000162
has_dbxref: KEGG:C00148
has_dbxref: KEGG:D00035
has_dbxref: KNApSAcK:C00001388
has_dbxref: MetaCyc:PRO
has_dbxref: PDBeChem:PRO
has_dbxref: PMID:11076505
has_dbxref: PMID:12770004
has_dbxref: PMID:14975886
has_dbxref: PMID:15576824
has_dbxref: PMID:15838615
has_dbxref: PMID:15894682
has_dbxref: PMID:15973048
has_dbxref: PMID:16033917
has_dbxref: PMID:16190672
has_dbxref: PMID:16501220
has_dbxref: PMID:16656443
has_dbxref: PMID:16657874
has_dbxref: PMID:16668324
has_dbxref: PMID:17127472
has_dbxref: PMID:17608428
has_dbxref: PMID:18551589
has_dbxref: PMID:18802692
has_dbxref: PMID:18973300
has_dbxref: PMID:19215998
has_dbxref: PMID:19580280
has_dbxref: PMID:19656302
has_dbxref: PMID:19688381
has_dbxref: PMID:19811425
has_dbxref: PMID:22139509
has_dbxref: PMID:22201772
has_dbxref: PMID:22451406
has_dbxref: PMID:22475019
has_dbxref: PMID:22482728
has_dbxref: PMID:22491679
has_dbxref: PMID:22770225
has_dbxref: Reaxys:80810
has_dbxref: Wikipedia:L-proline
has_exact_synonym: L-Proline
has_exact_synonym: L-proline
has_related_synonym: (-)-(S)-proline
has_related_synonym: (-)-2-pyrrolidinecarboxylic acid
has_related_synonym: (-)-proline
has_related_synonym: (2S)-pyrrolidine-2-carboxylic acid
has_related_synonym: (S)-2-carboxypyrrolidine
has_related_synonym: (S)-2-pyrrolidinecarboxylic acid
has_related_synonym: (S)-pyrrolidine-2-carboxylic acid
has_related_synonym: 2-Pyrrolidinecarboxylic acid
has_related_synonym: L-(-)-proline
has_related_synonym: L-Prolin
has_related_synonym: L-alpha-pyrrolidinecarboxylic acid
has_related_synonym: L-pyrrolidine-2-carboxylic acid
has_related_synonym: P
has_related_synonym: PROLINE
has_related_synonym: prolina
has_related_synonym: proline
has_related_synonym: prolinum
id: CHEBI:17203

L-glutamine
type: amino acid
definition: An optically active form of glutamine having L-configuration.
charge: 0
formula: C5H10N2O3
inchi: InChI=1S/C5H10N2O3/c6-3(5(9)10)1-2-4(7)8/h3H,1-2,6H2,(H2,7,8)(H,9,10)/t3-/m0/s1
inchikey: ZDXPYRJPNDTMRX-VKHMYHEASA-N
mass: 146.14458
monoisotopicmass: 146.06914
smiles: N[C@@H](CCC(N)=O)C(O)=O
has_alternative_id: CHEBI:13110
has_alternative_id: CHEBI:21308
has_alternative_id: CHEBI:42812
has_alternative_id: CHEBI:42814
has_alternative_id: CHEBI:42899
has_alternative_id: CHEBI:42943
has_alternative_id: CHEBI:6227
has_dbxref: Beilstein:1723797
has_dbxref: CAS:56-85-9
has_dbxref: DrugBank:DB00130
has_dbxref: Drug_Central:1311
has_dbxref: ECMDB:ECMDB00641
has_dbxref: Gmelin:3509
has_dbxref: HMDB:HMDB0000641
has_dbxref: KEGG:C00064
has_dbxref: KEGG:D00015
has_dbxref: KNApSAcK:C00001359
has_dbxref: LINCS:LSM-4741
has_dbxref: MetaCyc:GLN
has_dbxref: PDBeChem:GLN
has_dbxref: PMID:11139387
has_dbxref: PMID:15204730
has_dbxref: PMID:22055478
has_dbxref: PMID:22206385
has_dbxref: PMID:22451274
has_dbxref: PMID:22453904
has_dbxref: PMID:22575040
has_dbxref: PMID:22770225
has_dbxref: PMID:29438107
has_dbxref: Reaxys:1723797
has_dbxref: Wikipedia:Glutamine
has_dbxref: YMDB:YMDB00002
has_exact_synonym: L-Glutamine
has_exact_synonym: L-glutamine
has_related_synonym: (2S)-2,5-diamino-5-oxopentanoic acid
has_related_synonym: (2S)-2-amino-4-carbamoylbutanoic acid
has_related_synonym: (S)-2,5-diamino-5-oxopentanoic acid
has_related_synonym: GLUTAMINE
has_related_synonym: Glutamic acid 5-amide
has_related_synonym: Glutamic acid amide
has_related_synonym: L-(+)-glutamine
has_related_synonym: L-2-Aminoglutaramic acid
has_related_synonym: L-2-aminoglutaramic acid
has_related_synonym: L-Glutamin
has_related_synonym: L-Glutaminsaeure-5-amid
has_related_synonym: L-glutamic acid gamma-amide
has_related_synonym: Levoglutamide
has_related_synonym: Q
id: CHEBI:18050

L-arginine
type: AminAcid
definition: An L-alpha-amino acid that is the L-isomer of arginine.
charge: 0
formula: C6H14N4O2
inchi: InChI=1S/C6H14N4O2/c7-4(5(11)12)2-1-3-10-6(8)9/h4H,1-3,7H2,(H,11,12)(H4,8,9,10)/t4-/m0/s1
inchikey: ODKSFYDXXFIFQN-BYPYZUCNSA-N
mass: 174.20100
monoisotopicmass: 174.11168
smiles: N[C@@H](CCCNC(N)=N)C(O)=O
has_alternative_id: CHEBI:13077
has_alternative_id: CHEBI:21235
has_alternative_id: CHEBI:42927
has_alternative_id: CHEBI:6185
has_dbxref: Beilstein:1725413
has_dbxref: CAS:74-79-3
has_dbxref: DrugBank:DB00125
has_dbxref: Drug_Central:1549
has_dbxref: ECMDB:ECMDB00517
has_dbxref: Gmelin:83283
has_dbxref: HMDB:HMDB0000517
has_dbxref: KEGG:C00062
has_dbxref: KEGG:D02982
has_dbxref: KNApSAcK:C00001340
has_dbxref: MetaCyc:ARG
has_dbxref: PDBeChem:ARG
has_dbxref: PDBeChem:GND
has_dbxref: PMID:10848923
has_dbxref: PMID:11139824
has_dbxref: PMID:11300497
has_dbxref: PMID:11898853
has_dbxref: PMID:12812828
has_dbxref: PMID:15016745
has_dbxref: PMID:15465805
has_dbxref: PMID:16056256
has_dbxref: PMID:16416365
has_dbxref: PMID:17168727
has_dbxref: PMID:17439666
has_dbxref: PMID:19030957
has_dbxref: PMID:21600268
has_dbxref: PMID:21814794
has_dbxref: PMID:22179117
has_dbxref: PMID:22243793
has_dbxref: PMID:22251130
has_dbxref: PMID:22361732
has_dbxref: PMID:22425811
has_dbxref: PMID:22428068
has_dbxref: PMID:22439203
has_dbxref: PMID:22553931
has_dbxref: PMID:22619480
has_dbxref: PMID:22626826
has_dbxref: PMID:22652429
has_dbxref: PMID:22667467
has_dbxref: PMID:22709481
has_dbxref: PMID:8070089
has_dbxref: Reaxys:1725413
has_dbxref: Wikipedia:L-arginine
has_dbxref: YMDB:YMDB00592
has_exact_synonym: L-Arginine
has_exact_synonym: L-arginine
has_related_synonym: (2S)-2-amino-5-(carbamimidamido)pentanoic acid
has_related_synonym: (2S)-2-amino-5-guanidinopentanoic acid
has_related_synonym: (S)-2-Amino-5-guanidinovaleric acid
has_related_synonym: (S)-2-amino-5-guanidinopentanoic acid
has_related_synonym: Arg
has_related_synonym: L-(+)-arginine
has_related_synonym: L-Arg
has_related_synonym: L-Arginin
has_related_synonym: R
has_related_synonym: arginine
id: CHEBI:16467

L-serine
type: amino acid
definition: The L-enantiomer of serine.
charge: 0
formula: C3H7NO3
inchi: InChI=1S/C3H7NO3/c4-2(1-5)3(6)7/h2,5H,1,4H2,(H,6,7)/t2-/m0/s1
inchikey: MTCFGRXMJLQNBG-REOHCLBHSA-N
mass: 105.09262
monoisotopicmass: 105.04259
smiles: N[C@@H](CO)C(O)=O
has_alternative_id: CHEBI:13167
has_alternative_id: CHEBI:21387
has_alternative_id: CHEBI:45440
has_alternative_id: CHEBI:45451
has_alternative_id: CHEBI:45590
has_alternative_id: CHEBI:45597
has_alternative_id: CHEBI:45677
has_alternative_id: CHEBI:6301
has_dbxref: Beilstein:1721404
has_dbxref: CAS:56-45-1
has_dbxref: DrugBank:DB00133
has_dbxref: Drug_Central:4127
has_dbxref: ECMDB:ECMDB00187
has_dbxref: Gmelin:2570
has_dbxref: HMDB:HMDB0000187
has_dbxref: KEGG:C00065
has_dbxref: KEGG:D00016
has_dbxref: KNApSAcK:C00001393
has_dbxref: MetaCyc:SER
has_dbxref: PDBeChem:SER
has_dbxref: PMID:1650428
has_dbxref: PMID:17439666
has_dbxref: PMID:19062365
has_dbxref: PMID:21956576
has_dbxref: PMID:22265470
has_dbxref: PMID:22393170
has_dbxref: PMID:22547037
has_dbxref: PMID:22566084
has_dbxref: PMID:22566694
has_dbxref: Reaxys:1721404
has_dbxref: Wikipedia:L-serine
has_dbxref: YMDB:YMDB00112
has_exact_synonym: L-Serine
has_exact_synonym: L-serine
has_related_synonym: (2S)-2-amino-3-hydroxypropanoic acid
has_related_synonym: (S)-(-)-serine
has_related_synonym: (S)-2-amino-3-hydroxypropanoic acid
has_related_synonym: (S)-alpha-Amino-beta-hydroxypropionic acid
has_related_synonym: (S)-serine
has_related_synonym: L-(-)-serine
has_related_synonym: L-2-Amino-3-hydroxypropionic acid
has_related_synonym: L-3-Hydroxy-2-aminopropionic acid
has_related_synonym: L-3-Hydroxy-alanine
has_related_synonym: L-Ser
has_related_synonym: L-Serin
has_related_synonym: S
has_related_synonym: SERINE
has_related_synonym: Ser
has_related_synonym: Serine
has_related_synonym: beta-Hydroxy-L-alanine
has_related_synonym: beta-Hydroxyalanine
id: CHEBI:17115

L-threonine
type: amino acid
definition: An optically active form of threonine having L-configuration.
charge: 0
formula: C4H9NO3
inchi: InChI=1S/C4H9NO3/c1-2(6)3(5)4(7)8/h2-3,6H,5H2,1H3,(H,7,8)/t2-,3+/m1/s1
inchikey: AYFVYJQAPQTCCC-GBXIJSLDSA-N
mass: 119.11920
monoisotopicmass: 119.05824
smiles: C[C@@H](O)[C@H](N)C(O)=O
has_alternative_id: CHEBI:13175
has_alternative_id: CHEBI:21403
has_alternative_id: CHEBI:42083
has_alternative_id: CHEBI:45843
has_alternative_id: CHEBI:45983
has_alternative_id: CHEBI:6308
has_dbxref: Beilstein:1721646
has_dbxref: CAS:72-19-5
has_dbxref: DrugBank:DB00156
has_dbxref: Drug_Central:4254
has_dbxref: ECMDB:ECMDB00167
has_dbxref: Gmelin:82510
has_dbxref: HMDB:HMDB0000167
has_dbxref: KEGG:C00188
has_dbxref: KEGG:D00041
has_dbxref: KNApSAcK:C00001394
has_dbxref: PDBeChem:THR
has_dbxref: PMID:11964235
has_dbxref: PMID:12523390
has_dbxref: PMID:16659349
has_dbxref: PMID:17379183
has_dbxref: PMID:22289691
has_dbxref: PMID:22342587
has_dbxref: PMID:22513921
has_dbxref: PMID:22770225
has_dbxref: PMID:24671569
has_dbxref: Reaxys:1721646
has_dbxref: UM-BBD_compID:c0413
has_dbxref: Wikipedia:Threonine
has_dbxref: YMDB:YMDB00214
has_exact_synonym: L-Threonine
has_exact_synonym: L-threonine
has OBO namespace: chebi_ontology
has_related_synonym: (2S)-threonine
has_related_synonym: (2S,3R)-(-)-Threonine
has_related_synonym: (2S,3R)-2-amino-3-hydroxybutanoic acid
has_related_synonym: 2-Amino-3-hydroxybutyric acid
has_related_synonym: L-(-)-Threonine
has_related_synonym: L-2-Amino-3-hydroxybutyric acid
has_related_synonym: L-Threonin
has_related_synonym: L-alpha-amino-beta-hydroxybutyric acid
has_related_synonym: T
has_related_synonym: THREONINE
has_related_synonym: Thr
id: CHEBI:16857

tryptophan
type: amino acid
definition: An alpha-amino acid that is alanine bearing an indol-3-yl substituent at position 3.
charge: 0
formula: C11H12N2O2
inchi: InChI=1S/C11H12N2O2/c12-9(11(14)15)5-7-6-13-10-4-2-1-3-8(7)10/h1-4,6,9,13H,5,12H2,(H,14,15)
inchikey: QIVBCDIJIAJPQS-UHFFFAOYSA-N
mass: 204.22526
monoisotopicmass: 204.08988
smiles: NC(Cc1c[nH]c2ccccc12)C(O)=O
has_alternative_id: CHEBI:27163
has_alternative_id: CHEBI:9769
has_dbxref: Beilstein:86196
has_dbxref: CAS:54-12-6
has_dbxref: Gmelin:4532
has_dbxref: KEGG:C00806
has_dbxref: KNApSAcK:C00001396
has_dbxref: LINCS:LSM-36836
has_dbxref: PMID:17439666
has_dbxref: PMID:22264337
has_dbxref: Reaxys:86196
has_dbxref: Wikipedia:Tryptophan
has_exact_synonym: Tryptophan
has_exact_synonym: tryptophan
has_related_synonym: 2-amino-3-(1H-indol-3-yl)propanoic acid
has_related_synonym: Htrp
has_related_synonym: Trp
has_related_synonym: W
has_related_synonym: alpha-Amino-beta-(3-indolyl)-propionic acid
has_related_synonym: alpha-amino-beta-3-indolepropionic acid
has_related_synonym: beta-3-indolylalanine
has_related_synonym: triptofano
has_related_synonym: tryptophane
id: CHEBI:27897

tyrosine
type: amino acid
definition: An alpha-amino acid that is phenylalanine bearing a hydroxy substituent at position 4 on the phenyl ring.
charge: 0
formula: C9H11NO3
inchi: InChI=1S/C9H11NO3/c10-8(9(12)13)5-6-1-3-7(11)4-2-6/h1-4,8,11H,5,10H2,(H,12,13)
inchikey: OUYCCCASQSFEME-UHFFFAOYSA-N
mass: 181.18858
monoisotopicmass: 181.07389
smiles: NC(Cc1ccc(O)cc1)C(O)=O
has_alternative_id: CHEBI:15277
has_alternative_id: CHEBI:27176
has_alternative_id: CHEBI:9800
has_dbxref: Beilstein:515881
has_dbxref: CAS:55520-40-6
has_dbxref: CAS:556-03-6
has_dbxref: Gmelin:27744
has_dbxref: KEGG:C01536
has_dbxref: KNApSAcK:C00001397
has_dbxref: PMID:17190852
has_dbxref: Reaxys:515881
has_exact_synonym: Tyrosine
has_exact_synonym: tyrosine
has_related_synonym: 2-Amino-3-(p-hydroxyphenyl)propionic acid
has_related_synonym: 2-amino-3-(4-hydroxyphenyl)propanoic acid
has_related_synonym: 3-(p-Hydroxyphenyl)alanine
has_related_synonym: Tyr
has_related_synonym: Tyrosin
has_related_synonym: Y
has_related_synonym: tirosina
id: CHEBI:18186

L-valine
type: amino acid
definition: The L-enantiomer of valine.
charge: 0
formula: C5H11NO2
inchi: InChI=1S/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1
inchikey: KZSNJWFQEVHDMF-BYPYZUCNSA-N
mass: 117.14638
monoisotopicmass: 117.07898
smiles: CC(C)[C@H](N)C(O)=O
has_alternative_id: CHEBI:13186
has_alternative_id: CHEBI:21417
has_alternative_id: CHEBI:46282
has_alternative_id: CHEBI:46376
has_alternative_id: CHEBI:46418
has_alternative_id: CHEBI:46484
has_alternative_id: CHEBI:6321
has_dbxref: Beilstein:1721136
has_dbxref: CAS:72-18-4
has_dbxref: DrugBank:DB00161
has_dbxref: Drug_Central:4128
has_dbxref: Gmelin:2827
has_dbxref: HMDB:HMDB0000883
has_dbxref: KEGG:C00183
has_dbxref: KEGG:D00039
has_dbxref: KNApSAcK:C00001398
has_dbxref: MetaCyc:VAL
has_dbxref: PDBeChem:VAL
has_dbxref: PMID:14608070
has_dbxref: PMID:17670823
has_dbxref: PMID:21706252
has_dbxref: PMID:22138982
has_dbxref: PMID:22287678
has_dbxref: PMID:22585822
has_dbxref: Reaxys:1721136
has_dbxref: Wikipedia:L-valine
has_exact_synonym: L-Valine
has_exact_synonym: L-valine
has_related_synonym: (2S)-2-amino-3-methylbutanoic acid
has_related_synonym: (S)-valine
has_related_synonym: 2-Amino-3-methylbutyric acid
has_related_synonym: L-(+)-alpha-Aminoisovaleric acid
has_related_synonym: L-Valin
has_related_synonym: L-alpha-Amino-beta-methylbutyric acid
has_related_synonym: V
has_related_synonym: VALINE
has_related_synonym: Val
id: CHEBI:16414

amino acid
type: Concept
definition: A carboxylic acid containing one or more amino groups.
has_alternative_id: CHEBI:13815
has_alternative_id: CHEBI:22477
has_dbxref: Wikipedia:Amino_acid
has_related_synonym: Aminocarbonsaeure
has_related_synonym: Aminokarbonsaeure
has_related_synonym: Aminosaeure
has_related_synonym: amino acids
id: CHEBI:33709
is in scheme: chebi.owl

nucleotide
type: Concept
definition: A nucleotide is a nucleoside phosphate resulting from the condensation of the 3 or 5 hydroxy group of a nucleoside with phosphoric acid.
has_alternative_id: CHEBI:13215
has_alternative_id: CHEBI:13663
has_alternative_id: CHEBI:7656
has_dbxref: KEGG:C00215
has_exact_synonym: Nucleotide
has_related_synonym: nucleotides
id: CHEBI:36976
is in scheme: chebi.owl

nucleobase
type: Concept
definition: That part of DNA or RNA that may be involved in pairing.
has_alternative_id: CHEBI:13873
has_alternative_id: CHEBI:25598
has_alternative_id: CHEBI:2995
has_dbxref: KEGG:C00701
has_dbxref: Wikipedia:Nucleobase
has_related_synonym: Base
has_related_synonym: nucleobases
id: CHEBI:18282
is in scheme: chebi.owl

uracil
type: nucleotide
definition: A common and naturally occurring pyrimidine nucleobase in which the pyrimidine ring is substituted with two oxo groups at positions 2 and 4. Found in RNA, it base pairs with adenine and replaces thymine during DNA transcription.
charge: 0
formula: C4H4N2O2
inchi: InChI=1S/C4H4N2O2/c7-3-1-2-5-4(8)6-3/h1-2H,(H2,5,6,7,8)
inchikey: ISAKRJDGNUQOIC-UHFFFAOYSA-N
mass: 112.08684
monoisotopicmass: 112.02728
smiles: O=c1cc[nH]c(=O)[nH]1
has_alternative_id: CHEBI:15288
has_alternative_id: CHEBI:27210
has_alternative_id: CHEBI:46375
has_alternative_id: CHEBI:9882
has_dbxref: Beilstein:606623
has_dbxref: CAS:66-22-8
has_dbxref: DrugBank:DB03419
has_dbxref: Gmelin:2896
has_dbxref: HMDB:HMDB0000300
has_dbxref: KEGG:C00106
has_dbxref: KEGG:D00027
has_dbxref: KNApSAcK:C00001513
has_dbxref: MetaCyc:URACIL
has_dbxref: PDBeChem:URA
has_dbxref: PMID:11279060
has_dbxref: PMID:12855717
has_dbxref: PMID:15274295
has_dbxref: PMID:16834123
has_dbxref: PMID:17439666
has_dbxref: PMID:18533995
has_dbxref: PMID:18815805
has_dbxref: PMID:19175333
has_dbxref: PMID:22020693
has_dbxref: PMID:22074393
has_dbxref: PMID:22120518
has_dbxref: PMID:22171528
has_dbxref: PMID:22237209
has_dbxref: PMID:22299724
has_dbxref: PMID:22356544
has_dbxref: PMID:22447672
has_dbxref: PMID:22483865
has_dbxref: PMID:22567906
has_dbxref: PMID:22685418
has_dbxref: PMID:3654008
has_dbxref: Reaxys:606623
has_dbxref: Wikipedia:Uracil
has_exact_synonym: URACIL
has_exact_synonym: Uracil
has_exact_synonym: pyrimidine-2,4(1H,3H)-dione
has_exact_synonym: uracil
has_related_synonym: 2,4(1H,3H)-pyrimidinedione
has_related_synonym: 2,4-Dioxopyrimidine
has_related_synonym: 2,4-Pyrimidinedione
has_related_synonym: U
has_related_synonym: Ura
has_related_synonym: Urazil
id: CHEBI:17568

guanine
type: nucleotide
definition: A 2-aminopurine carrying a 6-oxo substituent.
charge: 0
formula: C5H5N5O
inchi: InChI=1S/C5H5N5O/c6-5-9-3-2(4(11)10-5)7-1-8-3/h1H,(H4,6,7,8,9,10,11)
inchikey: UYTPUPDQBNUYGX-UHFFFAOYSA-N
mass: 151.126
monoisotopicmass: 151.04941
smiles: C12=C(N=C(NC1=O)N)NC=N2
has_alternative_id: CHEBI:14371
has_alternative_id: CHEBI:14372
has_alternative_id: CHEBI:24443
has_alternative_id: CHEBI:42948
has_alternative_id: CHEBI:5563
has_dbxref: Beilstein:147911
has_dbxref: CAS:73-40-5
has_dbxref: DrugBank:DB02377
has_dbxref: Gmelin:431879
has_dbxref: HMDB:HMDB0000132
has_dbxref: KEGG:C00242
has_dbxref: KNApSAcK:C00001501
has_dbxref: MetaCyc:GUANINE
has_dbxref: PDBeChem:GUN
has_dbxref: PMID:22770225
has_dbxref: PMID:8070089
has_dbxref: Reaxys:147911
has_dbxref: Wikipedia:Guanine
has_exact_synonym: 2-amino-1,9-dihydro-6H-purin-6-one
has_exact_synonym: GUANINE
has_exact_synonym: Guanine
has_exact_synonym: guanine
has_related_synonym: 2-Amino-6-hydroxypurine
has_related_synonym: 2-amino-6-oxopurine
has_related_synonym: G
has_related_synonym: Gua
id: CHEBI:16235

adenine
type: nucleotide
definition: The parent compound of the 6-aminopurines, composed of a purine having an amino group at C-6.
charge: 0
formula: C5H5N5
inchi: InChI=1S/C5H5N5/c6-4-3-5(9-1-7-3)10-2-8-4/h1-2H,(H3,6,7,8,9,10)
inchikey: GFFGJBXGBJISGV-UHFFFAOYSA-N
mass: 135.12690
monoisotopicmass: 135.05450
smiles: Nc1ncnc2[nH]cnc12
has_alternative_id: CHEBI:13733
has_alternative_id: CHEBI:22236
has_alternative_id: CHEBI:2470
has_alternative_id: CHEBI:40579
has_dbxref: Beilstein:608603
has_dbxref: CAS:73-24-5
has_dbxref: DrugBank:DB00173
has_dbxref: Drug_Central:89
has_dbxref: Gmelin:3903
has_dbxref: HMDB:HMDB0000034
has_dbxref: KEGG:C00147
has_dbxref: KEGG:D00034
has_dbxref: KNApSAcK:C00001490
has_dbxref: MetaCyc:ADENINE
has_dbxref: PDBeChem:ADE
has_dbxref: PMID:11985597
has_dbxref: PMID:12829005
has_dbxref: PMID:12951489
has_dbxref: PMID:15063338
has_dbxref: PMID:15715490
has_dbxref: PMID:17439666
has_dbxref: PMID:8070089
has_dbxref: Reaxys:608603
has_dbxref: Wikipedia:Adenine
has_exact_synonym: 9H-purin-6-amine
has_exact_synonym: ADENINE
has_exact_synonym: Adenine
has_exact_synonym: adenine
has_related_synonym: 6-Aminopurine
has_related_synonym: A
has_related_synonym: Ade
has_related_synonym: Adenin
id: CHEBI:16708

cytosine
type: nucleotide
definition: An aminopyrimidine that is pyrimidin-2-one having the amino group located at position 4.
charge: 0
formula: C4H5N3O
inchi: InChI=1S/C4H5N3O/c5-3-1-2-6-4(8)7-3/h1-2H,(H3,5,6,7,8)
inchikey: OPTASPLRGRRNAP-UHFFFAOYSA-N
mass: 111.10212
monoisotopicmass: 111.04326
smiles: Nc1cc[nH]c(=O)n1
has_alternative_id: CHEBI:14066
has_alternative_id: CHEBI:23531
has_alternative_id: CHEBI:4072
has_alternative_id: CHEBI:41732
has_dbxref: Beilstein:2637
has_dbxref: CAS:71-30-7
has_dbxref: Gmelin:82472
has_dbxref: HMDB:HMDB0000630
has_dbxref: KEGG:C00380
has_dbxref: KNApSAcK:C00001498
has_dbxref: MetaCyc:CYTOSINE
has_dbxref: PDBeChem:CYT
has_dbxref: PMID:14253484
has_dbxref: PMID:22770225
has_dbxref: PMID:7877593
has_dbxref: Reaxys:2637
has_dbxref: Wikipedia:Cytosine
has_exact_synonym: 4-aminopyrimidin-2(1H)-one
has_exact_synonym: Cytosine
has_exact_synonym: cytosine
has_related_synonym: 4-amino-2(1H)-pyrimidinone
has_related_synonym: 4-amino-2-hydroxypyrimidine
has_related_synonym: C
has_related_synonym: Cyt
has_related_synonym: Cytosin
has_related_synonym: Zytosin
id: CHEBI:16040

thymine
type: nucleotide
definition: A pyrimidine nucleobase that is uracil in which the hydrogen at position 5 is replaced by a methyl group.
charge: 0
formula: C5H6N2O2
inchi: InChI=1S/C5H6N2O2/c1-3-2-6-5(9)7-4(3)8/h2H,1H3,(H2,6,7,8,9)
inchikey: RWQNBRDOKXIBIV-UHFFFAOYSA-N
mass: 126.11342
monoisotopicmass: 126.04293
smiles: Cc1c[nH]c(=O)[nH]c1=O
has_alternative_id: CHEBI:15247
has_alternative_id: CHEBI:27004
has_alternative_id: CHEBI:46017
has_alternative_id: CHEBI:9580
has_dbxref: Beilstein:607626
has_dbxref: CAS:65-71-4
has_dbxref: DrugBank:DB03462
has_dbxref: Gmelin:278790
has_dbxref: KEGG:C00178
has_dbxref: KNApSAcK:C00001511
has_dbxref: PDBeChem:TDR
has_dbxref: PMID:23237383
has_dbxref: Wikipedia:Thymine
has_exact_synonym: THYMINE
has_exact_synonym: Thymine
has_exact_synonym: thymine
has_related_synonym: 2,4-dihydroxy-5-methylpyrimidine
has_related_synonym: 5-Methyluracil
has_related_synonym: 5-methyl-2,4(1H,3H)-pyrimidinedione
has_related_synonym: 5-methylpyrimidine-2,4(1H,3H)-dione
has_related_synonym: 5-methyluracil
has_related_synonym: T
has_related_synonym: Thy
has_related_synonym: Thymin
id: CHEBI:17821

is encoded by
type: ObjectProperty
description: A relation between two objects, in which the first object is produced from the information contained in the second object.

probability measure
type: Concept
is in scheme: sio.owl
description: A probability measure is quantity of how likely it is that some event will occur.

stop codon
type: amino acid
description: A stop codon (or termination codon) is a nucleotide triplet within messenger RNA that signals a termination of translation.
alternative label: *

increased
type: Concept
subclass of: abnormal
disjoint with: decreased
description: A quality that has a value that is increased compared to normal or average.
is in scheme: sio.owl
alternative label: up

decreased
type: Concept
subclass of: abnormal
description: A quality that has a value that is decreased compared to normal or average.
is in scheme: sio.owl
alternative label: down

normal
type: Concept
disjoint with: abnormal
description: A quality that has a value that is normal or average.
is in scheme: sio.owl
alternative label: no change

abnormal
type: Concept
description: A quality that has a value that is outside normal or average.
is in scheme: sio.owl

chromosome
type: Concept
description: A chromosome is a molecular complex of circular or linear DNA and bound proteins.
is in scheme: sio.owl

curated information
type: Concept
IAO_0000111: curated information
example of usage: PMID: 17344875: A curated compendium of phosphorylation motifs.Nat Biotechnol. 2007 Mar;25(3):285-6.
definition: A information content entity that has undergone a digital curation performed by a curator for accuracy checks and compliance with curation requirements. Information which has been assessed for accuracy by domain experts.
editor note: 2010-01-31 Philippe Rocca-Serra: restriction now changed to be the output of a digital curation process + reflected in example of usage and reference
IAO_0000117: Person:Bjoern Peters
IAO_0000117: Person:Philippe Rocca-Serra
alternative label: Curated
is in scheme: obi.owl
License: http://creativecommons.org/licenses/by/4.0/

q-value
type: Concept
IAO_0000111: q-value
example of usage: PMID: 20483222. Comp Biochem Physiol Part D Genomics Proteomics. 2008 Sep;3(3):234-42. Analysis of Sus scrofa liver proteome and identification of proteins differentially expressed between genders, and conventional and genetically enhanced lines. "After controlling the false discovery rate (FDR</=0.1) using the Storey q value only four proteins (EPHX1, CAT, PAH, ST13) were shown to be differentially expressed between genders (Males/Females) and two proteins (SELENBP2, TAGLN) were differentially expressed between two lines (Transgenic/Conventional pigs)"
definition: A quantitative confidence value that measures the minimum false discovery rate that is incurred when calling that test significant. To compute q-values, it is necessary to know the p-value produced by a test and possibly set a false discovery rate level.
alternative label: FDR adjusted p-value
alternative term: FDR adjusted p-value
is in scheme: obi.owl
License: http://creativecommons.org/licenses/by/4.0/

p-value
type: Class
IAO_0000111: p-value
example of usage: PMID:19696660 in contrast to the in-vivo data AT-III increased significantly from 113.5% at baseline to 117% after 4 days (n = 10, P-value= 0.02; Table 2).
definition: A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.
IAO_0000119: WEB: http://en.wikipedia.org/wiki/P-value
is in scheme: obi.owl
License: http://creativecommons.org/licenses/by/4.0/

fold change
type: Class
definition: Fold change is a number describing how much a quantity changes going from an initial to a final value or one condition to another condition
IAO_0000117: Alejandra Gonzalez-Beltran
IAO_0000117: Orlaith Burke
IAO_0000117: Philippe Rocca-Serra
IAO_0000119: http://en.wikipedia.org/wiki/Fold_change
is in scheme: stato.owl
License: http://creativecommons.org/licenses/by/3.0/

alternative term
type: AnnotationProperty
IAO_0000111: alternative term
definition: An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)

approves
type: ObjectProperty
sub property of: governs
comment: An object property that specifies that a party governs the approval of a resource.
inverse of: is approved by
License: academic.php

is approved by
type: ObjectProperty
sub property of: is governed by
comment: References to which parties approve an entity.
License: academic.php

governs
type: ObjectProperty
comment: A super-property of governance properties: 'approves', 'gives concurrence for', 'reviews' and 'witness to'.
inverse of: is governed by
License: academic.php

is governed by
type: ObjectProperty
comment: A pointer to who is responsible for the governance of some entity of interest. This is a two-way reference with the inverse property 'governs'.
License: academic.php

Organization
type: Class
subclass of: Party
subclass of: Restriction
  all values from: Organization logo
  on property: has logo
subclass of: Restriction
  min cardinality: 0
  on property: url
subclass of: Restriction
  max cardinality: 1
  on property: has logo
License: academic.php

Organization logo
type: Class
subclass of: Logo
comment: A logo for an organization
License: academic.php

url
type: DatatypeProperty
range: anyURI
License: academic.php

Logo
type: Class
subclass of: Image
comment: Logo is ...
License: academic.php

Image
type: Class
subclass of: Thing
subclass of: Restriction
  max cardinality: 1
  on property: width
subclass of: Restriction
  max cardinality: 1
  on property: caption
subclass of: Restriction
  max cardinality: 1
  on property: height
subclass of: Restriction
  cardinality: 1
  on property: image
comment: Image is a class for figures, pictures, logos, and icons of various kinds
License: academic.php

image
type: DatatypeProperty
range: anyURI
comment: The property 'vaem:image' points to an image using a URL.
License: academic.php

height
type: DatatypeProperty
range: string
comment: Height is typically used to specify an image's height attribute.
License: academic.php

has logo
type: ObjectProperty
range: Logo
comment: A property to reference an image that is used as a logo.
License: academic.php

caption
type: DatatypeProperty
range: string
comment: A short description, typically used on a table or a figure.
License: academic.php

width
type: DatatypeProperty
comment: Width is typically used to specify an image's width attribute.
License: academic.php

Party
type: Class
subclass of: Restriction
  max cardinality: 1
  on property: id
subclass of: Restriction
  max cardinality: 1
  on property: short description
License: academic.php

id
sub property of: identifier
type: DatatypeProperty
range: anySimpleType
License: academic.php

short description
type: DatatypeProperty
range: string
License: academic.php

Early Detection Research Network
type: Organization
url: https://edrn.nci.nih.gov
id: EDRN
short description: The Early Detection Research Network (EDRN), an initatve of the National Cancer Institute (NCI), brings together dozens of institutions to help accelerate the translation of biomarker information into clinical applications and to evaluate new ways of testng cancer in its earliest stages and for cancer risk.
License: academic.php

Food and Drug Administration
type: Organization
url: https://www.fda.gov
id: FDA
short description: The Food and Drug Administration (FDA) is an agency within the U.S. Department of Health and Human Services. It consists of the Office of the Commissioner and four directorates overseeing the core functions of the agency: Medical Products and Tobacco, Foods and Veterinary Medicine, Global Regulatory Operations and Policy, and Operations.
License: academic.php

Disease-causing Mutation
type: Concept
comment: A gene alteration that causes or predisposes an individual to a specific disease.
has_exact_synonym: Disease-causing Mutation
has_exact_synonym: disease-causing mutation
is defined by: ncit.owl
is in scheme: NCI Thesaurus

Accepted
type: Biomarker quality assessment state
has_exact_synonym: Accepted
has_exact_synonym: Established
is defined by: ncit.owl
is in scheme: NCI Thesaurus

Prognosis
type: Concept
definition: Prediction of the probable course and outcome of a disease.
comment: The likely outcome or course of a disease; the chance of recovery or recurrence.
has_exact_synonym: Prediction of Outcome
has_exact_synonym: Prognosis
has_exact_synonym: prognosis
is in scheme: NCI Thesaurus

Prediction
type: Concept
definition: An extrapolation of given data into the future.
has_exact_synonym: Predicted
has_exact_synonym: Prediction
is in scheme: NCI Thesaurus

Diagnosis
type: Concept
definition: The investigation, analysis and recognition of the presence and nature of disease, condition, or injury from expressed signs and symptoms; also, the scientific determination of any kind; the concise results of such an investigation.
comment: The process of identifying a disease, such as cancer, from its signs and symptoms.
has_exact_synonym: DIAGNOSIS
has_exact_synonym: Diagnosed
has_exact_synonym: Diagnosis
has_exact_synonym: Diagnostic
has_exact_synonym: Dx
has_exact_synonym: diagnosis
is in scheme: NCI Thesaurus

Risk Assessment
type: Concept
definition: An estimated probability that one or more adverse event(s) will occur as a result of exposure to an actual or potential hazardous situation or chemical.
comment: A process used to estimate the risk that a certain event will happen. In medicine, this may include a person's risk of having a child with a certain condition or disease, such as cancer. It may also be used to estimate the risk of carrying a certain gene mutation (change), or of having an adverse event (unexpected medical problem) in response to certain types of drugs or other substances. A risk assessment may be done by collecting information about a person's age, sex, personal and family medical history, ethnic background, lifestyle, and other factors and using statistics tools to calculate risk.
has_exact_synonym: Risk Assessment
has_exact_synonym: risk assessment
is in scheme: NCI Thesaurus

Early Detection
type: Concept
definition: Use of a device, marker, or other means for the purpose of detecting the presence of a tumor early in its development.
has_exact_synonym: Early Detection
is in scheme: NCI Thesaurus

Susceptibility
type: Concept
definition: The constitutional or inborn state disposing to a disease, group of diseases, or metabolic or structural anomaly.
has_exact_synonym: Predisposition
has_exact_synonym: Susceptibility
has_exact_synonym: Susceptible
is in scheme: NCI Thesaurus

NCI Thesaurus
type: Concept Scheme
definition: The National Cancer Institute (NCI) reference terminology and ontology. NCI Thesaurus (NCIt) provides controlled terminology for clinical care, translational and basic research, public dissemination of information and associated administrative activities. NCIt is updated monthly to support precise coding of data based on the most recent developments in the cancer and biomedical research community. NCIt has rich textual and formal logic descriptions of biomedical concepts, including full text definitions, synonyms, a true is_a taxonomic structure, polyhierarchy, inferred partonomy, and other features that make it suitable for supporting accurate human understanding and complex computer processing. NCIt has been produced by NCI Enterprise Vocabulary Services (EVS) since 1997, and adopted since then for use by numerous federal agencies, standards development and research organizations.
has_exact_synonym: NCI Thesaurus
has_exact_synonym: NCIT
has_exact_synonym: NCIt
has_exact_synonym: Thesaurus

Statistical Significance
type: Concept
definition: In statistics, a number that expresses the probability that the result of a given experiment or study could have occurred purely by chance. This number can be a margin of error or it can indicate a confidence level.
has_exact_synonym: Significance
has_exact_synonym: Statistical Significance
has_exact_synonym: Statistically Significant
has_exact_synonym: significant
has_exact_synonym: statistical significance
has_exact_synonym: statistically significant
in subset: NCIT C61410
in subset: NCIT C67497
is in scheme: NCI Thesaurus

Human Chromosome
type: Concept
definition: A structure found in the nucleus of human cells that is comprised of a strand of linearized double-stranded DNA plus proteins that package the DNA in a condensed coil form and regulate chromosomal function.
DesignNote: Normal human somatic cells have 23 pairs of chromosomes.
has_exact_synonym: Human Chromosome
is in scheme: NCI Thesaurus

Chromosome 1
type: human chromosome
definition: The designation for each member of the largest human autosomal chromosome pair. Chromosome 1 spans about 247 million nucleotide base pairs and represents about 8% of the total DNA in normal diploid cells.

Chromosome 2
type: human chromosome
definition: The designation for each member of the second largest human autosomal chromosome pair. Chromosome 2 spans more than 237 million base pairs and represents almost 8% of the total DNA in normal diploid cells.

Chromosome 3
type: human chromosome
definition: The designation for each member of the third largest human autosomal chromosome pair. Chromosome 3 spans almost 200 million base pairs and represents about 6.5% of the total DNA in normal diploid cells.

Chromosome 4
type: human chromosome
definition: The designation for each member of the fourth largest human autosomal chromosome pair. Chromosome 4 spans more than 186 million base pairs and represents between 6 and 6.5% of the total DNA in normal diploid cells.

Chromosome 5
type: human chromosome
definition: The designation for each member of the fifth largest human autosomal chromosome pair. Chromosome 5 spans about 181 million base pairs and represents almost 6% of the total DNA in normal diploid cells.

Chromosome 6
type: human chromosome
definition: The designation for each member of the sixth largest human autosomal chromosome pair. Chromosome 6 spans more than 170 million base pairs and represents between 5.5 and 6% of the total DNA in normal diploid cells.

Chromosome 7
type: human chromosome
definition: The designation for each member of the seventh largest human autosomal chromosome pair. Chromosome 7 spans more than 158 million base pairs and represents between 5 and 5.5% of the total DNA in normal diploid cells.

Chromosome 8
type: human chromosome
definition: The designation for each member of the eighth largest human autosomal chromosome pair. Chromosome 8 spans about 145 million base pairs and represents between 4.5 and 5.0% of the total DNA in normal diploid cells.

Chromosome 9
type: human chromosome
definition: The designation for each member of the ninth largest human autosomal chromosome pair. Chromosome 9 spans about 145 million base pairs of nucleic acids and represents between 4 and 4.5% of the total DNA in normal diploid cells.

DesignNote
type: AnnotationProperty
definition: Design notes are notations made by NCI vocabulary curators. They are intended to provide supplemental, unstructured information to the user or additional insight about the concept.
range: string
is in scheme: NCI Thesaurus

Chromosome 10
type: human chromosome
definition: The designation for each member of the tenth largest human autosomal chromosome pair. Chromosome 10 spans about 135 million base pairs and represents between 4 and 4.5% of the total DNA in normal diploid cells.

Chromosome 11
type: human chromosome
definition: The designation for each member of the eleventh largest human autosomal chromosome pair. Chromosome 11 spans about 134.5 million base pairs and represents between 4 and 4.5% of the total DNA in normal diploid cells.

Chromosome 12
type: human chromosome
definition: The designation for each member of the twelfth largest human autosomal chromosome pair. Chromosome 12 spans about 143 million base pairs and represents between 4 and 4.5% of the total DNA in normal diploid cells.

Chromosome 13
type: human chromosome
definition: The designation for each member of the thirteenth largest human autosomal chromosome pair. Chromosome 13 spans about 113 million base pairs and represents between 3.5 and 4% of the total DNA in normal diploid cells.

Chromosome 14
type: human chromosome
definition: The designation for each member of the fourteenth largest human autosomal chromosome pair. Chromosome 14 spans about 105 million base pairs and represents between 3 and 3.5% of the total DNA in normal diploid cells.

Chromosome 15
type: human chromosome
definition: The designation for each member of the fifteenth largest human autosomal chromosome pair. Chromosome 15 spans about 106 million base pairs and represents between 3 and 3.5% of the total DNA in normal diploid cells.

Chromosome 16
type: human chromosome
definition: The designation for each member of the sixteenth largest human autosomal chromosome pair. Chromosome 16 spans about 90 million base pairs and represents just under 3% of the total DNA in normal diploid cells.

Chromosome 17
type: human chromosome
definition: The designation for each member of the seventeenth largest human autosomal chromosome pair. Chromosome 17 spans more than 81 million base pairs and represents between 2.5 and 3% of the total DNA in normal diploid cells.

Chromosome 18
type: human chromosome
definition: The designation for each member of the eighteenth largest human autosomal chromosome pair. Chromosome 18 spans about 76 million base pairs and represents about 2.5% of the total DNA in normal diploid cells.

Chromosome 19
type: human chromosome
definition: The designation for each member of the nineteenth largest human autosomal chromosome pair. Chromosome 19 spans more than 63 million base pairs and represents between 2 and 2.5% of the total DNA in normal diploid cells.

Chromosome 20
type: human chromosome
definition: The designation for each member of the third smallest human autosomal chromosome pair. Chromosome 20 spans around 63 million base pairs and represents between 2 and 2.5% of the total DNA in normal diploid cells.

Chromosome 21
type: human chromosome
definition: The designation for each member of the second smallest human autosomal chromosome pair. Chromosome 21 spans around 47 million nucleotides and represents about 1.5% of the total DNA in normal diploid cells.

Chromosome 22
type: human chromosome
definition: The designation for each member of the smallest human autosomal chromosome pair. Chromosome 22 spans about 49 million base pairs and represents between 1.5 and 2% of the total DNA in normal diploid cells.

Chromosome X
type: human chromosome
definition: The sex chromosome that is present in both sexes: singly in males and doubly in females.
has_exact_synonym: Chromosome X
has_exact_synonym: X Chromosome

Chromosome Y
type: human chromosome
definition: The y-shaped sex chromosome. In mammals, its presence or absence determines male or female sex.
has_exact_synonym: Chromosome Y
has_exact_synonym: Y Chromosome

Companion Diagnosis
type: Concept
definition: A companion diagnosis is a diagnostic test that provides essential information for the safe and effective use of a corresponding drug or biological product. The test helps a health care professional determine whether a particular therapeutic product’s benefits to patients will outweigh any potential serious side effects or risks.
comment: This term should be suggested as part of the NCI thesaurus.
has_exact_synonym: companion diagnostic
has_exact_synonym: companion diagnosis
is in scheme: cbio

has broader match
type: ObjectProperty
sub property of: has broader
sub property of: is in mapping relation with
inverse of: has narrower match
comment: If 'concept A has-broad-match concept B' then the set of resources properly indexed against concept A is a subset of the set of resources properly indexed against concept B.
definition: skos:broadMatch is used to state a hierarchical mapping link between two conceptual resources in different concept schemes.

has broader
type: ObjectProperty
sub property of: has broader transitive
inverse of: has narrower
comment: Broader concepts are typically rendered as parents in a concept hierarchy (tree).
definition: Relates a concept to a concept that is more general in meaning.
scope note: By convention, skos:broader is only used to assert an immediate (i.e. direct) hierarchical link between two conceptual resources.

has broader transitive
type: ObjectProperty
sub property of: is in semantic relation with
inverse of: has narrower transitive
type: TransitiveProperty
definition: skos:broaderTransitive is a transitive superproperty of skos:broader.
scope note: By convention, skos:broaderTransitive is not used to make assertions. Rather, the properties can be used to draw inferences about the transitive closure of the hierarchical relation, which is useful e.g. when implementing a simple query expansion algorithm in a search application.

has close match
type: ObjectProperty
sub property of: is in mapping relation with
type: SymmetricProperty
definition: skos:closeMatch is used to link two concepts that are sufficiently similar that they can be used interchangeably in some information retrieval applications. In order to avoid the possibility of "compound errors" when combining mappings across more than two concept schemes, skos:closeMatch is not declared to be a transitive property.

has exact match
type: ObjectProperty
sub property of: has close match
type: SymmetricProperty
type: TransitiveProperty
comment: skos:exactMatch is disjoint with each of the properties skos:broadMatch and skos:relatedMatch.
definition: skos:exactMatch is used to link two concepts, indicating a high degree of confidence that the concepts can be used interchangeably across a wide range of information retrieval applications. skos:exactMatch is a transitive property, and is a sub-property of skos:closeMatch.

is in mapping relation with
type: ObjectProperty
sub property of: is in semantic relation with
comment: These concept mapping relations mirror semantic relations, and the data model defined below is similar (with the exception of skos:exactMatch) to the data model defined for semantic relations. A distinct vocabulary is provided for concept mapping relations, to provide a convenient way to differentiate links within a concept scheme from links between concept schemes. However, this pattern of usage is not a formal requirement of the SKOS data model, and relies on informal definitions of best practice.
definition: Relates two concepts coming, by convention, from different schemes, and that have comparable meanings

has narrower match
type: ObjectProperty
sub property of: is in mapping relation with
sub property of: has narrower
comment: If 'concept A has-narrow-match concept B' then the set of resources properly indexed against concept A is a superset of the set of resources properly indexed against concept B.
definition: skos:narrowMatch is used to state a hierarchical mapping link between two conceptual resources in different concept schemes.

has narrower
type: ObjectProperty
sub property of: has narrower transitive
comment: Narrower concepts are typically rendered as children in a concept hierarchy (tree).
definition: Relates a concept to a concept that is more specific in meaning.
scope note: By convention, skos:broader is only used to assert an immediate (i.e. direct) hierarchical link between two conceptual resources.

has narrower transitive
type: ObjectProperty
sub property of: is in semantic relation with
type: TransitiveProperty
definition: skos:narrowerTransitive is a transitive superproperty of skos:narrower.
scope note: By convention, skos:narrowerTransitive is not used to make assertions. Rather, the properties can be used to draw inferences about the transitive closure of the hierarchical relation, which is useful e.g. when implementing a simple query expansion algorithm in a search application.

has related
type: ObjectProperty
sub property of: is in semantic relation with
type: SymmetricProperty
comment: skos:related is disjoint with skos:broaderTransitive
definition: Relates a concept to a concept with which there is an associative semantic relationship.

has related match
type: ObjectProperty
sub property of: is in mapping relation with
sub property of: has related
type: SymmetricProperty
definition: skos:relatedMatch is used to state an associative mapping link between two conceptual resources in different concept schemes.

is in semantic relation with
type: ObjectProperty
domain: Concept
range: Concept
definition: Links a concept to a concept related by meaning.
scope note: This property should not be used directly, but as a super-property for all properties denoting a relationship of meaning between concepts.

Concept Scheme
type: Class
definition: A set of concepts, optionally including statements about semantic relationships between those concepts.
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.
scope note: A concept scheme may be defined to include concepts from different sources.

is in scheme
type: ObjectProperty
range: Concept Scheme
definition: Relates a resource (for example a concept) to a concept scheme in which it is included.
scope note: A concept may be a member of more than one concept scheme.

Concept
type: Class
disjoint with: Concept Scheme
definition: An idea or notion; a unit of thought.

Article
type: Class
subclass of: Document
definition: The :Article class represents a scholarly work normally published as an item of a serial publication. In particular, this concept refers to the abstract notion of an article, rather than any of its realisations after it becomes embodied via a physical medium.
note: With reference to the FRBR model [http://www.ifla.org/publications/functional-requirements-for-bibliographic-records], an :Article can be mapped directly to the frbr:Expression concept. It is worth noting though that within the NPG core ontology we do not have any notion of a frbr:Work. Hence multiple versions of the same article (e.g. language translations, or revisions) are characterised as such simply by means of some relationship.
License: http://creativecommons.org/licenses/by/4.0/

Document
type: Class
subclass of: Publication
disjoint with: Component
disjoint with: Serial
definition: The :Document class groups together all publications which were created to be distributed and consumed as individual, self-contained entities.
License: http://creativecommons.org/licenses/by/4.0/

Component
type: Class
subclass of: Publication
disjoint with: Dataset
disjoint with: Document
disjoint with: Serial
definition: The :Component class groups together all individuals that normally come into existence as part of a :Document.
License: http://creativecommons.org/licenses/by/4.0/

Publication
type: Class
subclass of: Concept
definition: The :Publication class groups together all individuals (or part of) created as the result of the publishing process. Note that we are not referring here to the physical artefacts, but just their abstract counterparts.
License: http://creativecommons.org/licenses/by/4.0/

Dataset
type: Class
subclass of: Publication
definition: The :Dataset class represents a collection of related sets of information modelled in a known way and stored in a computer system.
note: We are currently using this class for RDF datasets.
License: http://creativecommons.org/licenses/by/4.0/

Serial
type: Class
subclass of: Publication
disjoint with: Component
disjoint with: Dataset
disjoint with: Document
definition: The :Serial class represents publications which appear in a new edition on a regular schedule. For example, a journal, a magazine or a blog. The :PublishEvent class is used to provide more details about the time, place and other contextual information relevant to when a new edition gets published.
License: http://creativecommons.org/licenses/by/4.0/

Concept
type: Class
subclass of: Thing
definition: The :Concept class groups together all individuals which do not exist in the physical world (i.e. have no extension in spacetime).
License: http://creativecommons.org/licenses/by/4.0/

Thing
type: Class
subclass of: Thing
definition: The :Thing class groups together all individuals used by Macmillan Science and Education within the NPG publishing world.
License: http://creativecommons.org/licenses/by/4.0/

tool
comment: A sub property of instrument. An object used (but not consumed) when performing instructions or a direction.
sub property of: instrument
type: Property
type: DatatypeProperty
domain: functional impact prediction
range: string

instrument
type: Property
comment: The object that helped the agent perform the action. e.g. John wrote a book with a pen.

has_exact_synonym
type: AnnotationProperty
comment: An alias in which the alias exhibits true synonymy. Example: ornithine cycle is an exact synonym of urea cycle
sub property of: has_synonym

has_synonym
type: AnnotationProperty
comment: A relation between a class and an alias term.
comment: Note that this should be a super-property of hasRelatedSynonym, hasExactSynonym etc; however, we cannot state this and remain in OWL-DL

has_alternative_id
type: AnnotationProperty

has_dbxref
type: AnnotationProperty

has_related_synonym
type: AnnotationProperty
comment: 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
sub property of: has_synonym