OHMI: Ontology of Host-Microbiome Interactions
type: Ontology
version IRI: ohmi.owl
Contributor: Barry Smith
creator: Alexander Alekseyenko
creator: Anna Maria Masci
creator: Haihe Wang
creator: Jianmin Wu
creator: Jie Zheng
creator: Jihad Obeid
creator: Kaiyong Liu
creator: Yongqun "Oliver" He (YH)
creator: Yu Hong
description: OHMI is a biomedical ontology that represents the entities and relations in the domain of host-microbiome interactions.
Format: OWL-DL
subject: OHMI: A biomedical ontology in the domain of host-microbiome interactions.
license: http://creativecommons.org/licenses/by/4.0/
version info: 2019-09-17

BFO OWL specification label
type: AnnotationProperty
textual definition: Relates an entity in the ontology to the name of the variable that is used to represent it in the code that generates the BFO OWL file from the lispy specification.
curator notes: Really of interest to developers only
sub property of: label

BFO CLIF specification label
type: AnnotationProperty
textual definition: Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2
definition source: Person:Alan Ruttenberg
curator notes: Really of interest to developers only
sub property of: label

editor preferred label
type: AnnotationProperty
editor preferred label: editor preferred label
editor preferred label: editor preferred term
editor preferred label: editor preferred term~editor preferred label
has curation status: IAO_0000122
textual definition: The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)
definition editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
label: editor preferred term
label: editor preferred term~editor preferred label

example of usage
type: AnnotationProperty
editor preferred label: example
has curation status: IAO_0000122
textual definition: A phrase describing how a class name should be used. May also include other kinds of examples that facilitate immediate understanding of a class semantics, such as widely known prototypical subclasses or instances of the class. Although essential for high level terms, examples for low level terms (e.g., Affymetrix HU133 array) are not
textual definition: A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold.
definition editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

has curation status
type: AnnotationProperty
editor preferred label: has curation status
definition editor: PERSON:Alan Ruttenberg
definition editor: PERSON:Bill Bug
definition editor: PERSON:Melanie Courtot
definition source: OBI_0000281

textual definition
type: AnnotationProperty
editor preferred label: definition
editor preferred label: textual definition
has curation status: IAO_0000122
textual definition: The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
textual definition: The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
editor note: 2012-04-05: Barry Smith The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. Alan Ruttenberg Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with.
definition editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
label: definition

editor note
type: AnnotationProperty
editor preferred label: editor note
has curation status: IAO_0000122
textual definition: An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology.
definition editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obfoundry.org/obo/obi>
database_cross_reference: IAO:0000116
has_obo_namespace: uberon
id: editor_note
is metadata tag: true
shorthand: editor_note

definition editor
type: AnnotationProperty
editor preferred label: term editor
has curation status: IAO_0000122
textual definition: Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people
editor note: 20110707, MC: label update to term editor and definition modified accordingly. See http://code.google.com/p/information-artifact-ontology/issues/detail?id=115.
editor note: 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115.
definition editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
label: term editor

alternative term
type: AnnotationProperty
editor preferred label: alternative term
has curation status: IAO_0000125
textual definition: An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)
definition editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

definition source
type: AnnotationProperty
editor preferred label: definition source
has curation status: IAO_0000122
textual definition: formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007
definition editor: PERSON:Daniel Schober
definition source: Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

curator notes
type: AnnotationProperty
editor preferred label: curator note
has curation status: IAO_0000122
textual definition: An administrative note of use for a curator but of no use for a user
definition editor: PERSON:Alan Ruttenberg
database_cross_reference: IAO:0000232
has_obo_namespace: uberon
id: curator_notes
is metadata tag: true
shorthand: curator_notes
label: curator note

term tracker item
type: AnnotationProperty
editor preferred label: term tracker item
example of usage: the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/
has curation status: IAO_0000125
textual definition: An IRI or similar locator for a request or discussion of an ontology term.
definition editor: Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
definition source: Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
comment: The 'tracker item' can associate a tracker with a specific ontology term.

imported from
type: AnnotationProperty
editor preferred label: imported from
has curation status: IAO_0000125
textual definition: For external terms/classes, the ontology from which the term was imported
definition editor: PERSON:Alan Ruttenberg
definition editor: PERSON:Melanie Courtot
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

expand expression to
type: AnnotationProperty

OBO foundry unique label
type: AnnotationProperty
editor preferred label: OBO foundry unique label
has curation status: IAO_0000125
textual definition: An alternative name for a class or property which is unique across the OBO Foundry.
editor note: The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools .
definition editor: PERSON:Alan Ruttenberg
definition editor: PERSON:Bjoern Peters
definition editor: PERSON:Chris Mungall
definition editor: PERSON:Melanie Courtot
definition source: GROUP:OBO Foundry <http://obofoundry.org/>

elucidation
type: AnnotationProperty
editor preferred label: elucidation
definition editor: person:Alan Ruttenberg
definition source: Person:Barry Smith
elucidation: Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms

has associated axiom(nl)
type: AnnotationProperty
editor preferred label: has associated axiom(nl)
definition editor: Person:Alan Ruttenberg
definition source: Person:Alan Ruttenberg
elucidation: An axiom associated with a term expressed using natural language

has associated axiom(fol)
type: AnnotationProperty
editor preferred label: has associated axiom(fol)
definition editor: Person:Alan Ruttenberg
definition source: Person:Alan Ruttenberg
elucidation: An axiom expressed in first order logic using CLIF syntax

has literature mining keywords
type: AnnotationProperty
textual definition: an annotation property that lists keyword(s) useful for literature tagging and retrieval of sentences containing the type (or kind) of entity (e.g., interaction) as shown by the ontology term label and definition.
definition editor: Yongqun He

ISA alternative term
type: AnnotationProperty
editor preferred label: ISA alternative term
has curation status: IAO_0000122
textual definition: An alternative term used by the ISA tools project (http://isa-tools.org).
editor note: Requested by Alejandra Gonzalez-Beltran https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891&atid=886178
definition editor: Person: Alejandra Gonzalez-Beltran
definition editor: Person: Philippe Rocca-Serra
definition source: ISA tools project (http://isa-tools.org)
sub property of: alternative term

NIAID GSCID-BRC alternative term
type: AnnotationProperty
editor preferred label: NIAID GSCID-BRC alternative term
has curation status: IAO_0000122
textual definition: An alternative term used by the National Institute of Allergy and Infectious Diseases (NIAID) Genomic Sequencing Centers for Infectious Diseases (GSCID) and Bioinformatics Resource Centers (BRC).
definition editor: PERSON: Chris Stoeckert, Jie Zheng
definition source: NIAID GSCID-BRC metadata working group
sub property of: alternative term

IEDB alternative term
type: AnnotationProperty
editor preferred label: IEDB alternative term
has curation status: IAO_0000122
textual definition: An alternative term used by the IEDB.
definition editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
sub property of: alternative term

evidence publication
type: AnnotationProperty
textual definition: An annotation property that represents a publication that includes the evidence of the presence of a class type.
definition editor: Jie Zheng, Jihad, Anna Maria, Haihe, Oliver

temporal interpretation
type: AnnotationProperty
textual definition: An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context.
sub property of: logical macro assertion on an object property

logical macro assertion
type: AnnotationProperty
textual definition: An assertion that involves at least one OWL object that is intended to be expanded into one or more logical axioms. The logical expansion can yield axioms expressed using any formal logical system, including, but not limited to OWL2-DL.

logical macro assertion on a property
type: AnnotationProperty
textual definition: A logical macro assertion whose domain is an IRI for a property
sub property of: logical macro assertion

logical macro assertion on an object property
type: AnnotationProperty
textual definition: Used to annotate object properties to describe a logical meta-property or characteristic of the object property.
sub property of: logical macro assertion on a property

logical macro assertion on an annotation property
type: AnnotationProperty
sub property of: logical macro assertion on a property

is direct form of
type: AnnotationProperty
textual definition: relation p is the direct form of relation q iff p is a subPropertyOf q, p does not have the Transitive characteristic, q does have the Transitive characteristic, and for all x, y: x q y -> exists z1, z2, ..., zn such that x p z1 ... z2n y
editor note: The general property hierarchy is: "directly P" SubPropertyOf "P" Transitive(P) Where we have an annotation assertion "directly P" "is direct form of" "P"
logical macro assertion on an annotation property: If we have the annotation P is-direct-form-of Q, and we have inverses P' and Q', then it follows that P' is-direct-form-of Q'
creator: Chris Mungall
sub property of: logical macro assertion on an object property

is indirect form of
type: AnnotationProperty
textual definition: relation p is the indirect form of relation q iff p is a subPropertyOf q, and there exists some p' such that p' is the direct form of q, p' o p' -> p, and forall x,y : x q y -> either (1) x p y or (2) x p' y
creator: Chris Mungall
sub property of: logical macro assertion on an object property

is directional form of
type: AnnotationProperty
textual definition: Used to annotate object properties representing a causal relationship where the value indicates a direction. Should be "+", "-" or "0"
created_by: cjm
creation_date: 2018-03-13T23:59:29Z
sub property of: logical macro assertion on an object property

is positive form of
type: AnnotationProperty
created_by: cjm
creation_date: 2018-03-14T00:03:16Z
sub property of: is directional form of

is negative form of
type: AnnotationProperty
created_by: cjm
creation_date: 2018-03-14T00:03:24Z
sub property of: is directional form of

external_definition
type: AnnotationProperty
textual definition: An alternate textual definition for a class taken unmodified from an external source. This definition may have been used to derive a generalized definition for the new class.
database_cross_reference: UBPROP:0000001
has_obo_namespace: uberon
id: external_definition
is metadata tag: true
shorthand: external_definition
comment: This annotation property may be replaced with an annotation property from an external ontology such as IAO

homology_notes
type: AnnotationProperty
textual definition: Notes on the homology status of this class.
database_cross_reference: UBPROP:0000003
has_obo_namespace: uberon
id: homology_notes
is metadata tag: true
shorthand: homology_notes
comment: This annotation property may be replaced with an annotation property from an external ontology such as IAO

has_relational_adjective
type: AnnotationProperty
curator notes: Used to connect a class to an adjectival form of its label. For example, a class with label 'intestine' may have a relational adjective 'intestinal'.
database_cross_reference: UBPROP:0000007
has_obo_namespace: uberon
id: has_relational_adjective
is metadata tag: true
shorthand: has_relational_adjective

taxon_notes
type: AnnotationProperty
textual definition: Notes on the how instances of this class vary across species.
database_cross_reference: UBPROP:0000008
has_obo_namespace: uberon
id: taxon_notes
is metadata tag: true
shorthand: taxon_notes

development_notes
type: AnnotationProperty
textual definition: Notes on the ontogenic development of instances of this class.
editor note: This annotation property may be replaced with an annotation property from an external ontology such as IAO
database_cross_reference: UBPROP:0000011
has_obo_namespace: uberon
id: development_notes
is metadata tag: true
shorthand: development_notes

external_ontology_notes
type: AnnotationProperty
textual definition: Notes on how similar or equivalent classes are represented in other ontologies.
editor note: This annotation property may be replaced with an annotation property from an external ontology such as IAO
database_cross_reference: UBPROP:0000012
has_obo_namespace: uberon
id: external_ontology_notes
is metadata tag: true
shorthand: external_ontology_notes

Contributor
type: AnnotationProperty
description: Examples of a Contributor include a person, an organisation, or a service. Typically, the name of a Contributor should be used to indicate the entity.
comment: An entity responsible for making contributions to the content of the resource.

Creator
type: AnnotationProperty
description: Examples of a Creator include a person, an organisation, or a service. Typically, the name of a Creator should be used to indicate the entity.
comment: An entity primarily responsible for making the content of the resource.

Date
type: AnnotationProperty
description: Typically, Date will be associated with the creation or availability of the resource. Recommended best practice for encoding the date value is defined in a profile of ISO 8601 [W3CDTF] and follows the YYYY-MM-DD format.
comment: A date associated with an event in the life cycle of the resource.

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

Format
type: AnnotationProperty
description: Typically, Format may include the media-type or dimensions of the resource. Format may be used to determine the software, hardware or other equipment needed to display or operate the resource. Examples of dimensions include size and duration. Recommended best practice is to select a value from a controlled vocabulary (for example, the list of Internet Media Types [MIME] defining computer media formats).
comment: The physical or digital manifestation of the resource.

Source
type: AnnotationProperty
description: The present resource may be derived from the Source resource in whole or in part. Recommended best practice is to reference the resource by means of a string or number conforming to a formal identification system.
comment: A reference to a resource from which the present resource is derived.

Subject and Keywords
type: AnnotationProperty
description: Typically, a Subject will be expressed as keywords, key phrases or classification codes that describe a topic of the resource. Recommended best practice is to select a value from a controlled vocabulary or formal classification scheme.
comment: The topic of the content of the resource.

license
type: AnnotationProperty
definition editor: Mark Miller
date: 2018-05-11T13:47:29Z

created_by
type: AnnotationProperty

creation_date
type: AnnotationProperty

has_alternative_id
type: AnnotationProperty

has_broad_synonym
type: AnnotationProperty

database_cross_reference
type: AnnotationProperty

has_exact_synonym
type: AnnotationProperty

has_narrow_synonym
type: AnnotationProperty

has_obo_namespace
type: AnnotationProperty
comment: disease_ontology

has_related_synonym
type: AnnotationProperty

id
type: AnnotationProperty

in_subset
type: AnnotationProperty

shorthand
type: AnnotationProperty

isDefinedBy
type: AnnotationProperty
OBO foundry unique label: is defined by

label
type: AnnotationProperty
editor preferred label: label

seeAlso
type: AnnotationProperty
id: seeAlso
is class level: true
is metadata tag: true
shorthand: seeAlso

part of
type: ObjectProperty
equivalent property:
  inverse of: has part
sub property of: overlaps
inverse of: has part
type: TransitiveProperty
editor preferred label: is part of
example of usage: my brain is part of my body (continuant parthood, two material entities)
example of usage: my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)
example of usage: this day is part of this year (occurrent parthood)
textual definition: a core relation that holds between a part and its whole
editor note: Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other.
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 can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'.
alternative term: part_of
imported from: obi.owl
imported from: ro.owl
temporal interpretation: RO_0001901

has part
type: ObjectProperty
equivalent property:
  inverse of: part of
sub property of: overlaps
type: TransitiveProperty
editor preferred label: has part
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)
textual 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'.
alternative term: has_part
imported from: obi.owl
imported from: ro.owl
temporal interpretation: RO_0001901

realized in
type: ObjectProperty
equivalent property:
  inverse of: realizes
inverse of: realizes
domain: realizable entity
range: process
editor preferred label: realized in
example of usage: this disease is realized in this disease course
example of usage: this fragility is realized in this shattering
example of usage: this investigator role is realized in this investigation
alternative term: is realized by
alternative term: realized_in
imported from: obi.owl
elucidation: [copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])
comment: Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process

realizes
type: ObjectProperty
equivalent property:
  inverse of: realized in
domain: process
range: realizable entity
editor preferred label: realizes
example of usage: this disease course realizes this disease
example of usage: this investigation realizes this investigator role
example of usage: this shattering realizes this fragility
imported from: obi.owl
imported from: ro.owl
elucidation: to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])
comment: Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process

obsolete preceded by
type: ObjectProperty
type: TransitiveProperty
imported from: ro.owl
comment: accidentally included in BFO 1.2 proposal - should have been BFO_0000062
deprecated: true

preceded by
type: ObjectProperty
sub property of: ends after
inverse of: precedes
type: TransitiveProperty
domain: occurrent
range: occurrent
property chain axiom: part of
property chain axiom: starts during
property chain axiom: happens during
editor preferred label: preceded by
textual definition: x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
editor note: An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other.
alternative term: is preceded by
alternative term: preceded_by
imported from: ro.owl
Source: http://www.obofoundry.org/ro/#OBO_REL:preceded_by
in_subset: ro-eco

precedes
type: ObjectProperty
sub property of: temporal relation
type: TransitiveProperty
domain: occurrent
range: occurrent
property chain axiom: part of
property chain axiom: happens during
editor preferred label: precedes
textual definition: x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
imported from: ro.owl
in_subset: ro-eco

occurs in
type: ObjectProperty
inverse of: contains process
domain: occurrent
range: independent continuant
property chain axiom: part of
editor preferred label: occurs in
textual definition: b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t
alternative term: occurs_in
alternative term: unfolds in
alternative term: unfolds_in
imported from: ro.owl
comment: Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant

contains process
type: ObjectProperty
editor preferred label: site of
textual definition: [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t
imported from: ro.owl
comment: Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant

has measurement unit label
type: ObjectProperty
sub property of: has part
type: FunctionalProperty
range: measurement unit label
imported from: obi.owl

is about
type: ObjectProperty
domain: information content entity
example of usage: This document is about information artifacts and their representations
has curation status: IAO_0000125
textual definition: is_about is a (currently) primitive relation that relates an information artifact to an entity.
editor note: 7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. We will try to build it back up by elaborating the various subproperties that are more precisely defined. Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic.
definition editor: person:Alan Ruttenberg
definition source: Smith, Ceusters, Ruttenberg, 2000 years of philosophy
imported from: obi.owl

is duration of
type: ObjectProperty
sub property of: is about
domain: time measurement datum
range: process
has curation status: IAO_0000120
textual definition: relates a process to a time-measurement-datum that represents the duration of the process
definition editor: Person:Alan Ruttenberg
imported from: obi.owl

has_specified_input
type: ObjectProperty
equivalent property:
  inverse of: is_specified_input_of
sub property of: has participant
inverse of: is_specified_input_of
domain: planned process
editor preferred label: has_specified_input
example of usage: see is_input_of example_of_usage
has curation status: IAO_0000122
textual definition: A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of.
editor note: 8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works.
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Bjoern Peters
definition editor: PERSON: Larry Hunter
definition editor: PERSON: Melanie Coutot
imported from: obi.owl

is_specified_input_of
type: ObjectProperty
equivalent property:
  inverse of: has_specified_input
sub property of: participates in
range: planned process
editor preferred label: is_specified_input_of
example of usage: some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay
has curation status: IAO_0000122
textual definition: A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of.
definition editor: Alan Ruttenberg
definition editor: PERSON:Bjoern Peters
imported from: obi.owl

has_specified_output
type: ObjectProperty
equivalent property:
  inverse of: is_specified_output_of
sub property of: has participant
inverse of: is_specified_output_of
domain: planned process
editor preferred label: has_specified_output
has curation status: IAO_0000122
textual definition: A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Bjoern Peters
definition editor: PERSON: Larry Hunter
definition editor: PERSON: Melanie Courtot
imported from: obi.owl

is_specified_output_of
type: ObjectProperty
equivalent property:
  inverse of: has_specified_output
sub property of: participates in
range: planned process
editor preferred label: is_specified_output_of
has curation status: IAO_0000122
textual definition: A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.
definition editor: Alan Ruttenberg
definition editor: PERSON:Bjoern Peters
imported from: obi.owl

achieves_planned_objective
type: ObjectProperty
inverse of: objective_achieved_by
domain: planned process
range: objective specification
editor preferred label: achieves_planned_objective
example of usage: A cell sorting process achieves the objective specification 'material separation objective'
has curation status: IAO_0000120
textual definition: This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process.
definition editor: BP, AR, PPPB branch
definition source: PPPB branch derived
curator notes: modified according to email thread from 1/23/09 in accordince with DT and PPPB branch
imported from: obi.owl

has grain
type: ObjectProperty
sub property of: has part
editor preferred label: has grain
has curation status: IAO_0000120
textual definition: the relation of the cells in the finger of the skin to the finger, in which an indeterminate number of grains are parts of the whole by virtue of being grains in a collective that is part of the whole, and in which removing one granular part does not nec- essarily damage or diminish the whole. Ontological Whether there is a fixed, or nearly fixed number of parts - e.g. fingers of the hand, chambers of the heart, or wheels of a car - such that there can be a notion of a single one being missing, or whether, by contrast, the number of parts is indeterminate - e.g., cells in the skin of the hand, red cells in blood, or rubber molecules in the tread of the tire of the wheel of the car.
editor note: Discussion in Karslruhe with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg. Definition take from the definition of granular parthood in the cited paper. Needs work to put into standard form
definition editor: PERSON: Alan Ruttenberg
definition source: PAPER: Granularity, scale and collectivity: When size does and does not matter, Alan Rector, Jeremy Rogers, Thomas Bittner, Journal of Biomedical Informatics 39 (2006) 333-349
imported from: obi.owl

objective_achieved_by
type: ObjectProperty
domain: objective specification
range: planned process
editor preferred label: objective_achieved_by
has curation status: IAO_0000122
textual definition: This relation obtains between a a objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process.
definition editor: OBI
definition source: OBI
imported from: obi.owl

has value specification
type: ObjectProperty
sub property of: has part
domain: information content entity
range: value specification
editor preferred label: has value specification
has curation status: IAO_0000120
textual definition: A relation between an information content entity and a value specification that specifies its value.
definition editor: PERSON: James A. Overton
definition source: OBI
imported from: obi.owl

microbe susceptibly expanded in host with disease
type: ObjectProperty
sub property of: microbe susceptibly changed in host with disease
inverse of: disease in host with susceptibly expanded microbe
domain: organism
range: disease
textual definition: An object property that represents the susceptible increase (compared to healthy control) of the population of a microbe in a host with a specific disease. This is a shortcut relation where the domain is microbe, and the range is a disease.
definition editor: Oliver He

microbe susceptibly expanded in human with disease
type: ObjectProperty
sub property of: microbe susceptibly expanded in host with disease
textual definition: An object property that represents the susceptible increase (compared to healthy control) of the population of a microbe in a human with a specific disease. This is a shortcut relation where the domain is microbe, and the range is a disease.
definition editor: Oliver He

microbe susceptibly expanded in gut of human with disease
type: ObjectProperty
sub property of: microbe susceptibly expanded in human with disease
textual definition: An object property that represents the susceptible increase (compared to healthy control) of the population of a microbe in the gut of a human with a specific disease. This is a shortcut relation where the domain is microbe, and the range is a disease.
definition editor: Oliver He

has disease
type: ObjectProperty
sub property of: has disposition

microbe susceptibly depleted in host with disease
type: ObjectProperty
sub property of: microbe susceptibly changed in host with disease
inverse of: disease in host with susceptibly depleted microbe
domain: organism
range: disease
textual definition: An object property that represents the susceptible decrease (compared to healthy control) of the population of a microbe in a host with a specific disease. The susceptibility is usually derived from peer-reviewed studies. This is a shortcut relation where the domain is microbe, and the range is a disease.
definition editor: Oliver He

microbial population phenotype in host
type: ObjectProperty
textual definition: this is a shortcut object property that represents the phenotype that exists in a microbial population inside a host.
definition editor: Yongqun He, Haihe Wang, Jie Zheng

microbe susceptibly depleted in human with disease
type: ObjectProperty
sub property of: microbe susceptibly depleted in host with disease
textual definition: An object property that represents the susceptible decrease (compared to healthy control) of the population of a microbe in a human with a specific disease. This is a shortcut relation where the domain is microbe, and the range is a disease.
definition editor: Oliver He

has phenotype
type: ObjectProperty
sub property of: has quality

microbe susceptibly depleted in gut of human with disease
type: ObjectProperty
sub property of: microbe susceptibly depleted in human with disease
textual definition: An object property that represents the susceptible decrease (compared to healthy control) of the population of a microbe in the gut of a human with a specific disease. This is a shortcut relation where the domain is microbe, and the range is a disease.
definition editor: Oliver He

microbe susceptibly depleted in rat with disease
type: ObjectProperty
sub property of: microbe susceptibly depleted in host with disease
textual definition: An object property that represents the susceptible decrease (compared to healthy control) of the population of a microbe in a rat with a specific disease. This is a shortcut relation where the domain is microbe, and the range is a disease.
definition editor: Oliver He

microbe susceptibly expanded in rat with disease
type: ObjectProperty
sub property of: microbe susceptibly expanded in host with disease
definition editor: An object property that represents the susceptible increase (compared to healthy control) of the population of a microbe in a rat with a specific disease. This is a shortcut relation where the domain is microbe, and the range is a disease.
definition editor: Oliver He

microbe susceptibly depleted in gut of rat with disease
type: ObjectProperty
sub property of: microbe susceptibly depleted in rat with disease
textual definition: An object property that represents the susceptible decrease (compared to healthy control) of the population of a microbe in the gut of a rat with a specific disease. This is a shortcut relation where the domain is microbe, and the range is a disease.
definition editor: Oliver He

microbe susceptibly expanded in gut of rat with disease
type: ObjectProperty
sub property of: microbe susceptibly expanded in rat with disease
textual definition: An object property that represents the susceptible increase (compared to healthy control) of the population of a microbe in the gut of a rat with a specific disease. This is a shortcut relation where the domain is microbe, and the range is a disease.
definition editor: Oliver He

disease in host with susceptibly expanded microbe
type: ObjectProperty
domain: disease
range: organism
textual definition: An object property that represents a disease in a host where the host has susceptibly increased population of a microbe. This is a shortcut relation where the domain is disease, and the range is a microbe.
definition editor: Oliver He

microbe susceptibly changed in host with disease
type: ObjectProperty
domain: organism
range: disease
textual definition: An object property that represents the susceptible change (compared to healthy control) of the population of a microbe in a host with a specific disease. This is a shortcut relation where the domain is microbe, and the range is a disease.
definition editor: Oliver He

disease in host with susceptibly depleted microbe
type: ObjectProperty
domain: disease
range: organism
textual definition: An object property that represents a disease in a host where the host has susceptibly decreased population of a microbe. This is a shortcut relation where the domain is disease, and the range is a microbe.
definition editor: Oliver He

microbe susceptibly depleted in respiratory airway of human with disease
type: ObjectProperty
sub property of: microbe susceptibly depleted in human with disease
textual definition: An object property that represents the susceptible decrease (compared to healthy control) of the population of a microbe in the respiratory airway of a human with a specific disease. This is a shortcut relation where the domain is microbe, and the range is a disease.
definition editor: Oliver He

microbe susceptibly expanded in respiratory airway of human with disease
type: ObjectProperty
sub property of: microbe susceptibly expanded in human with disease
textual definition: An object property that represents the susceptible increase (compared to healthy control) of the population of a microbe in the respiratory airway of a human with a specific disease. This is a shortcut relation where the domain is microbe, and the range is a disease.
definition editor: Oliver He

microbe susceptibly expanded in oral cavity of human with disease
type: ObjectProperty
sub property of: microbe susceptibly expanded in human with disease
textual definition: An object property that represents the susceptible increase (compared to healthy control) of the population of a microbe in the oral cavity of a human with a specific disease. This is a shortcut relation where the domain is microbe, and the range is a disease.
definition editor: Oliver He

microbe susceptibly depleted in oral cavity of human with disease
type: ObjectProperty
sub property of: microbe susceptibly depleted in human with disease
textual definition: An object property that represents the susceptible decrease (compared to healthy control) of the population of a microbe in the oral cavity of a human with a specific disease. This is a shortcut relation where the domain is microbe, and the range is a disease.
definition editor: Oliver He

microbe susceptibly expanded in mouse with disease
type: ObjectProperty
sub property of: microbe susceptibly expanded in host with disease

microbe susceptibly expanded in gut of mouse with disease
type: ObjectProperty
sub property of: microbe susceptibly expanded in mouse with disease

microbe susceptibly depleted in mouse with disease
type: ObjectProperty
sub property of: microbe susceptibly depleted in host with disease

microbe susceptibly depleted in gut of mouse with disease
type: ObjectProperty
sub property of: microbe susceptibly depleted in mouse with disease

has microbe depleted in diseased host
type: ObjectProperty
sub property of: has microbe population size altered in diseased host
domain: host-microbiome interaction
textual definition: an object property that represents the relation between a host-microbiome interaction and a microbe where the population of the microbe is depleted in a diseased host compared to a healthy host control.
definition editor: Oliver He

has microbe expanded in diseased host
type: ObjectProperty
sub property of: has microbe population size altered in diseased host
textual definition: an object property that represents the relation between a host-microbiome interaction and a microbe where the population of the microbe is expanded in a diseased host compared to a healthy host control.
definition editor: Oliver He

microbe susceptibly depleted (compared to fibromyalgia patients) in gut of human with disease
type: ObjectProperty
sub property of: topObjectProperty

has microbe population size altered in diseased host
type: ObjectProperty
sub property of: has participant
domain: host-microbiome interaction
textual definition: A subproperty of the 'has participant' object property that has the domain of host-microbiome interaction and range of a microbe where the population of the microbe has size altered in a disease host organism
definition editor: YH

has host
type: ObjectProperty
sub property of: has participant
definition editor: Oliver He
definition editor: an object subproperty of 'has participant' in which the participant is a host organism.

inheres in
type: ObjectProperty
equivalent property:
  inverse of: bearer of
sub property of: inheres in part of
inverse of: bearer of
editor preferred label: inheres in
example of usage: this fragility inheres in this vase
example of usage: this red color inheres in this apple
textual definition: a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence
editor note: A dependent inheres in its bearer at all times for which the dependent exists.
alternative term: inheres_in
imported from: obi.owl
imported from: ro.owl
temporal interpretation: RO_0001901

bearer of
type: ObjectProperty
equivalent property:
  inverse of: inheres in
range: specifically dependent continuant
editor preferred label: bearer of
example of usage: this apple is bearer of this red color
example of usage: this vase is bearer of this fragility
textual definition: a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence
editor note: A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist.
alternative term: bearer_of
alternative term: is bearer of
imported from: obi.owl
imported from: ro.owl
temporal interpretation: RO_0001901

participates in
type: ObjectProperty
equivalent property:
  inverse of: has participant
inverse of: has participant
domain: continuant
range: occurrent
editor preferred label: participates in
example of usage: this blood clot participates in this blood coagulation
example of usage: this input material (or this output material) participates in this process
example of usage: this investigator participates in this investigation
textual definition: a relation between a continuant and a process, in which the continuant is somehow involved in the process
alternative term: participates_in
imported from: obi.owl
imported from: ro.owl

has participant
type: ObjectProperty
equivalent property:
  inverse of: participates in
domain: occurrent
range: continuant
property chain axiom: has part
property chain axiom: realizes
property chain axiom: inheres in
editor preferred label: has participant
example of usage: this blood coagulation has participant this blood clot
example of usage: this investigation has participant this investigator
example of usage: this process has participant this input material (or this output material)
textual definition: a relation between a process and a continuant, in which the continuant is somehow involved in the process
editor note: Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time.
alternative term: has_participant
imported from: obi.owl
imported from: ro.owl
Source: http://www.obofoundry.org/ro/#OBO_REL:has_participant

is concretized as
type: ObjectProperty
equivalent property:
  inverse of: concretizes
inverse of: concretizes
domain: generically dependent continuant
range: specifically dependent continuant
example of usage: A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).
example of usage: An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process).
textual definition: A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants.
imported from: obi.owl

concretizes
type: ObjectProperty
equivalent property:
  inverse of: is concretized as
domain: specifically dependent continuant
range: generically dependent continuant
example of usage: A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).
example of usage: An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process).
textual definition: A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant.
imported from: obi.owl

function of
type: ObjectProperty
equivalent property:
  inverse of: has function
sub property of: inheres in
inverse of: has function
domain: function
example of usage: this catalysis function is a function of this enzyme
textual definition: a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence
editor note: A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists.
alternative term: function_of
alternative term: is function of
imported from: obi.owl

role of
type: ObjectProperty
equivalent property:
  inverse of: has role
sub property of: inheres in
inverse of: has role
example of usage: this investigator role is a role of this person
textual definition: a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence
editor note: A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists.
alternative term: is role of
alternative term: role_of
imported from: obi.owl

has function
type: ObjectProperty
equivalent property:
  inverse of: function of
sub property of: bearer of
domain: independent continuant
range: function
example of usage: this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)
textual definition: a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence
editor note: A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists.
alternative term: has_function
imported from: obi.owl

has quality
type: ObjectProperty
sub property of: bearer of
range: quality
example of usage: this apple has quality this red color
textual definition: a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence
editor note: A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist.
alternative term: has_quality
imported from: ro.owl

has role
type: ObjectProperty
equivalent property:
  inverse of: role of
sub property of: bearer of
domain: independent continuant
range: role
example of usage: this person has role this investigator role (more colloquially: this person has this role of investigator)
textual definition: a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence
editor note: A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists.
alternative term: has_role
imported from: obi.owl
imported from: ro.owl

has disposition
type: ObjectProperty
sub property of: bearer of
inverse of: disposition of
domain: independent continuant
range: disposition
textual definition: a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence
imported from: ro.owl

disposition of
type: ObjectProperty
sub property of: inheres in
textual definition: inverse of has disposition
imported from: ro.owl
in_subset: RO_0002259

derives from
type: ObjectProperty
equivalent property:
  inverse of: derives into
sub property of: topObjectProperty
inverse of: derives into
domain: independent continuant
range: independent continuant
editor preferred label: derives from
example of usage: this cell derives from this parent cell (cell division)
example of usage: this nucleus derives from this parent nucleus (nuclear division)
has curation status: IAO_0000125
textual definition: a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity
editor note: This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'.
alternative term: derives_from
imported from: obi.owl
imported from: ro.owl

derives into
type: ObjectProperty
equivalent property:
  inverse of: derives from
example of usage: this parent cell derives into this cell (cell division)
example of usage: this parent nucleus derives into this nucleus (nuclear division)
has curation status: IAO_0000125
textual definition: a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity
editor note: This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'.
alternative term: derives_into
imported from: obi.owl

located in
type: ObjectProperty
type: TransitiveProperty
domain: independent continuant
domain: Class
  intersection of: independent continuant
  intersection of: Class
    complement of: spatial region
range: independent continuant
range: Class
  intersection of: independent continuant
  intersection of: Class
    complement of: spatial region
editor preferred label: located in
example of usage: my brain is located in my head
example of usage: this rat is located in this cage
textual definition: a relation between two independent continuants, the target and the location, in which the target is entirely within the location
editor note: Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus
editor note: Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
alternative term: located_in
imported from: ro.owl
temporal interpretation: RO_0001901
Source: http://www.obofoundry.org/ro/#OBO_REL:located_in

has component activity
type: ObjectProperty
sub property of: has component process
imported from: ro.owl
created_by: dos
creation_date: 2017-05-24T09:44:33Z
comment: A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B.

has component process
type: ObjectProperty
sub property of: has component
textual definition: w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.
imported from: ro.owl
created_by: dos
creation_date: 2017-05-24T09:49:21Z

has effector activity
type: ObjectProperty
sub property of: has component activity
sub property of: regulates
type: FunctionalProperty
textual definition: A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.
imported from: ro.owl
created_by: dos
creation_date: 2017-09-22T14:14:36Z
comment: This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations.

before or simultaneous with
type: ObjectProperty
sub property of: temporal relation
definition editor: David Osumi-Sutherland
alternative term: <=
imported from: ro.owl
in_subset: ro-eco
comment: Primitive instance level timing relation between events

simultaneous with
type: ObjectProperty
sub property of: before or simultaneous with
type: TransitiveProperty
definition editor: David Osumi-Sutherland
imported from: ro.owl
in_subset: ro-eco
comment: t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2)

before
type: ObjectProperty
sub property of: before or simultaneous with
type: TransitiveProperty
definition editor: David Osumi-Sutherland
imported from: ro.owl
in_subset: ro-eco
comment: t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2)

during which ends
type: ObjectProperty
sub property of: temporal relation
inverse of: ends during
definition editor: David Osumi-Sutherland
imported from: ro.owl
in_subset: ro-eco
comment: Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range.

encompasses
type: ObjectProperty
sub property of: during which starts
inverse of: happens during
type: TransitiveProperty
definition editor: David Osumi-Sutherland
alternative term: di
imported from: ro.owl
comment: Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range.

ends after
type: ObjectProperty
sub property of: temporal relation
type: TransitiveProperty
property chain axiom: ends during
property chain axiom: preceded by
definition editor: David Osumi-Sutherland
imported from: ro.owl
in_subset: ro-eco
comment: X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)

immediately preceded by
type: ObjectProperty
sub property of: preceded by
inverse of: immediately precedes
property chain axiom: starts with
property chain axiom: ends with
definition editor: David Osumi-Sutherland
alternative term: starts_at_end_of
imported from: ro.owl
comment: X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)

during which starts
type: ObjectProperty
sub property of: temporal relation
inverse of: starts during
definition editor: David Osumi-Sutherland
imported from: ro.owl
in_subset: ro-eco
comment: Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range.

starts before
type: ObjectProperty
sub property of: temporal relation
type: TransitiveProperty
property chain axiom: starts during
property chain axiom: obsolete preceded by
definition editor: David Osumi-Sutherland
imported from: ro.owl
in_subset: ro-eco

immediately precedes
type: ObjectProperty
sub property of: precedes
property chain axiom: ends with
property chain axiom: starts with
definition editor: David Osumi-Sutherland
alternative term: ends_at_start_of
alternative term: meets
imported from: ro.owl
is direct form of: precedes
in_subset: ro-eco
comment: X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)

starts during
type: ObjectProperty
sub property of: temporal relation
domain: occurrent
range: occurrent
definition editor: David Osumi-Sutherland
alternative term: io
imported from: ro.owl
in_subset: ro-eco
comment: X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y))

happens during
type: ObjectProperty
sub property of: ends during
type: TransitiveProperty
definition editor: David Osumi-Sutherland
alternative term: d
alternative term: during
imported from: ro.owl
in_subset: ro-eco
comment: X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y))

ends during
type: ObjectProperty
sub property of: temporal relation
definition editor: David Osumi-Sutherland
alternative term: o
alternative term: overlaps
imported from: ro.owl
in_subset: ro-eco
comment: X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y).

overlaps
type: ObjectProperty
sub property of: mereotopologically related to
property chain axiom: part of
property chain axiom: has part
has curation status: IAO_0000125
textual definition: x overlaps y if and only if there exists some z such that x has part z and z part of y
imported from: ro.owl
expand expression to: http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)
temporal interpretation: RO_0001901
in_subset: ro-eco

has component
type: ObjectProperty
sub property of: has part
has curation status: IAO_0000125
textual definition: w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.
editor note: The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity.
curator notes: For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit.
imported from: ro.owl
temporal interpretation: RO_0001901
in_subset: ro-eco

regulates
type: ObjectProperty
sub property of: causally upstream of
inverse of: regulated by
type: TransitiveProperty
domain: process
range: process
property chain axiom: ends with
property chain axiom: directly regulates
has curation status: IAO_0000125
textual definition: process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2.
editor note: We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit
definition editor: Chris Mungall
definition editor: David Hill
definition editor: Tanya Berardini
definition source: causal-relations
definition source: GO
curator notes: Regulation precludes parthood; the regulatory process may not be within the regulated process.
imported from: ro.owl
OBO foundry unique label: regulates (processual)
elucidation: false

negatively regulates
type: ObjectProperty
sub property of: regulates
sub property of: causally upstream of, negative effect
inverse of: negatively regulated by
property chain axiom: ends with
textual definition: Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2.
definition editor: Chris Mungall
definition source: causal-relations
imported from: ro.owl
OBO foundry unique label: negatively regulates (process to process)
is negative form of: regulates

positively regulates
type: ObjectProperty
sub property of: regulates
sub property of: causally upstream of, positive effect
inverse of: positively regulated by
type: TransitiveProperty
property chain axiom: negatively regulates
property chain axiom: ends with
textual definition: Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2.
definition editor: Chris Mungall
definition source: causal-relations
imported from: ro.owl
OBO foundry unique label: positively regulates (process to process)
is positive form of: regulates

has prototype
type: ObjectProperty
domain: Class
  union of: independent continuant
  union of: process
example of usage: 'human p53 protein' SubClassOf some ('has prototype' some ('participates in' some 'DNA repair'))
example of usage: heart SubClassOf 'has prototype' some ('participates in' some 'blood circulation')
has curation status: IAO_0000125
textual definition: x has prototype y if and only if x is an instance of C and y is a prototypical instance of C. For example, every instance of heart, both normal and abnormal is related by the has prototype relation to some instance of a "canonical" heart, which participates in blood circulation.
editor note: Experimental. In future there may be a formalization in which this relation is treated as a shortcut to some modal logic axiom. We may decide to obsolete this and adopt a more specific evolutionary relationship (e.g. evolved from)
editor note: This property can be used to make weaker forms of certain relations by chaining an additional property. For example, we may say: retina SubClassOf has_prototype some 'detection of light'. i.e. every retina is related to a prototypical retina instance which is detecting some light. Note that this is very similar to 'capable of', but this relation affords a wider flexibility. E.g. we can make a relation between continuants.
definition editor: Chris Mungall
imported from: ro.owl

temporal relation
type: ObjectProperty
domain: occurrent
range: occurrent
has curation status: IAO_0000125
editor note: move to BFO?
definition editor: Chris Mungall
definition source: Allen's interval algebra
definition source: Allen
curator notes: Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends.
imported from: obi.owl
imported from: ro.owl
Source: https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit
in_subset: ro-eco
comment: A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.
label: temporally related to

starts
type: ObjectProperty
sub property of: part of
sub property of: temporal relation
inverse of: starts with
has curation status: IAO_0000125
textual definition: inverse of starts with
definition editor: Chris Mungall
definition source: Allen
imported from: obi.owl
imported from: ro.owl
in_subset: ro-eco

starts with
type: ObjectProperty
sub property of: has part
sub property of: temporal relation
type: TransitiveProperty
example of usage: Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor
has curation status: IAO_0000125
textual definition: x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
definition editor: Chris Mungall
alternative term: started by
imported from: ro.owl
in_subset: ro-eco

ends
type: ObjectProperty
sub property of: part of
sub property of: temporal relation
inverse of: ends with
has curation status: IAO_0000125
textual definition: inverse of ends with
definition editor: Chris Mungall
imported from: ro.owl
in_subset: ro-eco

ends with
type: ObjectProperty
sub property of: has part
sub property of: temporal relation
type: TransitiveProperty
has curation status: IAO_0000125
textual definition: x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
definition editor: Chris Mungall
alternative term: finished by
imported from: ro.owl
in_subset: ro-eco

has input
type: ObjectProperty
sub property of: has participant
inverse of: input of
domain: process
range: material entity
property chain axiom: starts with
has curation status: IAO_0000125
textual definition: p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p.
definition editor: Chris Mungall
alternative term: consumes
imported from: ro.owl
in_subset: ro-eco

has output
type: ObjectProperty
sub property of: has participant
inverse of: output of
property chain axiom: ends with
has curation status: IAO_0000125
textual definition: p has output c iff c is a participant in p, c is present at the end of p, and c is not present at the beginning of p.
definition editor: Chris Mungall
alternative term: produces
imported from: ro.owl
in_subset: ro-eco

causally upstream of, positive effect
type: ObjectProperty
sub property of: causally upstream of
sub property of: causally upstream of or within, positive effect
imported from: ro.owl
is positive form of: causally upstream of
creator: cjm
comment: holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y

causally upstream of, negative effect
type: ObjectProperty
sub property of: causally upstream of
sub property of: causally upstream of or within, negative effect
imported from: ro.owl
is negative form of: causally upstream of
creator: cjm
comment: holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y

inheres in part of
type: ObjectProperty
sub property of: depends on
property chain axiom: inheres in
property chain axiom: part of
textual definition: q inheres in part of w if and only if there exists some p such that q inheres in p and p part of w.
editor note: Because part_of is transitive, inheres in is a sub-relation of inheres in part of
definition editor: Chris Mungall
definition source: http://www.ncbi.nlm.nih.gov/pubmed/20064205
imported from: ro.owl
temporal interpretation: RO_0001901

mereotopologically related to
type: ObjectProperty
textual definition: A mereological relationship or a topological relationship
definition editor: Chris Mungall
curator notes: Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships
imported from: ro.owl
temporal interpretation: RO_0001901

functionally related to
type: ObjectProperty
textual definition: A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities.
definition editor: Chris Mungall
curator notes: This is a grouping relation that collects relations used for the purpose of connecting structure and function
imported from: ro.owl

regulated by
type: ObjectProperty
sub property of: causally downstream of or within
type: TransitiveProperty
domain: process
range: process
textual definition: inverse of regulates
definition editor: Chris Mungall
imported from: ro.owl
OBO foundry unique label: regulated by (processual)
in_subset: RO_0002259

negatively regulated by
type: ObjectProperty
sub property of: regulated by
textual definition: inverse of negatively regulates
definition editor: Chris Mungall
imported from: ro.owl
in_subset: RO_0002259

positively regulated by
type: ObjectProperty
sub property of: regulated by
textual definition: inverse of positively regulates
definition editor: Chris Mungall
imported from: ro.owl
in_subset: RO_0002259

has member
type: ObjectProperty
sub property of: has part
type: IrreflexiveProperty
textual definition: has member is a mereological relation between a collection and an item.
definition source: SIO
imported from: ro.owl
temporal interpretation: RO_0001901

input of
type: ObjectProperty
sub property of: participates in
sub property of: functionally related to
textual definition: inverse of has input
definition editor: Chris Mungall
imported from: ro.owl
in_subset: RO_0002259
in_subset: ro-eco

output of
type: ObjectProperty
sub property of: participates in
sub property of: functionally related to
textual definition: inverse of has output
definition editor: Chris Mungall
imported from: ro.owl
in_subset: RO_0002259
in_subset: ro-eco

has direct input
type: ObjectProperty
sub property of: has input
property chain axiom: starts with
example of usage: 'protein catabolic process' SubClassOf has_direct_input some protein
has curation status: IAO_0000428
textual definition: p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p.
definition editor: Chris Mungall
alternative term: directly consumes
curator notes: This is likely to be obsoleted. A candidate replacement would be a new relation 'has bound input' or 'has substrate'
imported from: ro.owl

obsolete has direct output
type: ObjectProperty
example of usage: translation SubClassOf has_direct_output some protein
has curation status: IAO_0000428
textual definition: p has direct input c iff c is a participanti n p, c is present at the end of p, and c is not present at the beginning of c.
definition editor: Chris Mungall
alternative term: directly produces
imported from: ro.owl
deprecated: true

causally downstream of
type: ObjectProperty
sub property of: preceded by
sub property of: causally downstream of or within
inverse of: causally upstream of
has curation status: IAO_0000428
textual definition: inverse of upstream of
definition editor: Chris Mungall
imported from: ro.owl

immediately causally downstream of
type: ObjectProperty
sub property of: immediately preceded by
sub property of: causally downstream of
inverse of: immediately causally upstream of
has curation status: IAO_0000428
definition editor: Chris Mungall
imported from: ro.owl

directly activates
type: ObjectProperty
sub property of: directly positively regulates
has curation status: IAO_0000428
textual definition: p directly activates q if and only if p is immediately upstream of q and p is the realization of a function to increase the rate or activity of q
definition editor: Chris Mungall
alternative term: directly positively regulates
definition source: causal-relations
imported from: ro.owl
OBO foundry unique label: directly activates (process to process)

indirectly activates
type: ObjectProperty
sub property of: positively regulates
type: TransitiveProperty
property chain axiom: directly activates
property chain axiom: indirectly inhibits
textual definition: p directly activates q if and only if p is immediately upstream of q and p is the realization of a function to increase the rate or activity of q
definition editor: Chris Mungall
alternative term: indirectly positively regulates
imported from: ro.owl
is indirect form of: positively regulates

directly inhibits
type: ObjectProperty
sub property of: directly negatively regulates
definition editor: Chris Mungall
alternative term: directly negatively regulates
definition source: causal-relations
imported from: ro.owl
OBO foundry unique label: directly inhibits (process to process)

indirectly inhibits
type: ObjectProperty
sub property of: negatively regulates
type: TransitiveProperty
property chain axiom: directly inhibits
has curation status: IAO_0000428
definition editor: Chris Mungall
alternative term: indirectly negatively regulates
imported from: ro.owl
is indirect form of: negatively regulates

causally related to
type: ObjectProperty
has curation status: IAO_0000428
textual definition: This relation groups causal relations between material entities and causal relations between processes
editor note: This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. To define causal relations in an activity-flow type network, we make use of 3 primitives: * Temporal: how do the intervals of the two occurrents relate? * Is the causal relation regulatory? * Is the influence positive or negative The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule. For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. Each of these 3 primitives can be composed to yiel…
definition editor: Chris Mungall
curator notes: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
imported from: ro.owl

causally upstream of
type: ObjectProperty
sub property of: precedes
sub property of: causally upstream of or within
type: TransitiveProperty
has curation status: IAO_0000428
textual definition: p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain
definition editor: Chris Mungall
imported from: ro.owl

immediately causally upstream of
type: ObjectProperty
sub property of: immediately precedes
sub property of: causally upstream of
has curation status: IAO_0000428
textual definition: p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q.
definition editor: Chris Mungall
imported from: ro.owl
is direct form of: causally upstream of

directly provides input for
type: ObjectProperty
sub property of: immediately causally upstream of
sub property of: transitively provides input for
property chain axiom: obsolete has direct output
property chain axiom: has direct input
has curation status: IAO_0000428
textual definition: p1 directly provides input for p2 iff there exists some c such that p1 has_output c and p2 has_input c
editor note: This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit
definition editor: Chris Mungall
definition source: causal-relations
imported from: ro.owl
OBO foundry unique label: directly provides input for (process to process)

transitively provides input for
type: ObjectProperty
sub property of: causally upstream of
type: TransitiveProperty
domain: process
range: process
has curation status: IAO_0000428
textual definition: transitive form of directly_provides_input_for
definition editor: Chris Mungall
curator notes: This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'directly provides input for' (which may later be relabeled simply to 'provides input for')
imported from: ro.owl
OBO foundry unique label: transitively provides input for (process to process)

causally upstream of or within
type: ObjectProperty
sub property of: causal relation between processes
inverse of: causally downstream of or within
type: TransitiveProperty
textual definition: p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q.
editor note: We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2
definition editor: Chris Mungall
alternative term: influences (processual)
imported from: ro.owl
has_related_synonym: affects

causally downstream of or within
type: ObjectProperty
sub property of: causal relation between processes
type: TransitiveProperty
textual definition: inverse of causally upstream of or within
definition editor: Chris Mungall
definition source: causal-relations
imported from: ro.owl
in_subset: RO_0002259

causal relation between processes
type: ObjectProperty
sub property of: causally related to
domain: occurrent
range: occurrent
textual definition: p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q.
definition editor: Chris Mungall
definition source: causal-relations
curator notes: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
imported from: ro.owl

depends on
type: ObjectProperty
definition editor: Chris Mungall
imported from: ro.owl

directly regulates
type: ObjectProperty
sub property of: regulates
sub property of: immediately causally upstream of
textual definition: Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2.
definition editor: Chris Mungall
definition source: causal-relations
imported from: ro.owl
OBO foundry unique label: directly regulates (processual)
is direct form of: regulates

directly positively regulates
type: ObjectProperty
sub property of: positively regulates
sub property of: directly regulates
textual definition: Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2.
definition source: causal-relations
imported from: ro.owl
OBO foundry unique label: directly positively regulates (process to process)
is positive form of: directly regulates

directly negatively regulates
type: ObjectProperty
sub property of: negatively regulates
sub property of: directly regulates
textual definition: Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2.
definition source: causal-relations
imported from: ro.owl
OBO foundry unique label: directly negatively regulates (process to process)
is negative form of: directly regulates

causally upstream of or within, negative effect
type: ObjectProperty
sub property of: causally upstream of or within
imported from: ro.owl
is negative form of: causally upstream of or within
created_by: cjm
creation_date: 2018-03-13T23:55:05Z

causally upstream of or within, positive effect
type: ObjectProperty
sub property of: causally upstream of or within
imported from: ro.owl
is positive form of: causally upstream of or within
created_by: cjm
creation_date: 2018-03-13T23:55:19Z

in similarity relationship with
type: ObjectProperty
type: SymmetricProperty
textual definition: Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison.
imported from: ro.owl
creator: bgee.unil.ch
Source: http://www.ncbi.nlm.nih.gov/pubmed/20116127
database_cross_reference: ECO:0000041
database_cross_reference: SO:similar_to
has_exact_synonym: sameness
has_exact_synonym: similar to
has_related_synonym: correspondence
has_related_synonym: resemblance

has measurement value
type: DatatypeProperty
sub property of: topDataProperty
type: FunctionalProperty
domain: scalar measurement datum
range: double
imported from: obi.owl

has specified numeric value
type: DatatypeProperty
sub property of: has specified value
domain: value specification
range: real
editor preferred label: has specified numeric value
has curation status: IAO_0000120
textual definition: A relation between a value specification and a number that quantifies it.
editor note: A range of 'real' might be better than 'float'. For now we follow 'has measurement value' until we can consider technical issues with SPARQL queries and reasoning.
definition editor: PERSON: James A. Overton
definition source: OBI
imported from: obi.owl

has specified value
type: DatatypeProperty
domain: value specification
editor preferred label: has specified value
has curation status: IAO_0000123
textual definition: A relation between a value specification and a literal.
editor note: This is not an RDF/OWL object property. It is intended to link a value found in e.g. a database column of 'M' (the literal) to an instance of a value specification class, which can then be linked to indicate that this is about the biological gender of a human subject.
definition source: OBI
imported from: obi.owl

entity
type: Class
subclass of: Thing
BFO OWL specification label: entity
BFO CLIF specification label: Entity
example of usage: Julius Caesar
example of usage: Verdi’s Requiem
example of usage: the Second World War
example of usage: your body mass index
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
imported from: obi.owl
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
subclass of: Restriction
  on property: has prototype
  all values from: continuant
subclass of: Restriction
  on property: in similarity relationship with
  all values from: continuant
BFO OWL specification label: continuant
BFO CLIF specification label: Continuant
textual definition: An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts.
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
imported from: obi.owl
imported from: ro.owl
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])
has associated axiom(nl): if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])
has associated axiom(nl): if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])
has associated axiom(nl): if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])
has associated axiom(fol): (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]
has associated axiom(fol): (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]
has associated axiom(fol): (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
has associated axiom(fol): (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]

occurrent
type: Class
subclass of: entity
subclass of: Restriction
  on property: in similarity relationship with
  all values from: occurrent
BFO OWL specification label: occurrent
BFO CLIF specification label: Occurrent
textual 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.
imported from: obi.owl
imported from: ro.owl
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])
has associated axiom(nl): Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])
has associated axiom(nl): b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])
has associated axiom(fol): (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001]
has associated axiom(fol): (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001]

independent continuant
type: Class
subclass of: continuant
BFO OWL specification label: ic
BFO CLIF specification label: IndependentContinuant
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
textual definition: A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.
textual 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])
imported from: obi.owl
imported from: ro.owl
has associated axiom(nl): For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])
has associated axiom(nl): For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])
has associated axiom(fol): (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]
has associated axiom(fol): (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002]
has associated axiom(fol): (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]

spatial region
type: Class
subclass of: immaterial entity
imported from: ro.owl

process
type: Class
subclass of: occurrent
subclass of: Restriction
  on property: has prototype
  all values from: process
BFO OWL specification label: process
BFO CLIF specification label: Process
example of usage: a process of cell-division, \ a beating of the heart
example of usage: a process of meiosis
example of usage: a process of sleeping
example of usage: the course of a disease
example of usage: the flight of a bird
example of usage: the life of an organism
example of usage: your process of aging.
textual definition: An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.
textual definition: p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])
editor note: BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war)
imported from: obi.owl
imported from: ro.owl
has associated axiom(fol): (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003]

disposition
type: Class
subclass of: realizable entity
BFO OWL specification label: disposition
BFO CLIF specification label: Disposition
example of usage: an atom of element X has the disposition to decay to an atom of element Y
example of usage: certain people have a predisposition to colon cancer
example of usage: children are innately disposed to categorize objects in certain ways.
example of usage: the cell wall is disposed to filter chemicals in endocytosis and exocytosis
editor note: BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type.
imported from: obi.owl
imported from: ro.owl
elucidation: b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])
has associated axiom(nl): If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002])
has associated axiom(fol): (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002]
has associated axiom(fol): (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002]

realizable entity
type: Class
subclass of: specifically dependent continuant
BFO OWL specification label: realizable
BFO CLIF specification label: RealizableEntity
example of usage: the disposition of this piece of metal to conduct electricity.
example of usage: the disposition of your blood to coagulate
example of usage: the function of your reproductive organs
example of usage: the role of being a doctor
example of usage: the role of this boundary to delineate where Utah and Colorado meet
textual definition: A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances.
imported from: obi.owl
imported from: ro.owl
elucidation: To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])
has associated axiom(nl): All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])
has associated axiom(fol): (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002]
has associated axiom(fol): (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002]

quality
type: Class
subclass of: specifically dependent continuant
BFO OWL specification label: quality
BFO CLIF specification label: Quality
example of usage: the ambient temperature of this portion of air
example of usage: the color of a tomato
example of usage: the length of the circumference of your waist
example of usage: the mass of this piece of gold.
example of usage: the shape of your nose
example of usage: the shape of your nostril
imported from: obi.owl
imported from: ro.owl
elucidation: a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])
has associated axiom(nl): If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001])
has associated axiom(fol): (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001]
has associated axiom(fol): (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001]

specifically dependent continuant
type: Class
subclass of: continuant
BFO OWL specification label: sdc
BFO CLIF specification label: SpecificallyDependentContinuant
example of usage: Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key
example of usage: of one-sided specifically dependent continuants: the mass of this tomato
example of usage: of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates.
example of usage: the disposition of this fish to decay
example of usage: the function of this heart: to pump blood
example of usage: the mutual dependence of proton donors and acceptors in chemical reactions [79
example of usage: the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction
example of usage: the pink color of a medium rare piece of grilled filet mignon at its center
example of usage: the role of being a doctor
example of usage: the shape of this hole.
example of usage: the smell of this portion of mozzarella
textual definition: A 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.
textual definition: b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n > 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i < j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004])
textual definition: b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])
editor note: Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc.
imported from: obi.owl
imported from: ro.owl
has associated axiom(fol): (iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004]
has associated axiom(fol): (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003]

role
type: Class
subclass of: realizable entity
BFO OWL specification label: role
BFO CLIF specification label: Role
example of usage: John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married.
example of usage: the priest role
example of usage: the role of a boundary to demarcate two neighboring administrative territories
example of usage: the role of a building in serving as a military target
example of usage: the role of a stone in marking a property boundary
example of usage: the role of subject in a clinical trial
example of usage: the student role
textual definition: A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts.
editor note: BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives.
imported from: obi.owl
imported from: ro.owl
elucidation: b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])
has associated axiom(fol): (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001]

generically dependent continuant
type: Class
subclass of: continuant
BFO OWL specification label: gdc
BFO CLIF specification label: GenericallyDependentContinuant
example of usage: The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity.
example of usage: the pdf file on your laptop, the pdf file that is a copy thereof on my laptop
example of usage: the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule.
textual definition: A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time.
textual definition: b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])
imported from: obi.owl
has associated axiom(fol): (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001]

function
type: Class
subclass of: disposition
BFO OWL specification label: function
BFO CLIF specification label: Function
example of usage: the function of a hammer to drive in nails
example of usage: the function of a heart pacemaker to regulate the beating of a heart through electricity
example of usage: the function of amylase in saliva to break down starch into sugar
editor note: BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc.
imported from: obi.owl
elucidation: A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])
has associated axiom(fol): (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001]

process boundary
type: Class
subclass of: occurrent
BFO OWL specification label: p-boundary
BFO CLIF specification label: ProcessBoundary
example of usage: the boundary between the 2nd and 3rd year of your life.
textual definition: p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001])
imported from: obi.owl
has associated axiom(nl): Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002])
has associated axiom(fol): (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002]
has associated axiom(fol): (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001]

material entity
type: Class
subclass of: independent continuant
BFO OWL specification label: material
BFO CLIF specification label: MaterialEntity
example of usage: a flame
example of usage: a forest fire
example of usage: a human being
example of usage: a hurricane
example of usage: a photon
example of usage: a puff of smoke
example of usage: a sea wave
example of usage: a tornado
example of usage: an aggregate of human beings.
example of usage: an energy wave
example of usage: an epidemic
example of usage: the undetached arm of a human being
textual definition: An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
editor note: BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60
editor note: BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity.
editor note: BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here.
imported from: envo.owl
imported from: obi.owl
imported from: ogg.owl
imported from: ro.owl
elucidation: A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])
has associated axiom(nl): Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])
has associated axiom(nl): every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])
has associated axiom(fol): (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002]
has associated axiom(fol): (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002]
has associated axiom(fol): (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002]

immaterial entity
type: Class
subclass of: independent continuant
imported from: ro.owl

organism or virus or viroid
type: Class
equivalent class: organism
subclass of: material entity
textual definition: Material anatomical entity that is a member of an individual species or is a viral or viroid particle.
imported from: pco.owl
OBO foundry unique label: organism or virus
IAO created by: Melissa Haendel
IAO creation date: 9/18/11

peptide
type: Class
subclass of: macromolecule
editor preferred label: peptide
textual definition: Amide derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another with formal loss of water. The term is usually applied to structures formed from alpha-amino acids, but it includes those derived from any amino carboxylic acid. X = OH, OR, NH2, NHR, etc.
imported from: chebi.owl
imported from: obi.owl

deoxyribonucleic acid
type: Class
subclass of: nucleic acid
editor preferred label: deoxyribonucleic acid
textual definition: High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms.
imported from: chebi.owl
imported from: obi.owl

molecular entity
type: Class
subclass of: material entity
editor preferred label: molecular entity
textual definition: Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.
editor note: We are assuming that every molecular entity has to be completely connected by chemical bonds. This excludes protein complexes, which are comprised of minimally two separate molecular entities. We will follow up with Chebi to ensure this is their understanding as well
imported from: chebi.owl
imported from: obi.owl

atom
type: Class
subclass of: material entity
editor preferred label: atom
textual definition: A chemical entity constituting the smallest component of an element having the chemical properties of the element.
imported from: chebi.owl
imported from: obi.owl

nucleic acid
type: Class
subclass of: macromolecule
editor preferred label: nucleic acid
textual definition: A macromolecule made up of nucleotide units and hydrolysable into certain pyrimidine or purine bases (usually adenine, cytosine, guanine, thymine, uracil), D-ribose or 2-deoxy-D-ribose and phosphoric acid.
imported from: chebi.owl
imported from: obi.owl

ribonucleic acid
type: Class
subclass of: nucleic acid
editor preferred label: ribonucleic acid
textual definition: High molecular weight, linear polymers, composed of nucleotides containing ribose and linked by phosphodiester bonds; RNA is central to the synthesis of proteins.
imported from: chebi.owl
imported from: obi.owl

macromolecule
type: Class
subclass of: molecular entity
editor preferred label: macromolecule
textual definition: A macromolecule is a molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
alternative term: polymer
imported from: chebi.owl
imported from: obi.owl

cell
type: Class
subclass of: material entity
editor preferred label: cell
example of usage: PMID:18089833.Cancer Res. 2007 Dec 15;67(24):12018-25. "...Epithelial cells were harvested from histologically confirmed adenocarcinomas .."
textual definition: A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.
imported from: cl.owl
imported from: obi.owl

cultured cell
type: Class
subclass of: experimentally modified cell in vitro
subclass of: Class
  union of: Restriction
    on property: is_specified_output_of
    some values from: establishing cell culture
  union of: Restriction
    on property: derives from
    some values from: Restriction
      on property: is_specified_output_of
      some values from: establishing cell culture
editor preferred label: cultured cell
textual definition: A cell in vitro that is or has been maintained or propagated as part of a cell culture.
imported from: cl.owl
imported from: obi.owl

experimentally modified cell in vitro
type: Class
subclass of: cell
subclass of: processed material
subclass of: Restriction
  on property: is_specified_output_of
  some values from: material processing
editor preferred label: experimentally modified cell in vitro
textual definition: A cell in vitro that has undergone physical changes as a consequence of a deliberate and specific experimental procedure.
imported from: cl.owl
imported from: obi.owl

clinical measurement
type: Class
subclass of: measurement datum
textual definition: A quantitative or qualitative value which is the result of an act of assessing a morphological or physiological state or property in a single individual or sample or a group of individuals or samples, based on direct observation or experimental manipulation.
imported from: cmo.owl
has_obo_namespace: Clinical_Measurement.ontology
id: CMO:0000000

serum immunoglobulin measurement
type: Class
subclass of: blood immunoglobulin measurement
textual definition: Any measurement related to immunoglobulin, any of several classes of proteins produced by plasma cells and lymphocytes which play essential roles in the immune system, for example, attaching to foreign substances in an effort to destroy them, in serum, the clear liquid that separates from blood after it has clotted completely, i.e. blood plasma from which fibrinogen has been removed.
imported from: cmo.owl
created_by: JSmith
creation_date: 2013-01-08T18:17:44Z
has_obo_namespace: Clinical_Measurement.ontology
id: CMO:0001276

blood immunoglobulin measurement
type: Class
subclass of: clinical measurement
textual definition: Any measurement related to immunoglobulins, any of several classes of proteins produced by plasma cells and lymphocytes which play essential roles in the immune system, for example, attaching to foreign substances in an effort to destroy them, in blood, the fluid that circulates through the heart, arteries, capillaries and veins carrying nutrients and oxygen to the body tissues and metabolites away from them.
imported from: cmo.owl
created_by: JSmith
creation_date: 2013-01-30T12:00:54Z
has_obo_namespace: Clinical_Measurement.ontology
id: CMO:0001531

serum immunoglobulin A level
type: Class
subclass of: serum immunoglobulin measurement
textual definition: The amount in a specified sample of serum of one or more types of immunoglobulin A (IgA), one of the most prevalent of the five classes of antibodies produced by the body. IgA is found in all secretions of the body and is the major antibody in the tears, saliva, and mucous membranes lining the intestines and bronchi, constituting an important factor in mucosal immunity.
imported from: cmo.owl
created_by: JSmith
creation_date: 2014-01-27T12:21:14Z
has_exact_synonym: serum IgA level
has_obo_namespace: Clinical_Measurement.ontology
id: CMO:0002095

serum immunoglobulin G level
type: Class
subclass of: serum immunoglobulin measurement
textual definition: The amount in a specified sample of serum of one or more types of immunoglobulin G (IgG), the most abundant class of antibodies found in blood serum and lymph. IgG antibodies are active against bacteria, fungi, viruses, and foreign particles, and trigger action of the complement system.
imported from: cmo.owl
created_by: JSmith
creation_date: 2014-01-27T12:33:22Z
has_exact_synonym: serum IgG level
has_obo_namespace: Clinical_Measurement.ontology
id: CMO:0002102

serum immunoglobulin M level
type: Class
subclass of: serum immunoglobulin measurement
textual definition: The amount in a specified sample of serum of one or more types of immunoglobulin M (IgM), one of the five classes of antibodies produced by the body. IgM is found in circulating body fluids and is the first class of antibodies to appear in response to an initial exposure to an antigen.
imported from: cmo.owl
created_by: JSmith
creation_date: 2014-01-27T12:35:25Z
has_exact_synonym: serum IgM level
has_obo_namespace: Clinical_Measurement.ontology
id: CMO:0002104

inflammatory bowel disease
type: Class
subclass of: intestinal disease
textual definition: An intestinal disease characterized by inflammation located_in all parts of digestive tract.
imported from: doid.owl
database_cross_reference: EFO:0003767
database_cross_reference: KEGG:05321
database_cross_reference: MESH:D015212
database_cross_reference: NCI:C3138
database_cross_reference: OMIM:PS266600
database_cross_reference: SNOMEDCT_US_2018_03_01:24526004
database_cross_reference: UMLS_CUI:C0021390
has_obo_namespace: disease_ontology
id: DOID:0050589
in_subset: DO FlyBase slim
in_subset: NCIthesaurus
comment: Xref MGI. OMIM mapping confirmed by DO. [SN].

organ system cancer
type: Class
subclass of: cancer
textual definition: A cancer that is classified based on the organ it starts in.
imported from: doid.owl
created_by: snadendla
creation_date: 2011-06-13T03:28:33Z
database_cross_reference: MESH:D009371
has_obo_namespace: disease_ontology
id: DOID:0050686

autoimmune disease of musculoskeletal system
type: Class
subclass of: musculoskeletal system disease
subclass of: autoimmune hypersensitivity disease
textual definition: An autoimmune hypersensitivity disease that is the abnormal functioning of the immune system that causes your immune system to produce antibodies or T cells against cells and/or tissues in the musculoskeletal system.
imported from: doid.owl
has_obo_namespace: disease_ontology
id: DOID:0060032

hepatobiliary system cancer
type: Class
subclass of: gastrointestinal system cancer
textual definition: A gastrointestinal system cancer that is located_in the hepatobiliary system
imported from: doid.owl
has_obo_namespace: disease_ontology
id: DOID:0080355

intestinal cancer
type: Class
subclass of: gastrointestinal system cancer
subclass of: intestinal disease
textual definition: A gastrointestinal system cancer that is located_in the intestine.
imported from: doid.owl
database_cross_reference: ICD10CM:C26.0
database_cross_reference: ICD9CM:159.0
database_cross_reference: MESH:D007414
database_cross_reference: NCI2004_11_17:C4572
database_cross_reference: NCI:C4572
database_cross_reference: SNOMEDCT_US_2018_03_01:93838000
database_cross_reference: UMLS_CUI:C0346627
has_exact_synonym: malignant intestinal tumors
has_exact_synonym: malignant neoplasm of intestine
has_obo_namespace: disease_ontology
id: DOID:10155
in_subset: NCIthesaurus
in_subset: TopNodes DOcancerslim

stomach cancer
type: Class
subclass of: gastrointestinal system cancer
textual definition: A gastrointestinal system cancer that is located_in the stomach.
imported from: doid.owl
has_alternative_id: DOID:10539
has_alternative_id: DOID:10542
has_alternative_id: DOID:10543
has_alternative_id: DOID:4713
database_cross_reference: GARD:7704
database_cross_reference: ICD10CM:C16
database_cross_reference: ICD10CM:C16.2
database_cross_reference: ICD10CM:C16.5
database_cross_reference: ICD10CM:C16.6
database_cross_reference: ICD10CM:C16.9
database_cross_reference: ICD9CM:151
database_cross_reference: ICD9CM:151.4
database_cross_reference: ICD9CM:151.5
database_cross_reference: ICD9CM:151.6
database_cross_reference: ICD9CM:151.9
database_cross_reference: MESH:D013274
database_cross_reference: NCI:C3387
database_cross_reference: NCI:C9331
database_cross_reference: OMIM:137215
database_cross_reference: OMIM:613659
database_cross_reference: SNOMEDCT_US_2018_03_01:93717002
database_cross_reference: SNOMEDCT_US_2018_03_01:93818001
database_cross_reference: SNOMEDCT_US_2018_03_01:93867004
database_cross_reference: SNOMEDCT_US_2018_03_01:94074003
database_cross_reference: UMLS_CUI:C0024623
database_cross_reference: UMLS_CUI:C0038356
database_cross_reference: UMLS_CUI:C0153421
database_cross_reference: UMLS_CUI:C0153422
database_cross_reference: UMLS_CUI:C0153423
has_exact_synonym: Ca body - stomach
has_exact_synonym: Ca lesser curvature - stomach
has_exact_synonym: ca greater curvature of stomach
has_exact_synonym: gastric cancer
has_exact_synonym: gastric neoplasm
has_exact_synonym: malignant neoplasm of body of stomach
has_exact_synonym: malignant neoplasm of lesser curve of stomach
has_exact_synonym: malignant tumor of body of stomach
has_exact_synonym: malignant tumor of greater curve of stomach
has_exact_synonym: malignant tumor of lesser curve of stomach
has_obo_namespace: disease_ontology
id: DOID:10534
in_subset: DO FlyBase slim
in_subset: DO cancer slim
in_subset: NCIthesaurus
in_subset: TopNodes DOcancerslim
comment: OMIM mapping confirmed by DO. [SN].

gout
type: Class
subclass of: arthritis
textual definition: An arthritis that has_material_basis_in uric acid crystal deposits located_in joint.
imported from: doid.owl
has_alternative_id: DOID:14144
database_cross_reference: EFO:0004274
database_cross_reference: ICD10CM:M10
database_cross_reference: ICD10CM:M10.9
database_cross_reference: ICD9CM:274
database_cross_reference: ICD9CM:274.0
database_cross_reference: ICD9CM:274.00
database_cross_reference: ICD9CM:274.9
database_cross_reference: MESH:D006073
database_cross_reference: MESH:D015210
database_cross_reference: NCI:C34650
database_cross_reference: SNOMEDCT_US_2018_03_01:48440001
database_cross_reference: SNOMEDCT_US_2018_03_01:90560007
database_cross_reference: UMLS_CUI:C0003868
database_cross_reference: UMLS_CUI:C0018099
has_exact_synonym: Articular gout
has_exact_synonym: Gouty arthropathy
has_exact_synonym: gouty arthritis
has_obo_namespace: disease_ontology
id: DOID:13189
in_subset: NCIthesaurus

diarrhea
type: Class
subclass of: gastrointestinal system disease
textual definition: A gastrointestinal system disease described as the condition of having frequent loose or liquid bowel movements. Acute diarrhea is a common cause of death in developing countries and the second most common cause of infant deaths worldwide. The loss of fluids through diarrhea can cause severe dehydration which is one cause of death in diarrhea sufferers. Along with water, sufferers also lose dangerous amounts of important salts, electrolytes, and other nutrients. There are at least four types of diarrhea: secretory diarrhea, osmotic diarrhea, motility-related diarrhea, and inflammatory diarrhea.
imported from: doid.owl
has_alternative_id: DOID:0050006
database_cross_reference: ICD9CM:009.2
database_cross_reference: MESH:D003967
database_cross_reference: SNOMEDCT_US_2018_03_01:19213003
database_cross_reference: UMLS_CUI:C0013369
has_obo_namespace: disease_ontology
has_related_synonym: diarrhea of presumed infectious origin
has_related_synonym: diarrhoea
id: DOID:13250
in_subset: GOLD

rheumatic disease
type: Class
subclass of: autoimmune disease of musculoskeletal system
subclass of: connective tissue disease
textual definition: An autoimmune hypersensitivity disease that involves inflammation or pain in the muscles, joints, or fibrous tissue.
imported from: doid.owl
has_obo_namespace: disease_ontology
id: DOID:1575

cancer
type: Class
subclass of: disease
textual definition: A disease of cellular proliferation that is malignant and primary, characterized by uncontrolled cellular proliferation, local cell invasion and metastasis.
imported from: doid.owl
database_cross_reference: ICD10CM:C80
database_cross_reference: ICD10CM:C80.1
database_cross_reference: ICD9CM:199
database_cross_reference: MESH:D009369
database_cross_reference: NCI:C9305
database_cross_reference: SNOMEDCT_US_2018_03_01:38807002
database_cross_reference: UMLS_CUI:C0006826
database_cross_reference: stedman:rlc
has_exact_synonym: malignant neoplasm
has_exact_synonym: malignant tumor
has_exact_synonym: primary cancer
has_obo_namespace: disease_ontology
id: DOID:162
in_subset: DO AGR slim
in_subset: DO FlyBase slim
in_subset: NCIthesaurus
comment: Updating out dated UMLS CUI.

musculoskeletal system disease
type: Class
subclass of: disease of anatomical entity
textual definition: A disease of anatomical entity that occurs in the muscular and/or skeletal system.
imported from: doid.owl
database_cross_reference: MESH:D009140
database_cross_reference: NCI:C107377
database_cross_reference: SNOMEDCT_US_2018_03_01:928000
database_cross_reference: UMLS_CUI:C0026857
has_obo_namespace: disease_ontology
id: DOID:17
in_subset: DO AGR slim
in_subset: DO MGI slim
in_subset: NCIthesaurus

endocrine gland cancer
type: Class
subclass of: organ system cancer
subclass of: endocrine system disease
textual definition: An organ system cancer located_in endocrine system that is characterized by uncontrolled cellular proliferation of the hormone producing glands of the endocrine system.
imported from: doid.owl
has_alternative_id: DOID:10009
database_cross_reference: CSP2005:2009-5861
database_cross_reference: ICD10CM:C75.9
database_cross_reference: ICD9CM:194.9
database_cross_reference: MESH:D004701
database_cross_reference: NCI2004_11_17:C3010
database_cross_reference: NCI2004_11_17:C3575
database_cross_reference: NCI:C3010
database_cross_reference: NCI:C3575
database_cross_reference: SNOMEDCT_US_2018_03_01:93780007
database_cross_reference: UMLS_CUI:C0014132
database_cross_reference: UMLS_CUI:C0153658
has_exact_synonym: Endocrine tumor
has_exact_synonym: endocrine neoplasm
has_exact_synonym: malignant Endocrine tumor
has_exact_synonym: malignant neoplasm of endocrine gland
has_exact_synonym: malignant tumour of endocrine gland
has_exact_synonym: neoplasm of endocrine gland
has_exact_synonym: neoplasm of endocrine system
has_obo_namespace: disease_ontology
id: DOID:170
in_subset: NCIthesaurus
in_subset: TopNodes DOcancerslim

pancreatic cancer
type: Class
subclass of: endocrine gland cancer
textual definition: An endocrine gland cancer located_in the pancreas.
imported from: doid.owl
has_alternative_id: DOID:14356
has_alternative_id: DOID:1797
has_alternative_id: DOID:3588
has_alternative_id: DOID:9859
database_cross_reference: CSP2005:2014-4876
database_cross_reference: GARD:9364
database_cross_reference: ICD10CM:C25.0
database_cross_reference: ICD10CM:C25.1
database_cross_reference: ICD10CM:C25.2
database_cross_reference: ICD9CM:157.0
database_cross_reference: ICD9CM:157.1
database_cross_reference: ICD9CM:157.2
database_cross_reference: ICD9CM:157.8
database_cross_reference: KEGG:05212
database_cross_reference: MESH:D010190
database_cross_reference: MTH:NOCODE
database_cross_reference: NCI2004_11_17:C3305
database_cross_reference: NCI:C3305
database_cross_reference: ORDO:1333
database_cross_reference: ORDO:217074
database_cross_reference: SNOMEDCT_US_2018_03_01:93715005
database_cross_reference: SNOMEDCT_US_2018_03_01:93823001
database_cross_reference: SNOMEDCT_US_2018_03_01:94082003
database_cross_reference: UMLS_CUI:C0030297
database_cross_reference: UMLS_CUI:C0153458
database_cross_reference: UMLS_CUI:C0153459
database_cross_reference: UMLS_CUI:C0153460
database_cross_reference: UMLS_CUI:C0153463
has_exact_synonym: Ca body of pancreas
has_exact_synonym: Ca head of pancreas
has_exact_synonym: Ca tail of pancreas
has_exact_synonym: malignant neoplasm of body of pancreas
has_exact_synonym: malignant neoplasm of head of pancreas
has_exact_synonym: malignant neoplasm of tail of pancreas
has_exact_synonym: pancreas neoplasm
has_exact_synonym: pancreatic neoplasm
has_exact_synonym: pancreatic tumor
has_obo_namespace: disease_ontology
id: DOID:1793
in_subset: DO rare slim
in_subset: NCIthesaurus
in_subset: TopNodes DOcancerslim
comment: Xref MGI.

colon cancer
type: Class
subclass of: large intestine cancer
textual definition: A large intestine cancer that is located_in the colon.
imported from: doid.owl
database_cross_reference: ICD10CM:C18
database_cross_reference: ICD10CM:C18.9
database_cross_reference: ICD9CM:153
database_cross_reference: ICD9CM:153.9
database_cross_reference: MESH:D003110
database_cross_reference: NCI:C9242
database_cross_reference: SNOMEDCT_US_2018_03_01:93761005
database_cross_reference: UMLS_CUI:C0007102
has_obo_namespace: disease_ontology
id: DOID:219
in_subset: DO cancer slim
in_subset: NCIthesaurus
in_subset: TopNodes DOcancerslim

endocrine system disease
type: Class
subclass of: disease of anatomical entity
textual definition: A disease of anatomical entity that is located_in endocrine glands which secretes a type of hormone directly into the bloodstream to regulate the body.
imported from: doid.owl
database_cross_reference: ICD10CM:E34.9
database_cross_reference: ICD9CM:259.9
database_cross_reference: MESH:D004700
database_cross_reference: NCI:C3009
database_cross_reference: SNOMEDCT_US_2018_03_01:67432001
database_cross_reference: UMLS_CUI:C0014130
has_obo_namespace: disease_ontology
id: DOID:28
in_subset: DO AGR slim
in_subset: DO MGI slim
in_subset: NCIthesaurus

immune system disease
type: Class
subclass of: disease of anatomical entity
textual definition: A disease of anatomical entity that is located_in the immune system.
imported from: doid.owl
database_cross_reference: EFO:0000540
database_cross_reference: ICD10CM:D89.9
database_cross_reference: ICD9CM:279
database_cross_reference: ICD9CM:279.9
database_cross_reference: UMLS_CUI:C0041806
has_obo_namespace: disease_ontology
id: DOID:2914
in_subset: DO AGR slim
in_subset: DO FlyBase slim
in_subset: DO MGI slim

carcinoma
type: Class
subclass of: cancer
textual definition: A cell type cancer that has_material_basis_in abnormally proliferating cells derives_from epithelial cells.
imported from: doid.owl
has_alternative_id: DOID:2428
has_alternative_id: DOID:6570
database_cross_reference: CSP2005:2000-5801
database_cross_reference: MESH:D002277
database_cross_reference: MESH:D009375
database_cross_reference: NCI2004_11_17:C6927
database_cross_reference: NCI:C2916
database_cross_reference: NCI:C3709
database_cross_reference: SNOMEDCT_US_2018_03_01:68453008
database_cross_reference: SNOMEDCT_US_2018_03_01:71298006
database_cross_reference: UMLS_CUI:C0007097
database_cross_reference: UMLS_CUI:C0553707
database_cross_reference: UMLS_CUI:C1368683
has_exact_synonym: epithelioma
has_exact_synonym: malignant Epithelioma
has_obo_namespace: disease_ontology
id: DOID:305
in_subset: DO FlyBase slim
in_subset: DO cancer slim
in_subset: NCIthesaurus

chronic obstructive pulmonary disease
type: Class
subclass of: disease of anatomical entity
imported from: doid.owl
has_alternative_id: DOID:11500
has_alternative_id: DOID:6144
database_cross_reference: CSP2005:4004-0004
database_cross_reference: EFO:0000341
database_cross_reference: ICD10CM:J44.9
database_cross_reference: MESH:D029424
database_cross_reference: NCI2004_11_17:C3199
database_cross_reference: NCI:C3199
database_cross_reference: OMIM:606963
database_cross_reference: SNOMEDCT_US_2018_03_01:13645005
database_cross_reference: UMLS_CUI:C0024117
has_exact_synonym: COLD
has_exact_synonym: COPD
has_exact_synonym: chronic obstructive airway disease
has_exact_synonym: chronic obstructive lung disease
has_obo_namespace: disease_ontology
id: DOID:3083
in_subset: NCIthesaurus

hepatobiliary disease
type: Class
subclass of: gastrointestinal system disease
textual definition: A gastrointestinal system disease that is located_in the liver and/or biliary tract.
imported from: doid.owl
database_cross_reference: NCI:C3959
database_cross_reference: UMLS_CUI:C0267792
has_exact_synonym: liver and biliary tract disease
has_obo_namespace: disease_ontology
id: DOID:3118
in_subset: NCIthesaurus

gastrointestinal system cancer
type: Class
subclass of: organ system cancer
subclass of: gastrointestinal system disease
textual definition: An organ system cancer located_in gastrointestinal tract that is manifested in organs of the gastrointestinal system.
imported from: doid.owl
has_alternative_id: DOID:4945
has_alternative_id: DOID:8377
database_cross_reference: ICD10CM:C26.9
database_cross_reference: ICD9CM:239.0
database_cross_reference: MESH:D004067
database_cross_reference: MESH:D005770
database_cross_reference: NCI2004_11_17:C3052
database_cross_reference: NCI2004_11_17:C4890
database_cross_reference: NCI:C3052
database_cross_reference: NCI:C4890
database_cross_reference: SNOMEDCT_US_2018_03_01:93811007
database_cross_reference: UMLS_CUI:C0012243
database_cross_reference: UMLS_CUI:C0017185
database_cross_reference: UMLS_CUI:C0685938
has_exact_synonym: GI tumor
has_exact_synonym: digestive system cancer
has_exact_synonym: gastrointestinal tract cancer
has_obo_namespace: disease_ontology
id: DOID:3119
in_subset: DO FlyBase slim
in_subset: NCIthesaurus
in_subset: TopNodes DOcancerslim

bone inflammation disease
type: Class
subclass of: connective tissue disease
textual definition: A bone disease that results_in inflammation of the located_in bone.
imported from: doid.owl
database_cross_reference: CSP2005:2715-2703
database_cross_reference: MESH:D010000
database_cross_reference: SNOMEDCT_US_2018_03_01:44462005
database_cross_reference: UMLS_CUI:C0029400
has_exact_synonym: Inflammatory disorder of bone
has_exact_synonym: bone inflammatory disease
has_exact_synonym: osteitis
has_obo_namespace: disease_ontology
id: DOID:3342

liver cancer
type: Class
subclass of: hepatobiliary system cancer
subclass of: endocrine gland cancer
subclass of: liver disease
textual definition: A hepatobiliary system cancer that is located_in the liver.
imported from: doid.owl
has_alternative_id: DOID:12300
has_alternative_id: DOID:269
has_alternative_id: DOID:7330
has_alternative_id: DOID:915
has_alternative_id: DOID:919
database_cross_reference: CSP2005:2003-2810
database_cross_reference: ICD10CM:C22.0
database_cross_reference: ICD10CM:C22.9
database_cross_reference: ICD9CM:155.0
database_cross_reference: ICD9CM:155.2
database_cross_reference: ICD9CM_2006:155.0
database_cross_reference: ICD9CM_2006:155.2
database_cross_reference: MESH:D008113
database_cross_reference: NCI2004_11_17:C34803
database_cross_reference: NCI2004_11_17:C7692
database_cross_reference: NCI:C34803
database_cross_reference: NCI:C7692
database_cross_reference: SNOMEDCT_US_2018_03_01:93870000
database_cross_reference: SNOMEDCT_US_2018_03_01:95214007
database_cross_reference: UMLS_CUI:C0023903
database_cross_reference: UMLS_CUI:C0024620
database_cross_reference: UMLS_CUI:C0345904
database_cross_reference: UMLS_CUI:C0854795
has_exact_synonym: Ca liver - primary
has_exact_synonym: Resectable malignant neoplasm of Liver
has_exact_synonym: ca liver - primary
has_exact_synonym: hepatic cancer
has_exact_synonym: hepatic neoplasm
has_exact_synonym: malignant hepato-biliary neoplasm
has_exact_synonym: malignant neoplasm of liver
has_exact_synonym: malignant neoplasm of liver, not specified as primary or secondary
has_exact_synonym: malignant neoplasm of liver, primary
has_exact_synonym: malignant tumor of liver
has_exact_synonym: neoplasm of liver
has_exact_synonym: non-resectable primary hepatic malignant neoplasm
has_exact_synonym: primary liver cancer
has_exact_synonym: primary malignant neoplasm of Liver
has_exact_synonym: primary malignant neoplasm of liver
has_exact_synonym: resectable malignant neoplasm of the liver
has_obo_namespace: disease_ontology
id: DOID:3571
in_subset: NCIthesaurus
in_subset: TopNodes DOcancerslim

disease
type: Class
subclass of: disposition
textual definition: A disease is a disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism.
imported from: doid.owl
database_cross_reference: MESH:D004194
database_cross_reference: NCI:C2991
database_cross_reference: SNOMEDCT_US_2018_03_01:64572001
database_cross_reference: UMLS_CUI:C0012634
has_obo_namespace: disease_ontology
id: DOID:4
in_subset: NCIthesaurus

liver disease
type: Class
subclass of: endocrine system disease
subclass of: hepatobiliary disease
imported from: doid.owl
has_alternative_id: DOID:2164
has_alternative_id: DOID:2165
has_alternative_id: DOID:46
database_cross_reference: ICD10CM:K70-K77
database_cross_reference: ICD10CM:K76.9
database_cross_reference: ICD9CM:573.9
database_cross_reference: MESH:D008107
database_cross_reference: NCI2004_11_17:C3196
database_cross_reference: NCI:C3196
database_cross_reference: SNOMEDCT_US_2018_03_01:62857009
database_cross_reference: UMLS_CUI:C0023895
has_exact_synonym: disorder of liver
has_exact_synonym: hepatic disorder
has_obo_namespace: disease_ontology
id: DOID:409
in_subset: NCIthesaurus

autoimmune hypersensitivity disease
type: Class
subclass of: immune system disease
textual definition: An immune system disease that is an overactive immune response of the body against substances and tissues normally present in the body resulting from an abnormal functioning of the immune system that results in the production of antibodies or T cell directed against the host tissues.
imported from: doid.owl
database_cross_reference: ICD9CM:720
database_cross_reference: OMIM:109100
database_cross_reference: UMLS_CUI:C0003089
database_cross_reference: ls:IEDB
has_exact_synonym: autoimmune disease
has_exact_synonym: hypersensitivity reaction type II disease
has_obo_namespace: disease_ontology
id: DOID:417
comment: Xref MGI.

bile duct cancer
type: Class
subclass of: hepatobiliary system cancer
subclass of: hepatobiliary disease
textual definition: A biliary tract cancer that is located_in the bile duct.
imported from: doid.owl
has_alternative_id: DOID:10019
database_cross_reference: ICD10CM:C24.0
database_cross_reference: ICD9CM:156.1
database_cross_reference: MESH:D001650
database_cross_reference: NCI2004_11_17:C2898
database_cross_reference: NCI2004_11_17:C7483
database_cross_reference: NCI:C2898
database_cross_reference: NCI:C7483
database_cross_reference: SNOMEDCT_US_2018_03_01:93790004
database_cross_reference: UMLS_CUI:C0005396
database_cross_reference: UMLS_CUI:C0153453
has_exact_synonym: Ca extrahepatic bile ducts
has_exact_synonym: bile duct tumor
has_exact_synonym: malignant neoplasm of the extrahepatic bile duct
has_obo_namespace: disease_ontology
id: DOID:4606
in_subset: NCIthesaurus
in_subset: TopNodes DOcancerslim

esophageal cancer
type: Class
subclass of: gastrointestinal system cancer
textual definition: A gastrointestinal system cancer that is located_in the esophagus.
imported from: doid.owl
has_alternative_id: DOID:10291
has_alternative_id: DOID:10292
has_alternative_id: DOID:10448
has_alternative_id: DOID:1102
has_alternative_id: DOID:1104
database_cross_reference: GARD:6383
database_cross_reference: ICD10CM:C15.3
database_cross_reference: ICD10CM:C15.4
database_cross_reference: ICD10CM:C15.5
database_cross_reference: ICD9CM:150.2
database_cross_reference: ICD9CM:150.3
database_cross_reference: ICD9CM:150.4
database_cross_reference: ICD9CM:150.5
database_cross_reference: ICD9CM:150.8
database_cross_reference: MESH:D004938
database_cross_reference: MTHICD9_2006:150.3
database_cross_reference: MTHICD9_2006:150.5
database_cross_reference: NCI2004_11_17:C3533
database_cross_reference: NCI2004_11_17:C3534
database_cross_reference: NCI2004_11_17:C3535
database_cross_reference: NCI2004_11_17:C4764
database_cross_reference: NCI:C3028
database_cross_reference: NCI:C3533
database_cross_reference: NCI:C3534
database_cross_reference: NCI:C3535
database_cross_reference: NCI:C4764
database_cross_reference: OMIM:133239
database_cross_reference: SNOMEDCT_US_2018_03_01:93656003
database_cross_reference: SNOMEDCT_US_2018_03_01:93877002
database_cross_reference: SNOMEDCT_US_2018_03_01:93895004
database_cross_reference: SNOMEDCT_US_2018_03_01:94119000
database_cross_reference: UMLS_CUI:C0014859
database_cross_reference: UMLS_CUI:C0153413
database_cross_reference: UMLS_CUI:C0153414
database_cross_reference: UMLS_CUI:C0153415
database_cross_reference: UMLS_CUI:C0153416
database_cross_reference: UMLS_CUI:C0496775
has_exact_synonym: Ca lower third oesophagus
has_exact_synonym: Ca middle third oesophagus
has_exact_synonym: esophagus cancer
has_exact_synonym: malignant neoplasm of distal third of esophagus
has_exact_synonym: malignant neoplasm of lower third of oesophagus
has_exact_synonym: malignant neoplasm of middle third of oesophagus
has_exact_synonym: malignant neoplasm of proximal third of esophagus
has_exact_synonym: malignant neoplasm of upper third esophagus
has_exact_synonym: malignant tumor of Distal Third of esophagus
has_exact_synonym: malignant tumor of Proximal Third of esophagus
has_exact_synonym: malignant tumor of abdominal esophagus
has_exact_synonym: malignant tumor of the middle Third of the esophagus
has_obo_namespace: disease_ontology
id: DOID:5041
in_subset: NCIthesaurus
in_subset: TopNodes DOcancerslim

intestinal disease
type: Class
subclass of: gastrointestinal system disease
textual definition: A gastrointestinal system disease that is located_in the intestine.
imported from: doid.owl
has_alternative_id: DOID:10759
has_alternative_id: DOID:11222
has_alternative_id: DOID:11789
has_alternative_id: DOID:8531
has_alternative_id: DOID:8558
has_alternative_id: DOID:8591
database_cross_reference: ICD10CM:K63.9
database_cross_reference: ICD9CM:569.9
database_cross_reference: MESH:D007410
database_cross_reference: NCI:C26801
database_cross_reference: SNOMEDCT_US_2018_03_01:85919009
database_cross_reference: UMLS_CUI:C0021831
has_obo_namespace: disease_ontology
id: DOID:5295
in_subset: NCIthesaurus

stomach carcinoma
type: Class
subclass of: stomach cancer
subclass of: carcinoma
textual definition: A stomach cancer that is located_in the stomach.
imported from: doid.owl
database_cross_reference: EFO:0000178
database_cross_reference: NCI2004_11_17:C4911
database_cross_reference: NCI:C4911
database_cross_reference: UMLS_CUI:C0699791
has_exact_synonym: cancer of the stomach
has_exact_synonym: carcinoma of stomach
has_exact_synonym: gastric carcinoma
has_obo_namespace: disease_ontology
id: DOID:5517
in_subset: NCIthesaurus

large intestine cancer
type: Class
subclass of: intestinal cancer
textual definition: An intestinal cancer that effects the long, tube-like organ that is connected to the small intestine at one end and the anus at the other.
imported from: doid.owl
has_alternative_id: DOID:1994
has_alternative_id: DOID:1997
database_cross_reference: ICD10CM:C18.9
database_cross_reference: MESH:D015179
database_cross_reference: NCI:C2955
database_cross_reference: NCI:C4978
database_cross_reference: NCI:C5105
database_cross_reference: SNOMEDCT_US_2018_03_01:93854002
database_cross_reference: UMLS_CUI:C0009402
database_cross_reference: UMLS_CUI:C0346629
database_cross_reference: UMLS_CUI:C1319315
has_obo_namespace: disease_ontology
id: DOID:5672
in_subset: NCIthesaurus
in_subset: TopNodes DOcancerslim

reactive arthritis
type: Class
subclass of: arthritis
textual definition: An arthritis that is an autoimmune disease which develops due to an infection located elsewhere in the body. [database_cross_reference: url:http://emedicine.medscape.com/article/331347-overview][database_cross_reference: url:http://en.wikipedia.org/wiki/Reactive_arthritis]
alternative term: Fiessinger Leroy Reiter syndrome; Post-bacterial arthropathy; postdysenteric arthropathy; Reiter's disease; Reactive arthritis; Reiter disease

connective tissue disease
type: Class
subclass of: musculoskeletal system disease
textual definition: A musculoskeletal system disease that affects tissues such as skin, tendons, and cartilage.
imported from: doid.owl
database_cross_reference: CSP2005:0729-7208
database_cross_reference: MESH:D003240
database_cross_reference: NCI:C26729
database_cross_reference: UMLS_CUI:C0009782
has_exact_synonym: connective tissue disorder
has_exact_synonym: disorder of connective tissue
has_obo_namespace: disease_ontology
id: DOID:65
in_subset: NCIthesaurus

juvenile rheumatoid arthritis
type: Class
subclass of: rheumatoid arthritis
textual definition: A rheumatoid arthritis that involves an autoimmune disease onset in children under 16 which attacks the healthy cells and tissue of located_in joint.
imported from: doid.owl
has_alternative_id: DOID:10129
has_alternative_id: DOID:1264
has_alternative_id: DOID:675
database_cross_reference: ICD10CM:M08.4
database_cross_reference: ICD10CM:M08.40
database_cross_reference: ICD9CM:714.3
database_cross_reference: ICD9CM:714.31
database_cross_reference: ICD9CM:714.32
database_cross_reference: ICD9CM:714.33
database_cross_reference: NCI:C26979
database_cross_reference: NCI:C61279
database_cross_reference: OMIM:604302
database_cross_reference: ORDO:92
database_cross_reference: SNOMEDCT_US_2018_03_01:74391003
database_cross_reference: SNOMEDCT_US_2018_03_01:7441009
database_cross_reference: SNOMEDCT_US_2018_03_01:75822003
database_cross_reference: SNOMEDCT_US_2018_03_01:83793004
database_cross_reference: UMLS_CUI:C0157916
database_cross_reference: UMLS_CUI:C0157917
database_cross_reference: UMLS_CUI:C0157918
database_cross_reference: UMLS_CUI:C0409667
has_exact_synonym: Pauciarticular onset juvenile chronic arthritis
has_exact_synonym: acute juvenile rheumatoid arthritis
has_exact_synonym: juvenile chronic polyarthritis
has_exact_synonym: juvenile idiopathic arthritis
has_exact_synonym: monarticular juvenile rheumatoid arthritis
has_exact_synonym: pauciarticular juvenile arthritis
has_exact_synonym: systemic juvenile rheumatoid arthritis
has_obo_namespace: disease_ontology
id: DOID:676
in_subset: DO rare slim
in_subset: NCIthesaurus
comment: Xref MGI.

hepatocellular carcinoma
type: Class
subclass of: liver carcinoma
textual definition: A liver carcinoma that has_material_basis_in undifferentiated hepatocytes.
imported from: doid.owl
has_alternative_id: DOID:5005
database_cross_reference: EFO:0000182
database_cross_reference: NCI2004_11_17:C3099
database_cross_reference: NCI2004_11_17:C7956
database_cross_reference: NCI:C7956
database_cross_reference: OMIM:114550
database_cross_reference: UMLS_CUI:C0279607
has_exact_synonym: HCC
has_exact_synonym: Hepatoma
has_exact_synonym: adult Hepatoma
has_exact_synonym: adult primary hepatocellular carcinoma
has_obo_namespace: disease_ontology
id: DOID:684
in_subset: DO cancer slim
in_subset: NCIthesaurus
comment: OMIM mapping confirmed by DO. [SN].

liver carcinoma
type: Class
subclass of: carcinoma
subclass of: liver cancer
textual definition: A liver cancer that has_material_basis_in epithelial cells.
imported from: doid.owl
database_cross_reference: NCI2004_11_17:C7927
database_cross_reference: NCI:C7927
database_cross_reference: UMLS_CUI:C0279000
has_exact_synonym: Liver and Intrahepatic bile duct carcinoma
has_obo_namespace: disease_ontology
id: DOID:686
in_subset: NCIthesaurus

disease of anatomical entity
type: Class
subclass of: disease
textual definition: A disease that manifests in a defined anatomical structure.
imported from: doid.owl
has_alternative_id: DOID:1
has_alternative_id: DOID:2
has_alternative_id: DOID:5
has_alternative_id: DOID:71
has_alternative_id: DOID:72
has_alternative_id: DOID:8
has_obo_namespace: disease_ontology
id: DOID:7

ankylosing spondylitis
type: Class
subclass of: rheumatic disease
subclass of: bone inflammation disease
textual definition: A bone inflammation disease that results_in inflammation in the joints of the spine and pelvis. The disease has_symptom pain, has_symptom stiffness in the spine, has_symptom stiffness in the neck, has_symptom stiffness in the hips, has_symptom stiffness in the jaw and has_symptom stiffness in the rib cage.
imported from: doid.owl
database_cross_reference: EFO:0003898
database_cross_reference: GARD:9518
database_cross_reference: ICD10CM:M45
database_cross_reference: ICD9CM:720.0
database_cross_reference: MESH:D013167
database_cross_reference: NCI:C84564
database_cross_reference: ORDO:825
database_cross_reference: SNOMEDCT_US_2018_03_01:9631008
database_cross_reference: UMLS_CUI:C0038013
database_cross_reference: ls:IEDB
has_exact_synonym: Bekhterev syndrome
has_exact_synonym: Bekhterev's disease
has_exact_synonym: Marie-Strumpell disease
has_obo_namespace: disease_ontology
id: DOID:7147
in_subset: DO rare slim
in_subset: NCIthesaurus

rheumatoid arthritis
type: Class
subclass of: arthritis
textual definition: An arthritis that is an autoimmune disease which attacks healthy cells and tissue located_in joint.
imported from: doid.owl
database_cross_reference: EFO:0000685
database_cross_reference: ICD10CM:M06.9
database_cross_reference: ICD9CM:714.0
database_cross_reference: KEGG:05323
database_cross_reference: MESH:D001172
database_cross_reference: MTHICD9_2006:714.0
database_cross_reference: NCI2004_11_17:C27206
database_cross_reference: NCI:C2884
database_cross_reference: OMIM:180300
database_cross_reference: SNOMEDCT_US_2018_03_01:69896004
database_cross_reference: UMLS_CUI:C0003873
has_exact_synonym: Arthritis or polyarthritis, rheumatic
has_exact_synonym: atrophic Arthritis
has_obo_namespace: disease_ontology
id: DOID:7148
in_subset: NCIthesaurus
comment: OMIM mapping confirmed by DO. [SN].

gastrointestinal system disease
type: Class
subclass of: disease of anatomical entity
textual definition: A disease of anatomical entity that is located_in the gastrointestinal tract.
imported from: doid.owl
has_alternative_id: DOID:27
has_alternative_id: DOID:944
database_cross_reference: CSP2005:1248-3545
database_cross_reference: ICD10CM:K92.9
database_cross_reference: ICD9CM:520-579.99
database_cross_reference: MESH:D004066
database_cross_reference: SNOMEDCT_US_2018_03_01:53619000
database_cross_reference: UMLS_CUI:C0012242
has_exact_synonym: GIT disease
has_exact_synonym: Gastroenteropathy
has_exact_synonym: alimentary system disease
has_exact_synonym: digestive system disorder
has_exact_synonym: gastrointestinal disease
has_exact_synonym: gastrointestinal disorder
has_obo_namespace: disease_ontology
id: DOID:77
in_subset: DO AGR slim
in_subset: DO MGI slim

arthritis
type: Class
subclass of: rheumatic disease
subclass of: bone inflammation disease
textual definition: A bone inflammation disease that involves a response to irritation or injury, characterized by joint pain, swelling, stiffness located_in joint and/or redness located_in skin over the joint.
imported from: doid.owl
database_cross_reference: ICD10CM:M19.90
database_cross_reference: MESH:D001168
database_cross_reference: NCI:C2883
database_cross_reference: SNOMEDCT_US_2018_03_01:3723001
database_cross_reference: UMLS_CUI:C0003864
database_cross_reference: ls:IEDB
has_exact_synonym: Inflammatory disorder of joint
has_obo_namespace: disease_ontology
id: DOID:848
in_subset: NCIthesaurus

psoriatic arthritis
type: Class
subclass of: arthritis
textual definition: A syndrome that occurs in humans with psoriasis who also experience symptoms similar to arthritis.
imported from: doid.owl
database_cross_reference: EFO:0003778
database_cross_reference: ICD10CM:L40.5
database_cross_reference: ICD10CM:L40.50
database_cross_reference: ICD9CM:696.0
database_cross_reference: MESH:D015535
database_cross_reference: NCI:C61277
database_cross_reference: SNOMEDCT_US_2018_03_01:33339001
database_cross_reference: UMLS_CUI:C0003872
has_exact_synonym: arthritis psoriatica
has_exact_synonym: arthropathic psoriasis
has_obo_namespace: disease_ontology
has_related_synonym: psoriatic arthropathy
id: DOID:9008
in_subset: NCIthesaurus

systemic lupus erythematosus
type: Class
subclass of: rheumatic disease
textual definition: A lupus erythematosus that is an inflammation of connective tissue marked by skin rashes, joint pain and swelling, inflammation of the kidneys and inflammation of the tissue surrounding the heart.
imported from: doid.owl
database_cross_reference: CSP2005:0729-7721
database_cross_reference: EFO:0002690
database_cross_reference: GARD:10253
database_cross_reference: ICD10CM:M32
database_cross_reference: ICD10CM:M32.9
database_cross_reference: ICD9CM:710.0
database_cross_reference: KEGG:05322
database_cross_reference: MESH:D008180
database_cross_reference: MTH:U002054
database_cross_reference: NCI2004_11_17:C3201
database_cross_reference: NCI:C3201
database_cross_reference: OMIM:152700
database_cross_reference: OMIM:300809
database_cross_reference: OMIM:605480
database_cross_reference: OMIM:608437
database_cross_reference: OMIM:609903
database_cross_reference: OMIM:609939
database_cross_reference: OMIM:610065
database_cross_reference: OMIM:610066
database_cross_reference: OMIM:612254
database_cross_reference: OMIM:612378
database_cross_reference: OMIM:613145
database_cross_reference: OMIM:614420
database_cross_reference: ORDO:536
database_cross_reference: SNOMEDCT_US_2018_03_01:55464009
database_cross_reference: UMLS_CUI:C0024141
database_cross_reference: ls:IEDB
has_exact_synonym: Lupus Erythematosus, systemic
has_exact_synonym: SLE - Lupus Erythematosus, systemic
has_exact_synonym: disseminated lupus erythematosus
has_obo_namespace: disease_ontology
id: DOID:9074
in_subset: DO rare slim
in_subset: NCIthesaurus
comment: Xref MGI.

colorectal cancer
type: Class
subclass of: large intestine cancer
textual definition: A large intestine cancer that is located_in the colon and/or located_in the rectum.
imported from: doid.owl
database_cross_reference: KEGG:05210
database_cross_reference: MESH:D015179
database_cross_reference: OMIM:114500
database_cross_reference: OMIM:611469
database_cross_reference: OMIM:612230
database_cross_reference: OMIM:612231
database_cross_reference: OMIM:612232
database_cross_reference: OMIM:612589
database_cross_reference: OMIM:612590
database_cross_reference: OMIM:612592
database_cross_reference: UMLS_CUI:C1527249
has_obo_namespace: disease_ontology
id: DOID:9256
in_subset: DO FlyBase slim
comment: Xref MGI. OMIM mapping confirmed by DO. [SN].

drug product
type: Class
subclass of: material entity
textual definition: a material entity (1) containing at least one scattered molecular aggregate as part that is the bearer of an active ingredient role and (2) that is itself the bearer of a clinical drug role
definition editor: William Hogan
imported from: dron.owl
creator: William Hogan

biome
type: Class
subclass of: ecosystem
textual definition: A biome is an ecosystem to which resident ecological communities have evolved adaptations.
imported from: envo.owl
database_cross_reference: EcoLexicon:biome
database_cross_reference: LTER:173
has_exact_synonym: major habitat type
has_related_synonym: EcosytemType
comment: There has been some concern raised (see Issue #143) about the usefulness of the assertion that organisms have evolved within a given biome. They may have evolved adaptations elsewhere and demonstrating one or the other is often not feasible. Consider relabelling to "environmental system determined by an ecological community" or similar.

environmental material
type: Class
subclass of: material entity
editor preferred label: environmental material
textual definition: A portion of environmental material is a fiat object which forms the medium or part of the medium of an environmental system.
imported from: envo.owl
imported from: obi.owl

environmental system
type: Class
subclass of: RO_0002577
textual definition: A system which has the disposition to environ one or more material entities.
imported from: envo.owl
creation_date: 2013-09-23T16:04:08Z
database_cross_reference: EcoLexicon:environment
has_exact_synonym: environment
comment: In ENVO's alignment with the Basic Formal Ontology, this class is being considered as a subclass of a proposed BFO class "system". The relation "environed_by" is also under development. Roughly, a system which includes a material entity (at least partially) within its site and causally influences that entity may be considered to environ it. Following the completion of this alignment, this class' definition and the definitions of its subclasses will be revised.

habitat
type: Class
subclass of: ecosystem
textual definition: An environmental system which can sustain and allow the growth of an ecological population.
imported from: envo.owl
database_cross_reference: EcoLexicon:habitat
database_cross_reference: LTER:238
database_cross_reference: SWEETRealm:Habitat
database_cross_reference: https://en.wikipedia.org/wiki/Habitat
comment: A habitat's specificity to an ecological population differentiates it from other environment classes.

ecosystem
type: Class
subclass of: environmental system
textual definition: An environmental system which includes both living and non-living components.
imported from: envo.owl
comment: This class will be primarily filled by inference, any environmental system which necessarily includes living parts should be autoclassified here.

biological_process
type: Class
subclass of: process
editor preferred label: biological_process
textual definition: A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.
imported from: go.owl
imported from: obi.owl
created_by: janelomax
creation_date: 2012-09-19T15:05:24Z
has_alternative_id: GO:0000004
has_alternative_id: GO:0007582
has_alternative_id: GO:0044699
database_cross_reference: Wikipedia:Biological_process
has_exact_synonym: biological process
has_exact_synonym: physiological process
has_obo_namespace: biological_process
has_related_synonym: single organism process
has_related_synonym: single-organism process
id: GO:0008150
in_subset: goslim aspergillus
in_subset: goslim candida
in_subset: goslim chembl
in_subset: goslim generic
in_subset: goslim metagenomics
in_subset: goslim pir
in_subset: goslim plant
in_subset: goslim pombe
in_subset: goslim yeast
comment: Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code "no data" (ND), is used to indicate this.

gene expression
type: Class
subclass of: biological_process
editor preferred label: gene expression
textual definition: The process in which a gene's sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
imported from: go.owl
imported from: obi.owl

interspecies interaction between organisms
type: Class
subclass of: multi-organism process
textual definition: Any process in which an organism has an effect on an organism of a different species.
imported from: go.owl
has_exact_synonym: interaction with another species
has_exact_synonym: interspecies interaction
has_exact_synonym: interspecies interaction with other organisms
has_obo_namespace: biological_process
id: GO:0044419
in_subset: goslim candida
in_subset: goslim pir

interaction with host
type: Class
subclass of: interspecies interaction between organisms
textual definition: An interaction between two organisms living together in more or less intimate association. The term host is used for the larger (macro) of the two members of a symbiosis; the various forms of symbiosis include parasitism, commensalism and mutualism.
imported from: go.owl
has_obo_namespace: biological_process
id: GO:0051701

multi-organism process
type: Class
subclass of: biological_process
textual definition: A biological process which involves another organism of the same or different species.
imported from: go.owl
has_alternative_id: GO:0051706
has_exact_synonym: interaction between organisms
has_exact_synonym: physiological interaction between organisms
has_exact_synonym: physiological interaction with other organism
has_obo_namespace: biological_process
id: GO:0051704
in_subset: goslim pir

Phenotypic abnormality
type: Class
subclass of: UPHENO_0001002
textual definition: A phenotypic abnormality.
imported from: hp.owl
database_cross_reference: UMLS:C4021819
has_exact_synonym: Organ abnormality
has_obo_namespace: human_phenotype
id: HP:0000118
comment: This is the root of the phenotypic abnormality subontology of the HPO.

Obesity
type: Class
subclass of: Phenotypic abnormality
textual definition: Accumulation of substantial excess body fat.
imported from: hp.owl
database_cross_reference: MSH:D009765
database_cross_reference: SNOMEDCT_US:414915002
database_cross_reference: SNOMEDCT_US:414916001
database_cross_reference: UMLS:C0028754
has_exact_synonym: Having too much body fat
has_exact_synonym: Obesity
has_obo_namespace: human_phenotype
id: HP:0001513

Diarrhea
type: Class
subclass of: Phenotypic abnormality
textual definition: Abnormally increased frequency of loose or watery bowel movements.
imported from: hp.owl
database_cross_reference: MSH:D003967
database_cross_reference: SNOMEDCT_US:267060006
database_cross_reference: SNOMEDCT_US:62315008
database_cross_reference: UMLS:C0011991
has_exact_synonym: Diarrhea
has_exact_synonym: Diarrhoea
has_exact_synonym: Watery stool
has_obo_namespace: human_phenotype
id: HP:0002014

Chronic diarrhea
type: Class
subclass of: Diarrhea
textual definition: The presence of chronic diarrhea, which is usually taken to mean diarrhea that has persisted for over 4 weeks.
imported from: hp.owl
database_cross_reference: SNOMEDCT_US:236071009
database_cross_reference: UMLS:C0401151
has_exact_synonym: Chronic diarrhea
has_obo_namespace: human_phenotype
has_related_synonym: Diarrhea, recurrent
has_related_synonym: Recurrent diarrhea
id: HP:0002028

measurement unit label
type: Class
subclass of: datum label
editor preferred label: measurement unit label
example of usage: Examples of measurement unit labels are liters, inches, weight per volume.
has curation status: IAO_0000125
textual definition: A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure.
editor note: 2009-03-16: provenance: a term measurement unit was proposed for OBI (OBI_0000176) , edited by Chris Stoeckert and Cristian Cocos, and subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definition of this, different, term.
editor note: 2009-03-16: review of this term done during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI.
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Melanie Courtot
imported from: obi.owl

objective specification
type: Class
subclass of: directive information entity
editor preferred label: objective specification
example of usage: In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction.
has curation status: IAO_0000122
textual definition: a directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved.
editor note: 2009-03-16: original definition when imported from OBI read: "objective is an non realizable information entity which can serve as that proper part of a plan towards which the realization of the plan is directed."
editor note: 2014-03-31: In the example of usage ("In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction") there is a protocol which is the ChIP assay protocol. In addition to being concretized on paper, the protocol can be concretized as a realizable entity, such as a plan that inheres in a person. The objective specification is the part that says that some protein and DNA interactions are identified. This is a specification of a process endpoint: the boundary in the process before which they are not identified and after which they are. During the realization of the plan, the goal is to get to the point of having the interactions, and participants in the realization of the plan try to do that.
editor note: Answers the question, why did you do this experiment?
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Barry Smith
definition editor: PERSON: Bjoern Peters
definition editor: PERSON: Jennifer Fostel
alternative term: goal specification
definition source: OBI Plan and Planned Process/Roles Branch
definition source: OBI_0000217
imported from: obi.owl

action specification
type: Class
subclass of: directive information entity
example of usage: Pour the contents of flask 1 into flask 2
has curation status: IAO_0000122
textual definition: a directive information entity that describes an action the bearer will take
definition editor: Alan Ruttenberg
definition source: OBI Plan and Planned Process branch
imported from: obi.owl

datum label
type: Class
subclass of: information content entity
editor preferred label: datum label
has curation status: IAO_0000123
textual definition: A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label
editor note: http://www.golovchenko.org/cgi-bin/wnsearch#4n
definition editor: GROUP: IAO
curator notes: 9/22/11 BP: changed the rdfs:label for this class from 'label' to 'datum label' to convey that this class is not intended to cover all kinds of labels (stickers, radiolabels, etc.), and not even all kind of textual labels, but rather the kind of labels occuring in a datum.
imported from: obi.owl

data item
type: Class
subclass of: information content entity
editor preferred label: data item
example of usage: Data items include counts of things, analyte concentrations, and statistical summaries.
has curation status: IAO_0000125
textual definition: a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements.
editor note: 2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers.
editor note: 2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum.
editor note: 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym.
editor note: 2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/
editor note: JAR: datum -- well, this will be very tricky to define, but maybe some information-like stuff that might be put into a computer and that is meant, by someone, to denote and/or to be interpreted by some process... I would include lists, tables, sentences... I think I might defer to Barry, or to Brian Cantwell Smith JAR: A data item is an approximately justified approximately true approximate belief
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Chris Stoeckert
definition editor: PERSON: Jonathan Rees
alternative term: data
imported from: obi.owl

information content entity
type: Class
subclass of: generically dependent continuant
subclass of: Restriction
  on property: is about
  some values from: entity
editor preferred label: information content entity
example of usage: Examples of information content entites include journal articles, data, graphical layouts, and graphs.
has curation status: IAO_0000122
textual definition: A generically dependent continuant that is about some thing.
editor note: 2014-03-10: The use of "thing" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ).
editor note: information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity.
definition editor: PERSON: Chris Stoeckert
definition source: OBI_0000142
imported from: obi.owl

scalar measurement datum
type: Class
subclass of: measurement datum
subclass of: Restriction
  on property: has value specification
  some values from: scalar value specification
subclass of: Restriction
  on property: has measurement unit label
  min cardinality: 1
subclass of: Restriction
  on property: has measurement value
  min cardinality: 1
example of usage: 10 feet. 3 ml.
has curation status: IAO_0000120
textual definition: a scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label.
editor note: 2009-03-16: we decided to keep datum singular in scalar measurement datum, as in this case we explicitly refer to the singular form
editor note: Would write this as: has_part some 'measurement unit label' and has_part some numeral and has_part exactly 2, except for the fact that this won't let us take advantage of OWL reasoning over the numbers. Instead use has measurment value property to represent the same. Use has measurement unit label (subproperty of has_part) so we can easily say that there is only one of them.
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Melanie Courtot
imported from: obi.owl

directive information entity
type: Class
subclass of: information content entity
subclass of: Restriction
  on property: is about
  some values from: realizable entity
has curation status: IAO_0000122
textual definition: An information content entity whose concretizations indicate to their bearer how to realize them in a process.
editor note: 2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was "is the specification of a process that can be concretized and realized by an actor" with alternative term "instruction".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term.
editor note: 2013-05-30 Alan Ruttenberg: What differentiates a directive information entity from an information concretization is that it can have concretizations that are either qualities or realizable entities. The concretizations that are realizable entities are created when an individual chooses to take up the direction, i.e. has the intention to (try to) realize it.
editor note: 8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO
editor note: Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Bjoern Peters
imported from: obi.owl

curation status specification
type: Class
equivalent class: Class
  one of: IAO_0000002
  one of: IAO_0000120
  one of: IAO_0000121
  one of: IAO_0000122
  one of: IAO_0000123
  one of: IAO_0000124
  one of: IAO_0000125
  one of: IAO_0000423
  one of: IAO_0000428
subclass of: data about an ontology part
editor preferred label: curation status specification
has curation status: IAO_0000125
textual definition: The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.
editor note: Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)
definition editor: PERSON:Bill Bug
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
definition source: OBI_0000266
imported from: obi.owl

data about an ontology part
type: Class
subclass of: data item
textual definition: data about an ontology part is a data item about a part of an ontology, for example a term
definition editor: Person:Alan Ruttenberg
imported from: obi.owl

plan specification
type: Class
subclass of: directive information entity
subclass of: Restriction
  on property: has part
  some values from: objective specification
subclass of: Restriction
  on property: has part
  some values from: action specification
editor preferred label: plan specification
example of usage: PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice.
has curation status: IAO_0000122
textual definition: A directive information entity with action specifications and objective specifications as parts that, when concretized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified.
editor note: 2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was " a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term.
editor note: 2014-03-31: A plan specification can have other parts, such as conditional specifications.
editor note: Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved
definition editor: Alan Ruttenberg
definition source: OBI Plan and Planned Process branch
definition source: OBI_0000344
imported from: obi.owl
comment: 2/3/2009 Comment from OBI review. Action specification not well enough specified. Conditional specification not well enough specified. Question whether all plan specifications have objective specifications. Request that IAO either clarify these or change definitions not to use them

measurement datum
type: Class
subclass of: data item
subclass of: Restriction
  on property: has value specification
  some values from: value specification
editor preferred label: measurement datum
example of usage: Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}.
has curation status: IAO_0000125
textual definition: A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device.
editor note: 2/2/2009 is_specified_output of some assay?
definition editor: person:Chris Stoeckert
definition source: OBI_0000305
definition source: group:OBI
imported from: obi.owl

time measurement datum
type: Class
subclass of: scalar measurement datum
subclass of: Class
  intersection of: Restriction
    on property: has measurement unit label
    all values from: UO_0000003
  intersection of: Restriction
    on property: is duration of
    all values from: process
has curation status: IAO_0000123
textual definition: A scalar measurement datum that is the result of measuring a temporal interval
editor note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
definition editor: Person:Alan Ruttenberg
imported from: obi.owl

infection
type: Class
subclass of: material entity
editor preferred label: infection
textual definition: A part of an extended organism that itself has as part a population of one or more infectious agents and that (1) exists as a result of processes initiated by members of the infectious agent population and is (2) clinically abnormal in virtue of the presence of this infectious agent population, or (3) has a disposition to bring clinical abnormality to immunocompetent organisms of the same Species as the host (the organism corresponding to the extended organism) through transmission of a member or offspring of a member of the infectious agent population.
imported from: ido.owl
imported from: obi.owl

interaction
type: Class
subclass of: process
textual definition: Interaction is a processual entity that has two or more participants (i.e., interactors) that have an effect upon one another.
definition editor: YH, ZX
imported from: ino.owl
has literature mining keywords: interact, interacted, interacting, interaction, interaction, interactor, interactors, interacts, participates; plays a role, contribute, contributed, contributes, contributing, engagement, engagements, engages, engaging, involve, involved, involves, involving, act, acted, acting, acts

enthesitis-related juvenile idiopathic arthritis
type: Class
subclass of: juvenile rheumatoid arthritis
textual definition: Enthesitis-related juvenile idiopathic arthritis is a subtype of juvenile idiopathic arthritis that is characterized by both arthritis and inflammation of an enthesitis site (the point at which a ligament, tendon, or joint capsule attaches to the bone). Signs and symptoms generally develop in late childhood or early adolescence and include pain, tenderness, and swelling in joints and at the enthesis. The knee and the back of the ankle (at the Achilles tendon) are the most commonly affected parts of the body. The underlying cause of enthesitis-related juvenile idiopathic arthritis is currently unknown (idiopathic). It is very rare for more than one member of a family to have juvenile arthritis; however, research suggests that having a family member with juvenile arthritis or any autoimmune disease may increase the risk of having juvenile arthritis, in general. Treatment usually involves different types of medications to help manage symptoms and/or physical therapy .
imported from: mondo.owl
database_cross_reference: GARD:0010969
database_cross_reference: ICD10:M08.8
database_cross_reference: NCIT:C119024
database_cross_reference: Orphanet:85438
database_cross_reference: SCTID:410801005
has_exact_synonym: enthesitis-related JIA
has_exact_synonym: era
has_related_synonym: enthesitis related arthritis, juvenile
has_related_synonym: enthesitis-related arthritis
has_related_synonym: juvenile enthesitis-related arthritis
has_related_synonym: juvenile spondylarthropathy
id: MONDO:0019437
in_subset: gard rare
in_subset: ordo malformation syndrome

Coprobacillus
type: Class
subclass of: Erysipelotrichaceae
editor preferred label: Coprobacillus
imported from: ncbitaxon.owl

Mus musculus
type: Class
subclass of: Murinae
editor preferred label: Mus musculus
alternative term: house mouse
alternative term: mouse
imported from: ncbitaxon.owl

Rattus
type: Class
subclass of: Murinae
editor preferred label: Rattus
alternative term: rat
alternative term: rats
imported from: ncbitaxon.owl

Rattus norvegicus
type: Class
subclass of: Rattus
editor preferred label: Rattus norvegicus
alternative term: Norway rat
alternative term: Rattus sp. strain Wistar
alternative term: brown rat
alternative term: rat
alternative term: rats
imported from: ncbitaxon.owl

Capnocytophaga
type: Class
subclass of: Bacteroidetes
editor preferred label: Capnocytophaga
imported from: ncbitaxon.owl

Capnocytophaga gingivalis
type: Class
subclass of: Capnocytophaga

Beggiatoa
type: Class
subclass of: Gammaproteobacteria
editor preferred label: Beggiatoa
imported from: ncbitaxon.owl

Collinsella
type: Class
subclass of: Coriobacteriaceae
editor preferred label: Collinsella
imported from: ncbitaxon.owl

Solobacterium moorei
type: Class
subclass of: Solobacterium
editor preferred label: Solobacterium moorei
imported from: ncbitaxon.owl

Viruses
type: Class
subclass of: OHMI_0000460
subclass of: Restriction
  on property: has quality
  some values from: OHMI_0000462
editor preferred label: Viruses
imported from: ncbitaxon.owl
imported from: obi.owl

Hepatitis B virus
type: Class
subclass of: Viruses
editor preferred label: Hepatitis B virus
imported from: ncbitaxon.owl

Leptotrichia sp.
type: Class
subclass of: Leptotrichia
subclass of: Restriction
  on property: microbe susceptibly expanded in oral cavity of human with disease
  some values from: rheumatoid arthritis
editor preferred label: Leptotrichia sp.
imported from: ncbitaxon.owl

Badula fragilis
type: Class
subclass of: Pentapetalae
editor preferred label: Badula fragilis
imported from: ncbitaxon.owl

Anaerovorax
type: Class
subclass of: Clostridiales Family XIII. Incertae Sedis
editor preferred label: Anaerovorax
imported from: ncbitaxon.owl

Hepacivirus C
type: Class
subclass of: Viruses
editor preferred label: Hepacivirus C
imported from: ncbitaxon.owl

Leptotrichiaceae
type: Class
subclass of: Fusobacteriales
editor preferred label: Leptotrichiaceae
imported from: ncbitaxon.owl

Fusicatenibacter saccharivorans
type: Class
subclass of: Lachnospiraceae
editor preferred label: Fusicatenibacter saccharivorans
imported from: ncbitaxon.owl

Parasporobacterium
type: Class
subclass of: Lachnospiraceae
editor preferred label: Parasporobacterium
imported from: ncbitaxon.owl

Coprococcus catus
type: Class
subclass of: Coprococcus
editor preferred label: Coprococcus catus
imported from: ncbitaxon.owl

Euteleostomi
type: Class
subclass of: Vertebrata <Metazoa>
editor preferred label: Euteleostomi
alternative term: bony vertebrates
imported from: ncbitaxon.owl

Cutibacterium acnes 17B
type: Class
subclass of: Propionibacteriaceae
editor preferred label: Cutibacterium acnes 17B
imported from: ncbitaxon.owl

Methylobacteriaceae
type: Class
subclass of: Proteobacteria
editor preferred label: Methylobacteriaceae
imported from: ncbitaxon.owl

Burkholderiaceae
type: Class
subclass of: Burkholderiales
editor preferred label: Burkholderiaceae
imported from: ncbitaxon.owl

Ecdysozoa
type: Class
subclass of: Bilateria
editor preferred label: Ecdysozoa
imported from: ncbitaxon.owl

Solobacterium sp. S4-A19
type: Class
subclass of: Solobacterium
editor preferred label: Solobacterium sp. S4-A19
imported from: ncbitaxon.owl

Proteobacteria
type: Class
subclass of: Bacteria
editor preferred label: Proteobacteria
alternative term: purple bacteria
alternative term: purple bacteria and relatives
alternative term: purple non-sulfur bacteria
alternative term: purple photosynthetic bacteria
alternative term: purple photosynthetic bacteria and relatives
imported from: ncbitaxon.owl

Solobacterium
type: Class
subclass of: Erysipelotrichaceae
editor preferred label: Solobacterium
imported from: ncbitaxon.owl

Gammaproteobacteria
type: Class
subclass of: Proteobacteria
editor preferred label: Gammaproteobacteria
imported from: ncbitaxon.owl

Firmicutes
type: Class
subclass of: Terrabacteria group
editor preferred label: Firmicutes
alternative term: low G+C Gram-positive bacteria
alternative term: low GC Gram+
imported from: ncbitaxon.owl

Peptostreptococcus
type: Class
subclass of: Peptostreptococcaceae
editor preferred label: Peptostreptococcus
imported from: ncbitaxon.owl

Peptostreptococcus anaerobius
type: Class
subclass of: Peptostreptococcus
editor preferred label: Peptostreptococcus anaerobius
imported from: ncbitaxon.owl

Ruminococcus
type: Class
subclass of: Ruminococcaceae
editor preferred label: Ruminococcus
imported from: ncbitaxon.owl

Ruminococcus albus
type: Class
subclass of: Ruminococcus
editor preferred label: Ruminococcus albus
imported from: ncbitaxon.owl

Micrococcaceae
type: Class
subclass of: Micrococcales
editor preferred label: Micrococcaceae
imported from: ncbitaxon.owl

Micrococcus
type: Class
subclass of: Micrococcaceae
subclass of: Restriction
  on property: microbe susceptibly expanded in respiratory airway of human with disease
  some values from: rheumatoid arthritis

Human immunodeficiency virus
type: Class
subclass of: Viruses
editor preferred label: Human immunodeficiency virus
imported from: ncbitaxon.owl

Erysipelotrichaceae
type: Class
subclass of: Firmicutes
editor preferred label: Erysipelotrichaceae
imported from: ncbitaxon.owl

Acidovorax
type: Class
subclass of: Burkholderiales
editor preferred label: Acidovorax
alternative term: Acidivorax
imported from: ncbitaxon.owl

Streptococcaceae
type: Class
subclass of: Lactobacillales
editor preferred label: Streptococcaceae
imported from: ncbitaxon.owl

Streptococcus
type: Class
subclass of: Streptococcaceae
editor preferred label: Streptococcus
imported from: ncbitaxon.owl

Streptococcus sanguinis
type: Class
subclass of: Streptococcus

Streptococcus thermophilus
type: Class
subclass of: Streptococcus
editor preferred label: Streptococcus thermophilus
alternative term: Streptococcus salivarius thermophilus
imported from: ncbitaxon.owl

Streptococcus pyogenes
type: Class
subclass of: Streptococcus
editor preferred label: Streptococcus pyogenes
imported from: ncbitaxon.owl

Streptococcus equinus
type: Class
subclass of: Streptococcus
editor preferred label: Streptococcus equinus
imported from: ncbitaxon.owl

Enterococcus
type: Class
subclass of: Enterococcaceae
editor preferred label: Enterococcus
imported from: ncbitaxon.owl

Enterococcus faecalis
type: Class
subclass of: Enterococcus
editor preferred label: Enterococcus faecalis
imported from: ncbitaxon.owl

Escherichia coli #1/H766
type: Class
subclass of: Escherichia coli
editor preferred label: Escherichia coli #1/H766
imported from: ncbitaxon.owl

Spirochaetaceae
type: Class
subclass of: Bacteria
editor preferred label: Spirochaetaceae
imported from: ncbitaxon.owl

Atopobium
type: Class
subclass of: Coriobacteriales
editor preferred label: Atopobium
imported from: ncbitaxon.owl

Atopobium parvulum
type: Class
subclass of: Atopobium
editor preferred label: Atopobium parvulum
imported from: ncbitaxon.owl

Lachnobacterium bovis
type: Class
subclass of: Lachnospiraceae
editor preferred label: Lachnobacterium bovis
imported from: ncbitaxon.owl

Fretibacterium
type: Class
subclass of: Bacteria
editor preferred label: Fretibacterium
imported from: ncbitaxon.owl

Mesangiospermae
type: Class
subclass of: Eukaryota
editor preferred label: Mesangiospermae
imported from: ncbitaxon.owl

Pentapetalae
type: Class
subclass of: Mesangiospermae
editor preferred label: Pentapetalae
imported from: ncbitaxon.owl

Clostridium
type: Class
subclass of: Clostridiaceae
editor preferred label: Clostridium
imported from: ncbitaxon.owl

Clostridioides difficile
type: Class
subclass of: Peptostreptococcaceae
editor preferred label: Clostridioides difficile
alternative term: [Clostridium] difficile
imported from: ncbitaxon.owl

Clostridium perfringens
type: Class
subclass of: Clostridium
subclass of: Restriction
  on property: microbe susceptibly expanded in gut of human with disease
  some values from: rheumatoid arthritis
editor preferred label: Clostridium perfringens
imported from: ncbitaxon.owl

Anoxybacillus
type: Class
subclass of: Bacillaceae
editor preferred label: Anoxybacillus
imported from: ncbitaxon.owl

Erysipelatoclostridium
type: Class
subclass of: Erysipelotrichaceae
editor preferred label: Erysipelatoclostridium
imported from: ncbitaxon.owl

Lachnoclostridium
type: Class
subclass of: Lachnospiraceae
editor preferred label: Lachnoclostridium
imported from: ncbitaxon.owl

[Clostridium] clostridioforme
type: Class
subclass of: Lachnoclostridium
editor preferred label: [Clostridium] clostridioforme
alternative term: Clostridium clostridioforme
imported from: ncbitaxon.owl

Blautia coccoides
type: Class
subclass of: Blautia
subclass of: Restriction
  on property: microbe susceptibly depleted (compared to fibromyalgia patients) in gut of human with disease
  some values from: rheumatoid arthritis
editor preferred label: Blautia coccoides
imported from: ncbitaxon.owl

Candida <Debaryomycetaceae>
type: Class
subclass of: Saccharomycetales
editor preferred label: Candida <Debaryomycetaceae>
alternative term: Candida
imported from: ncbitaxon.owl

Fusobacterium nucleatum subsp. vincentii
type: Class
subclass of: Fusobacterium nucleatum
editor preferred label: Fusobacterium nucleatum subsp. vincentii
alternative term: Fusibacterium nucleatum subsp. fusiforme
alternative term: Fusibacterium nucleatum subsp. vincentii
imported from: ncbitaxon.owl

Treponema
type: Class
subclass of: Spirochaetaceae
subclass of: Restriction
  on property: microbe susceptibly depleted in respiratory airway of human with disease
  some values from: rheumatoid arthritis
editor preferred label: Treponema
imported from: ncbitaxon.owl

Lactobacillus
type: Class
subclass of: Lactobacillaceae
editor preferred label: Lactobacillus
imported from: ncbitaxon.owl

Lactobacillus acidophilus
type: Class
subclass of: Lactobacillus
editor preferred label: Lactobacillus acidophilus
imported from: ncbitaxon.owl

Treponema denticola
type: Class
subclass of: Treponema

Lactobacillus casei
type: Class
subclass of: Lactobacillus
editor preferred label: Lactobacillus casei
imported from: ncbitaxon.owl

Fusobacterium hwasookii
type: Class
subclass of: Fusobacterium
editor preferred label: Fusobacterium hwasookii
imported from: ncbitaxon.owl

Megamonas hypermegale
type: Class
subclass of: Selenomonadaceae
subclass of: Restriction
  on property: microbe susceptibly depleted in gut of human with disease
  some values from: rheumatoid arthritis
editor preferred label: Megamonas hypermegale
imported from: ncbitaxon.owl

Lactobacillus sp.
type: Class
subclass of: Lactobacillus
subclass of: Restriction
  on property: microbe susceptibly expanded in gut of human with disease
  some values from: rheumatoid arthritis
editor preferred label: Lactobacillus sp.
imported from: ncbitaxon.owl

Lactobacillus reuteri
type: Class
subclass of: Lactobacillus
editor preferred label: Lactobacillus reuteri
imported from: ncbitaxon.owl

Lactobacillus fermentum
type: Class
subclass of: Lactobacillus
editor preferred label: Lactobacillus fermentum
imported from: ncbitaxon.owl

Lactobacillus murinus
type: Class
subclass of: Lactobacillus
editor preferred label: Lactobacillus murinus
imported from: ncbitaxon.owl

Lactobacillus salivarius
type: Class
subclass of: Lactobacillus
subclass of: Restriction
  on property: microbe susceptibly expanded in oral cavity of human with disease
  some values from: rheumatoid arthritis
editor preferred label: Lactobacillus salivarius
imported from: ncbitaxon.owl

Eggerthellaceae
type: Class
subclass of: Coriobacteriia
editor preferred label: Eggerthellaceae
imported from: ncbitaxon.owl

Prevotella copri
type: Class
subclass of: Prevotella
subclass of: Restriction
  on property: microbe susceptibly expanded in gut of human with disease
  some values from: rheumatoid arthritis
subclass of: Restriction
  on property: microbe susceptibly depleted in gut of human with disease
  some values from: juvenile rheumatoid arthritis
subclass of: Restriction
  on property: microbe susceptibly depleted in gut of human with disease
  some values from: colorectal cancer
subclass of: Restriction
  on property: microbe susceptibly expanded in gut of mouse with disease
  some values from: arthritis
editor preferred label: Prevotella copri
imported from: ncbitaxon.owl

Actinomyces
type: Class
subclass of: Actinobacteria <class>
subclass of: Restriction
  on property: microbe susceptibly depleted in respiratory airway of human with disease
  some values from: rheumatoid arthritis
subclass of: Restriction
  on property: microbe susceptibly expanded in oral cavity of human with disease
  some values from: rheumatoid arthritis
editor preferred label: Actinomyces
imported from: ncbitaxon.owl

Bifidobacterium
type: Class
subclass of: Bifidobacteriales
editor preferred label: Bifidobacterium
imported from: ncbitaxon.owl

Bifidobacterium bifidum
type: Class
subclass of: Bifidobacterium
subclass of: Restriction
  on property: microbe susceptibly depleted in gut of human with disease
  some values from: rheumatoid arthritis
subclass of: Restriction
  on property: microbe susceptibly depleted (compared to fibromyalgia patients) in gut of human with disease
  some values from: rheumatoid arthritis
editor preferred label: Bifidobacterium bifidum
imported from: ncbitaxon.owl

Bifidobacterium dentium
type: Class
subclass of: Bifidobacterium
subclass of: Restriction
  on property: microbe susceptibly expanded in gut of human with disease
  some values from: rheumatoid arthritis
editor preferred label: Bifidobacterium dentium
imported from: ncbitaxon.owl

Bacteroidales
type: Class
subclass of: Bacteroidia
editor preferred label: Bacteroidales
imported from: ncbitaxon.owl

Rikenellaceae
type: Class
subclass of: Bacteroidales
editor preferred label: Rikenellaceae
imported from: ncbitaxon.owl

Porphyromonadaceae
type: Class
subclass of: Bacteroidales
editor preferred label: Porphyromonadaceae
imported from: ncbitaxon.owl

Prevotellaceae
type: Class
subclass of: Bacteroidales
subclass of: Restriction
  on property: microbe susceptibly expanded in gut of human with disease
  some values from: rheumatoid arthritis
editor preferred label: Prevotellaceae
imported from: ncbitaxon.owl

Corynebacterium diphtheriae
type: Class
subclass of: Corynebacteriales
editor preferred label: Corynebacterium diphtheriae
imported from: ncbitaxon.owl

Rothia aeria
type: Class
subclass of: Micrococcaceae
subclass of: Restriction
  on property: microbe susceptibly depleted in oral cavity of human with disease
  some values from: rheumatoid arthritis
editor preferred label: Rothia aeria
imported from: ncbitaxon.owl

Eubacterium
type: Class
subclass of: Eubacteriaceae

Propionibacterium
type: Class
subclass of: Propionibacteriaceae
editor preferred label: Propionibacterium
alternative term: Propionicibacterium
imported from: ncbitaxon.owl

Actinobacteria <class>
type: Class
subclass of: Actinobacteria <phylum>
editor preferred label: Actinobacteria <class>
alternative term: Actinobacteria
alternative term: high G+C Gram-positive bacteria
imported from: ncbitaxon.owl

Mycobacterium
type: Class
subclass of: Corynebacteriales
editor preferred label: Mycobacterium
imported from: ncbitaxon.owl

Mycobacterium avium
type: Class
subclass of: Mycobacterium
editor preferred label: Mycobacterium avium
imported from: ncbitaxon.owl

PVC group
type: Class
subclass of: Bacteria
editor preferred label: PVC group
imported from: ncbitaxon.owl

Terrabacteria group
type: Class
subclass of: Bacteria
editor preferred label: Terrabacteria group
imported from: ncbitaxon.owl

Rhodococcus
type: Class
subclass of: Nocardiaceae

Selenomonadaceae
type: Class
subclass of: Negativicutes
editor preferred label: Selenomonadaceae
imported from: ncbitaxon.owl

Pseudonocardia
type: Class
subclass of: Pseudonocardiaceae
subclass of: Restriction
  on property: microbe susceptibly expanded in respiratory airway of human with disease
  some values from: rheumatoid arthritis

Clostridia
type: Class
subclass of: Firmicutes
subclass of: Restriction
  on property: microbe susceptibly expanded in gut of human with disease
  some values from: rheumatoid arthritis
editor preferred label: Clostridia
imported from: ncbitaxon.owl

Clostridiales
type: Class
subclass of: Clostridia
editor preferred label: Clostridiales
imported from: ncbitaxon.owl

Lachnospiraceae
type: Class
subclass of: Clostridiales
editor preferred label: Lachnospiraceae
imported from: ncbitaxon.owl

Peptostreptococcaceae
type: Class
subclass of: Clostridiales
editor preferred label: Peptostreptococcaceae
imported from: ncbitaxon.owl

Eubacteriaceae
type: Class
subclass of: Clostridiales
editor preferred label: Eubacteriaceae
imported from: ncbitaxon.owl

unclassified Clostridiales
type: Class
subclass of: Clostridiales
editor preferred label: unclassified Clostridiales
imported from: ncbitaxon.owl

Bacillaceae
type: Class
subclass of: Bacilli
editor preferred label: Bacillaceae
imported from: ncbitaxon.owl

Lactobacillales
type: Class
subclass of: Bacilli
editor preferred label: Lactobacillales
imported from: ncbitaxon.owl

Atopobium sp.
type: Class
subclass of: Atopobium
subclass of: Restriction
  on property: microbe susceptibly expanded in oral cavity of human with disease
  some values from: rheumatoid arthritis
editor preferred label: Atopobium sp.
imported from: ncbitaxon.owl

Subdoligranulum sp. 60_17
type: Class
subclass of: Subdoligranulum
editor preferred label: Subdoligranulum sp. 60_17
imported from: ncbitaxon.owl

Lachnospiraceae bacterium
type: Class
subclass of: Lachnospiraceae
subclass of: Restriction
  on property: microbe susceptibly expanded in gut of human with disease
  some values from: rheumatoid arthritis
editor preferred label: Lachnospiraceae bacterium
imported from: ncbitaxon.owl

Yersiniaceae
type: Class
subclass of: Enterobacterales
editor preferred label: Yersiniaceae
imported from: ncbitaxon.owl

Morganellaceae
type: Class
subclass of: Enterobacterales
editor preferred label: Morganellaceae
imported from: ncbitaxon.owl

Neisseria sp.
type: Class
subclass of: Neisseriaceae
subclass of: Restriction
  on property: microbe susceptibly depleted in oral cavity of human with disease
  some values from: rheumatoid arthritis
editor preferred label: Neisseria sp.
imported from: ncbitaxon.owl

Campylobacter
type: Class
subclass of: Campylobacteraceae
editor preferred label: Campylobacter
imported from: ncbitaxon.owl

Desulfovibrionaceae
type: Class
subclass of: delta/epsilon subdivisions
editor preferred label: Desulfovibrionaceae
imported from: ncbitaxon.owl

Campylobacter jejuni
type: Class
subclass of: Campylobacter
editor preferred label: Campylobacter jejuni
imported from: ncbitaxon.owl

Pancrustacea
type: Class
subclass of: Ecdysozoa
editor preferred label: Pancrustacea
imported from: ncbitaxon.owl

Bacteria
type: Class
subclass of: OHMI_0000460
subclass of: Restriction
  on property: has quality
  some values from: OHMI_0000462
editor preferred label: Bacteria
alternative term: eubacteria
imported from: ncbitaxon.owl
imported from: obi.owl

Tannerellaceae
type: Class
subclass of: Bacteroidales
editor preferred label: Tannerellaceae
imported from: ncbitaxon.owl

Bacteroidia
type: Class
subclass of: Bacteroidetes
editor preferred label: Bacteroidia
imported from: ncbitaxon.owl

Crenothrix
type: Class
subclass of: Gammaproteobacteria
editor preferred label: Crenothrix
imported from: ncbitaxon.owl

Chloroflexi
type: Class
subclass of: Terrabacteria group

Actinobacteria <phylum>
type: Class
subclass of: Terrabacteria group
subclass of: Restriction
  on property: microbe susceptibly expanded in gut of human with disease
  some values from: rheumatoid arthritis
editor preferred label: Actinobacteria <phylum>
alternative term: Actinobacteria
imported from: ncbitaxon.owl

Fusobacteriales
type: Class
subclass of: Fusobacteria
editor preferred label: Fusobacteriales
imported from: ncbitaxon.owl

Fusobacteriaceae
type: Class
subclass of: Fusobacteriales
editor preferred label: Fusobacteriaceae
imported from: ncbitaxon.owl

Pseudonocardiaceae
type: Class
subclass of: Actinobacteria <class>
editor preferred label: Pseudonocardiaceae
imported from: ncbitaxon.owl

Helicobacter
type: Class
subclass of: Campylobacterales
editor preferred label: Helicobacter
imported from: ncbitaxon.owl

Helicobacter pylori
type: Class
subclass of: Helicobacter
editor preferred label: Helicobacter pylori
imported from: ncbitaxon.owl

Mycoplasma fermentans
type: Class
subclass of: Terrabacteria group
editor preferred label: Mycoplasma fermentans
imported from: ncbitaxon.owl

Campylobacterales
type: Class
subclass of: Epsilonproteobacteria
editor preferred label: Campylobacterales
imported from: ncbitaxon.owl

Archaea
type: Class
subclass of: organism or virus or viroid
subclass of: organism
editor preferred label: Archaea
imported from: ncbitaxon.owl
imported from: obi.owl

Bifidobacterium longum
type: Class
subclass of: Bifidobacterium
editor preferred label: Bifidobacterium longum
imported from: ncbitaxon.owl

Faecalibacterium
type: Class
subclass of: Ruminococcaceae
subclass of: Restriction
  on property: microbe susceptibly depleted in gut of human with disease
  some values from: rheumatoid arthritis
editor preferred label: Faecalibacterium
imported from: ncbitaxon.owl

Dialister invisus
type: Class
subclass of: Dialister
editor preferred label: Dialister invisus
imported from: ncbitaxon.owl

Moniliophthora
type: Class
subclass of: Basidiomycota
subclass of: OHMI_0000460
subclass of: Restriction
  on property: has quality
  some values from: OHMI_0000462
editor preferred label: Moniliophthora
imported from: ncbitaxon.owl

Candidatus Portiera
type: Class
subclass of: Gammaproteobacteria
editor preferred label: Candidatus Portiera
imported from: ncbitaxon.owl

Alistipes
type: Class
subclass of: Rikenellaceae
editor preferred label: Alistipes
imported from: ncbitaxon.owl

Akkermansia
type: Class
subclass of: Verrucomicrobia
editor preferred label: Akkermansia
imported from: ncbitaxon.owl

Akkermansia muciniphila
type: Class
subclass of: Akkermansia
editor preferred label: Akkermansia muciniphila
imported from: ncbitaxon.owl

Anaerotruncus
type: Class
subclass of: Ruminococcaceae
editor preferred label: Anaerotruncus
imported from: ncbitaxon.owl

Acetanaerobacterium
type: Class
subclass of: Ruminococcaceae
editor preferred label: Acetanaerobacterium
imported from: ncbitaxon.owl

Sulfurovum
type: Class
subclass of: Epsilonproteobacteria
editor preferred label: Sulfurovum
imported from: ncbitaxon.owl

Cardiobacterium
type: Class
subclass of: Gammaproteobacteria
subclass of: Restriction
  on property: microbe susceptibly depleted in oral cavity of human with disease
  some values from: rheumatoid arthritis
editor preferred label: Cardiobacterium
imported from: ncbitaxon.owl

Eukaryota
type: Class
subclass of: organism or virus or viroid
subclass of: organism
editor preferred label: Eukaryota
alternative term: eucaryotes
alternative term: eukaryotes
imported from: ncbitaxon.owl
imported from: obi.owl

Bifidobacterium animalis
type: Class
subclass of: Bifidobacterium
editor preferred label: Bifidobacterium animalis
imported from: ncbitaxon.owl

Lachnospira pectinoschiza
type: Class
subclass of: Lachnospiraceae
editor preferred label: Lachnospira pectinoschiza
imported from: ncbitaxon.owl

Tannerella forsythia
type: Class
subclass of: Tannerellaceae
subclass of: Restriction
  on property: microbe susceptibly expanded in oral cavity of human with disease
  some values from: rheumatoid arthritis
editor preferred label: Tannerella forsythia
imported from: ncbitaxon.owl

Bacteroides ovatus
type: Class
subclass of: Bacteroides
editor preferred label: Bacteroides ovatus
imported from: ncbitaxon.owl

Alistipes putredinis
type: Class
subclass of: Alistipes
editor preferred label: Alistipes putredinis
imported from: ncbitaxon.owl

Prevotella intermedia
type: Class
subclass of: Prevotella
subclass of: Restriction
  on property: microbe susceptibly expanded in oral cavity of human with disease
  some values from: rheumatoid arthritis
editor preferred label: Prevotella intermedia
imported from: ncbitaxon.owl

Prevotella oris
type: Class
subclass of: Prevotella
editor preferred label: Prevotella oris
imported from: ncbitaxon.owl

Prevotella oulorum
type: Class
subclass of: Prevotella

Betaproteobacteria
type: Class
subclass of: Proteobacteria
editor preferred label: Betaproteobacteria
imported from: ncbitaxon.owl

Odoribacter
type: Class
subclass of: Bacteroidales
editor preferred label: Odoribacter
imported from: ncbitaxon.owl

Pseudomonas
type: Class
subclass of: Pseudomonadales
editor preferred label: Pseudomonas
imported from: ncbitaxon.owl

Salmonella enterica
type: Class
subclass of: Salmonella
editor preferred label: Salmonella enterica
imported from: ncbitaxon.owl

Anaerolineae
type: Class
subclass of: Chloroflexi

Anaerolineaceae
type: Class
subclass of: Anaerolineales

Anaerolineales
type: Class
subclass of: Terrabacteria group
editor preferred label: Anaerolineales
imported from: ncbitaxon.owl

Subdoligranulum
type: Class
subclass of: Ruminococcaceae
editor preferred label: Subdoligranulum
imported from: ncbitaxon.owl

[Clostridium] scindens
type: Class
subclass of: Lachnoclostridium
editor preferred label: [Clostridium] scindens
alternative term: Clostridium scindens
imported from: ncbitaxon.owl

Veillonella
type: Class
subclass of: Veillonellaceae
subclass of: Restriction
  on property: microbe susceptibly depleted in gut of human with disease
  some values from: rheumatoid arthritis
subclass of: Restriction
  on property: microbe susceptibly depleted in oral cavity of human with disease
  some values from: rheumatoid arthritis
editor preferred label: Veillonella
imported from: ncbitaxon.owl

Bacteroides sp.
type: Class
subclass of: Bacteroides
subclass of: Restriction
  on property: microbe susceptibly expanded in gut of human with disease
  some values from: gout
subclass of: Restriction
  on property: microbe susceptibly expanded in gut of human with disease
  some values from: rheumatoid arthritis
editor preferred label: Bacteroides sp.
imported from: ncbitaxon.owl

Epsilonproteobacteria
type: Class
subclass of: delta/epsilon subdivisions
editor preferred label: Epsilonproteobacteria
imported from: ncbitaxon.owl

Roseburia hominis
type: Class
subclass of: Roseburia
editor preferred label: Roseburia hominis
imported from: ncbitaxon.owl

Bifidobacterium animalis subsp. lactis
type: Class
subclass of: Bifidobacterium animalis
editor preferred label: Bifidobacterium animalis subsp. lactis
imported from: ncbitaxon.owl

Clostridium sp. cp01.19
type: Class
subclass of: Clostridium
editor preferred label: Clostridium sp. cp01.19
imported from: ncbitaxon.owl

Pseudomonas sp.
type: Class
subclass of: Pseudomonas

Bacteroides plebeius
type: Class
subclass of: Bacteroides
editor preferred label: Bacteroides plebeius
imported from: ncbitaxon.owl

Euarchontoglires
type: Class
subclass of: Mammalia
editor preferred label: Euarchontoglires
imported from: ncbitaxon.owl

Streptococcus gallolyticus
type: Class
subclass of: Streptococcus
editor preferred label: Streptococcus gallolyticus
imported from: ncbitaxon.owl

Propionibacteriaceae
type: Class
subclass of: Actinobacteria <class>
editor preferred label: Propionibacteriaceae
alternative term: Propionicibacteriaceae
imported from: ncbitaxon.owl

Veillonellaceae
type: Class
subclass of: Negativicutes
editor preferred label: Veillonellaceae
imported from: ncbitaxon.owl

Clostridiaceae
type: Class
subclass of: Clostridiales
editor preferred label: Clostridiaceae
imported from: ncbitaxon.owl

Burkholderia
type: Class
subclass of: Burkholderiaceae
subclass of: Restriction
  on property: microbe susceptibly depleted in respiratory airway of human with disease
  some values from: rheumatoid arthritis

Helicobacter hepaticus
type: Class
subclass of: Helicobacter
editor preferred label: Helicobacter hepaticus
imported from: ncbitaxon.owl

unclassified Proteobacteria
type: Class
subclass of: Proteobacteria
subclass of: Restriction
  on property: microbe susceptibly expanded in gut of human with disease
  some values from: diarrhea
editor preferred label: unclassified Proteobacteria
imported from: ncbitaxon.owl

Fusobacteria
type: Class
subclass of: Bacteria
editor preferred label: Fusobacteria
imported from: ncbitaxon.owl

Leptotrichia
type: Class
subclass of: Leptotrichiaceae
editor preferred label: Leptotrichia
imported from: ncbitaxon.owl

Kingella
type: Class
subclass of: Neisseriaceae
subclass of: Restriction
  on property: microbe susceptibly depleted in oral cavity of human with disease
  some values from: rheumatoid arthritis
editor preferred label: Kingella
imported from: ncbitaxon.owl

Tetrapoda
type: Class
subclass of: Euteleostomi
editor preferred label: Tetrapoda
alternative term: tetrapods
imported from: ncbitaxon.owl

Amniota
type: Class
subclass of: Tetrapoda
editor preferred label: Amniota
alternative term: amniotes
imported from: ncbitaxon.owl

Bacteroides intestinalis
type: Class
subclass of: Bacteroides
editor preferred label: Bacteroides intestinalis
imported from: ncbitaxon.owl

Phascolarctobacterium
type: Class
subclass of: Negativicutes
editor preferred label: Phascolarctobacterium
imported from: ncbitaxon.owl

Parvimonas micra
type: Class
subclass of: Parvimonas
editor preferred label: Parvimonas micra
imported from: ncbitaxon.owl

Coprococcus
type: Class
subclass of: Lachnospiraceae
editor preferred label: Coprococcus
imported from: ncbitaxon.owl

Opisthokonta
type: Class
subclass of: Eukaryota
editor preferred label: Opisthokonta
imported from: ncbitaxon.owl

Bilateria
type: Class
subclass of: Opisthokonta
editor preferred label: Bilateria
imported from: ncbitaxon.owl

[Clostridium] asparagiforme
type: Class
subclass of: Lachnoclostridium
subclass of: Restriction
  on property: microbe susceptibly expanded in gut of human with disease
  some values from: rheumatoid arthritis
editor preferred label: [Clostridium] asparagiforme
alternative term: Clostridium asparagiforme
imported from: ncbitaxon.owl

Bacteroides finegoldii
type: Class
subclass of: Bacteroides
editor preferred label: Bacteroides finegoldii
imported from: ncbitaxon.owl

Microbacterium
type: Class
subclass of: Micrococcales
editor preferred label: Microbacterium
alternative term: Aureibacterium
imported from: ncbitaxon.owl

Lactobacillaceae
type: Class
subclass of: Lactobacillales
editor preferred label: Lactobacillaceae
imported from: ncbitaxon.owl

Streptobacillus
type: Class
subclass of: Leptotrichiaceae
editor preferred label: Streptobacillus
imported from: ncbitaxon.owl

Peptostreptococcus stomatis
type: Class
subclass of: Peptostreptococcus
editor preferred label: Peptostreptococcus stomatis
imported from: ncbitaxon.owl

Bilophila
type: Class
subclass of: Desulfovibrionaceae
editor preferred label: Bilophila
imported from: ncbitaxon.owl

Bilophila wadsworthia
type: Class
subclass of: Bilophila
editor preferred label: Bilophila wadsworthia
imported from: ncbitaxon.owl

Prevotella stercorea
type: Class
subclass of: Prevotella
editor preferred label: Prevotella stercorea
imported from: ncbitaxon.owl

Streptococcus sp. 'group A'
type: Class
subclass of: Streptococcus
editor preferred label: Streptococcus sp. 'group A'
imported from: ncbitaxon.owl

Arabidopsis thaliana
type: Class
subclass of: Pentapetalae
editor preferred label: Arabidopsis thaliana
alternative term: mouse-ear cress
alternative term: thale cress
alternative term: thale-cress
imported from: ncbitaxon.owl

Bacteroides xylanisolvens
type: Class
subclass of: Bacteroides
editor preferred label: Bacteroides xylanisolvens
imported from: ncbitaxon.owl

Parabacteroides
type: Class
subclass of: Tannerellaceae
editor preferred label: Parabacteroides
imported from: ncbitaxon.owl

Escherichia coli B
type: Class
subclass of: Escherichia coli
subclass of: Restriction
  on property: microbe susceptibly expanded in gut of human with disease
  some values from: colorectal cancer
editor preferred label: Escherichia coli B
imported from: ncbitaxon.owl

Murinae
type: Class
subclass of: Rodentia
editor preferred label: Murinae
imported from: ncbitaxon.owl

Dorea formicigenerans
type: Class
subclass of: Lachnospiraceae
editor preferred label: Dorea formicigenerans
imported from: ncbitaxon.owl

Eubacterium ventriosum
type: Class
subclass of: Eubacteriaceae
editor preferred label: Eubacterium ventriosum
alternative term: [Eubacterium] ventriosum
imported from: ncbitaxon.owl

Barnesiella
type: Class
subclass of: Bacteroidales
editor preferred label: Barnesiella
imported from: ncbitaxon.owl

Dialister
type: Class
subclass of: Veillonellaceae
editor preferred label: Dialister
imported from: ncbitaxon.owl

Dialister pneumosintes
type: Class
subclass of: Dialister
editor preferred label: Dialister pneumosintes
imported from: ncbitaxon.owl

Blautia obeum
type: Class
subclass of: Blautia
editor preferred label: Blautia obeum
imported from: ncbitaxon.owl

Sutterella wadsworthensis
type: Class
subclass of: Burkholderiales
subclass of: Restriction
  on property: microbe susceptibly depleted in gut of human with disease
  some values from: rheumatoid arthritis
editor preferred label: Sutterella wadsworthensis
imported from: ncbitaxon.owl

Mammalia
type: Class
subclass of: Amniota
editor preferred label: Mammalia
alternative term: mammals
imported from: ncbitaxon.owl

Methylobacterium
type: Class
subclass of: Methylobacteriaceae
subclass of: Restriction
  on property: microbe susceptibly expanded in respiratory airway of human with disease
  some values from: rheumatoid arthritis

Prevotella pleuritidis
type: Class
subclass of: Prevotella

Cronobacter
type: Class
subclass of: Enterobacteriaceae
editor preferred label: Cronobacter
imported from: ncbitaxon.owl

Aggregatibacter
type: Class
subclass of: Pasteurellaceae
subclass of: Restriction
  on property: microbe susceptibly depleted in oral cavity of human with disease
  some values from: rheumatoid arthritis
editor preferred label: Aggregatibacter
imported from: ncbitaxon.owl

Ruminococcus sp.
type: Class
subclass of: Ruminococcus
editor preferred label: Ruminococcus sp.
imported from: ncbitaxon.owl

Filifactor
type: Class
subclass of: Peptostreptococcaceae
editor preferred label: Filifactor
imported from: ncbitaxon.owl

Dictyostelium discoideum
type: Class
subclass of: Eukaryota
editor preferred label: Dictyostelium discoideum
imported from: ncbitaxon.owl

Eleutherodactylus lentus
type: Class
subclass of: Anura
editor preferred label: Eleutherodactylus lentus
alternative term: Virgin Islands robber frog
imported from: ncbitaxon.owl

Dikarya
type: Class
subclass of: Fungi
editor preferred label: Dikarya
imported from: ncbitaxon.owl

Oscillibacter
type: Class
subclass of: Clostridiales
editor preferred label: Oscillibacter
imported from: ncbitaxon.owl

Pseudobutyrivibrio
type: Class
subclass of: Lachnospiraceae
editor preferred label: Pseudobutyrivibrio
imported from: ncbitaxon.owl

Pseudobutyrivibrio ruminis
type: Class
subclass of: Pseudobutyrivibrio
editor preferred label: Pseudobutyrivibrio ruminis
imported from: ncbitaxon.owl

Ruminococcus lactaris
type: Class
subclass of: Ruminococcus
editor preferred label: Ruminococcus lactaris
imported from: ncbitaxon.owl

Acinetobacter
type: Class
subclass of: Pseudomonadales
editor preferred label: Acinetobacter
imported from: ncbitaxon.owl

Gordonibacter pamelaeae
type: Class
subclass of: Eggerthellaceae
subclass of: Restriction
  on property: microbe susceptibly expanded in gut of human with disease
  some values from: rheumatoid arthritis
editor preferred label: Gordonibacter pamelaeae
imported from: ncbitaxon.owl

Natronobacillus
type: Class
subclass of: Bacillaceae
subclass of: Restriction
  on property: microbe susceptibly expanded in gut of human with disease
  some values from: diarrhea
editor preferred label: Natronobacillus
imported from: ncbitaxon.owl

Fungi
type: Class
subclass of: Opisthokonta
editor preferred label: Fungi
alternative term: fungi
imported from: ncbitaxon.owl

Bacteroides caccae
type: Class
subclass of: Bacteroides
editor preferred label: Bacteroides caccae
imported from: ncbitaxon.owl

Lactobacillus rhamnosus
type: Class
subclass of: Lactobacillus
editor preferred label: Lactobacillus rhamnosus
imported from: ncbitaxon.owl

Neisseriaceae
type: Class
subclass of: Betaproteobacteria
editor preferred label: Neisseriaceae
imported from: ncbitaxon.owl

Ascomycota
type: Class
subclass of: Dikarya
editor preferred label: Ascomycota
alternative term: ascomycetes
alternative term: sac fungi
imported from: ncbitaxon.owl

Saccharomycetales
type: Class
subclass of: saccharomyceta
editor preferred label: Saccharomycetales
alternative term: budding yeasts
imported from: ncbitaxon.owl

Schizosaccharomyces pombe
type: Class
subclass of: Ascomycota
subclass of: OHMI_0000460
subclass of: Restriction
  on property: has quality
  some values from: OHMI_0000462
editor preferred label: Schizosaccharomyces pombe
alternative term: fission yeast
imported from: ncbitaxon.owl

Saccharomyces cerevisiae
type: Class
subclass of: Saccharomycetales
editor preferred label: Saccharomyces cerevisiae
alternative term: baker's yeast
alternative term: brewer's yeast
imported from: ncbitaxon.owl

Treponema maltophilum
type: Class
subclass of: Treponema

Neurospora
type: Class
subclass of: leotiomyceta
editor preferred label: Neurospora
imported from: ncbitaxon.owl

Basidiomycota
type: Class
subclass of: Dikarya
editor preferred label: Basidiomycota
alternative term: basidiomycetes
imported from: ncbitaxon.owl

Eikenella
type: Class
subclass of: Neisseriaceae
subclass of: Restriction
  on property: microbe susceptibly depleted in oral cavity of human with disease
  some values from: rheumatoid arthritis
editor preferred label: Eikenella
imported from: ncbitaxon.owl

Clostridiales incertae sedis
type: Class
subclass of: Clostridiales
editor preferred label: Clostridiales incertae sedis
imported from: ncbitaxon.owl

Ruminococcaceae
type: Class
subclass of: Clostridiales
editor preferred label: Ruminococcaceae
imported from: ncbitaxon.owl

Enterobacteriaceae
type: Class
subclass of: Enterobacterales
editor preferred label: Enterobacteriaceae
imported from: ncbitaxon.owl

Parvimonas
type: Class
subclass of: Firmicutes
editor preferred label: Parvimonas
imported from: ncbitaxon.owl

Clostridiales Family XIII. Incertae Sedis
type: Class
subclass of: Clostridiales incertae sedis
editor preferred label: Clostridiales Family XIII. Incertae Sedis
imported from: ncbitaxon.owl

Citrobacter
type: Class
subclass of: Enterobacteriaceae
editor preferred label: Citrobacter
imported from: ncbitaxon.owl

Candida albicans
type: Class
subclass of: Candida <Debaryomycetaceae>
editor preferred label: Candida albicans
imported from: ncbitaxon.owl

Klebsiella aerogenes
type: Class
subclass of: Klebsiella
editor preferred label: Klebsiella aerogenes
alternative term: [Enterobacter] aerogenes
imported from: ncbitaxon.owl

Diutina rugosa
type: Class
subclass of: Saccharomycetales
editor preferred label: Diutina rugosa
imported from: ncbitaxon.owl

Malassezia
type: Class
subclass of: Basidiomycota
subclass of: OHMI_0000460
subclass of: Restriction
  on property: has quality
  some values from: OHMI_0000462
editor preferred label: Malassezia
imported from: ncbitaxon.owl

Malassezia furfur
type: Class
subclass of: Malassezia
editor preferred label: Malassezia furfur
alternative term: Pityriasis (Tinea) versicolor infection agent
imported from: ncbitaxon.owl

Escherichia
type: Class
subclass of: Enterobacteriaceae
subclass of: Restriction
  on property: microbe susceptibly expanded in gut of human with disease
  some values from: colorectal cancer
editor preferred label: Escherichia
imported from: ncbitaxon.owl

Escherichia coli
type: Class
subclass of: Escherichia
subclass of: Restriction
  on property: microbe susceptibly expanded in gut of human with disease
  some values from: rheumatoid arthritis
subclass of: Restriction
  on property: microbe susceptibly expanded in gut of rat with disease
  some values from: arthritis
editor preferred label: Escherichia coli
alternative term: E. coli
alternative term: Escherichia/Shigella coli
imported from: ncbitaxon.owl

Klebsiella
type: Class
subclass of: Enterobacteriaceae
editor preferred label: Klebsiella
imported from: ncbitaxon.owl

Blautia
type: Class
subclass of: Lachnospiraceae
editor preferred label: Blautia
imported from: ncbitaxon.owl

Klebsiella pneumoniae
type: Class
subclass of: Klebsiella
subclass of: Restriction
  on property: microbe susceptibly depleted in gut of human with disease
  some values from: rheumatoid arthritis
editor preferred label: Klebsiella pneumoniae
imported from: ncbitaxon.owl

Paraprevotella
type: Class
subclass of: Prevotellaceae
editor preferred label: Paraprevotella
imported from: ncbitaxon.owl

Kluyvera
type: Class
subclass of: Enterobacteriaceae
editor preferred label: Kluyvera
imported from: ncbitaxon.owl

Proteus mirabilis
type: Class
subclass of: Morganellaceae
subclass of: Restriction
  on property: microbe susceptibly expanded in gut of human with disease
  some values from: rheumatoid arthritis
editor preferred label: Proteus mirabilis
imported from: ncbitaxon.owl

Providencia
type: Class
subclass of: Morganellaceae
editor preferred label: Providencia
imported from: ncbitaxon.owl

Robinsoniella
type: Class
subclass of: Lachnospiraceae
editor preferred label: Robinsoniella
imported from: ncbitaxon.owl

Salmonella
type: Class
subclass of: Enterobacteriaceae
editor preferred label: Salmonella
imported from: ncbitaxon.owl

Salmonella enterica subsp. enterica
type: Class
subclass of: Salmonella enterica
editor preferred label: Salmonella enterica subsp. enterica
imported from: ncbitaxon.owl

Holdemania
type: Class
subclass of: Erysipelotrichaceae
editor preferred label: Holdemania
imported from: ncbitaxon.owl

Serratia
type: Class
subclass of: Yersiniaceae
editor preferred label: Serratia
imported from: ncbitaxon.owl

Shigella
type: Class
subclass of: Enterobacteriaceae
editor preferred label: Shigella
imported from: ncbitaxon.owl

Shigella dysenteriae
type: Class
subclass of: Shigella
editor preferred label: Shigella dysenteriae
alternative term: Escherichia/Shigella dysenteriae
imported from: ncbitaxon.owl

Caenorhabditis elegans
type: Class
subclass of: Ecdysozoa
editor preferred label: Caenorhabditis elegans
alternative term: roundworm
imported from: ncbitaxon.owl

Yersinia
type: Class
subclass of: Yersiniaceae

Yersinia enterocolitica
type: Class
subclass of: Yersiniaceae
editor preferred label: Yersinia enterocolitica
imported from: ncbitaxon.owl

Vibrionaceae
type: Class
subclass of: Gammaproteobacteria
editor preferred label: Vibrionaceae
imported from: ncbitaxon.owl

Fretibacterium fastidiosum
type: Class
subclass of: Fretibacterium

Acidaminobacter
type: Class
subclass of: Clostridiales incertae sedis
editor preferred label: Acidaminobacter
imported from: ncbitaxon.owl

Photobacterium
type: Class
subclass of: Vibrionaceae
editor preferred label: Photobacterium
imported from: ncbitaxon.owl

Bacteroides xylanisolvens XB1A
type: Class
subclass of: Bacteroides xylanisolvens
editor preferred label: Bacteroides xylanisolvens XB1A
alternative term: Bacteroides xylanisolvens str. XB1A
alternative term: Bacteroides xylanisolvens strain XB1A
imported from: ncbitaxon.owl

Vibrio
type: Class
subclass of: Vibrionaceae
editor preferred label: Vibrio
imported from: ncbitaxon.owl

Daphnia
type: Class
subclass of: Pancrustacea
editor preferred label: Daphnia
alternative term: common water fleas
imported from: ncbitaxon.owl

Citrobacter farmeri
type: Class
subclass of: Citrobacter
editor preferred label: Citrobacter farmeri
imported from: ncbitaxon.owl

Citrobacter rodentium
type: Class
subclass of: Citrobacter
editor preferred label: Citrobacter rodentium
imported from: ncbitaxon.owl

delta/epsilon subdivisions
type: Class
subclass of: Proteobacteria
editor preferred label: delta/epsilon subdivisions
imported from: ncbitaxon.owl

Fusobacterium sp.
type: Class
subclass of: Fusobacterium
editor preferred label: Fusobacterium sp.
imported from: ncbitaxon.owl

Escherichia coli ETEC TW03439
type: Class
subclass of: Escherichia coli
subclass of: Restriction
  on property: microbe susceptibly expanded in gut of human with disease
  some values from: gout
editor preferred label: Escherichia coli ETEC TW03439
imported from: ncbitaxon.owl

Catenisphaera adipataccumulans
type: Class
subclass of: Erysipelotrichaceae
editor preferred label: Catenisphaera adipataccumulans
imported from: ncbitaxon.owl

Pasteurellaceae
type: Class
subclass of: Gammaproteobacteria
editor preferred label: Pasteurellaceae
imported from: ncbitaxon.owl

Aggregatibacter actinomycetemcomitans
type: Class
subclass of: Aggregatibacter
editor preferred label: Aggregatibacter actinomycetemcomitans
imported from: ncbitaxon.owl

saccharomyceta
type: Class
subclass of: Ascomycota
subclass of: OHMI_0000460
subclass of: Restriction
  on property: has quality
  some values from: OHMI_0000462
editor preferred label: saccharomyceta
imported from: ncbitaxon.owl

leotiomyceta
type: Class
subclass of: saccharomyceta
editor preferred label: leotiomyceta
imported from: ncbitaxon.owl

Drosophila melanogaster
type: Class
subclass of: Pancrustacea
editor preferred label: Drosophila melanogaster
alternative term: fruit fly
imported from: ncbitaxon.owl

Pseudomonadales
type: Class
subclass of: Gammaproteobacteria
editor preferred label: Pseudomonadales
imported from: ncbitaxon.owl

Campylobacteraceae
type: Class
subclass of: Campylobacterales
editor preferred label: Campylobacteraceae
imported from: ncbitaxon.owl

Haemophilus
type: Class
subclass of: Pasteurellaceae
subclass of: Restriction
  on property: microbe susceptibly depleted in oral cavity of human with disease
  some values from: rheumatoid arthritis
editor preferred label: Haemophilus
imported from: ncbitaxon.owl

Haemophilus parainfluenzae
type: Class
subclass of: Haemophilus

[Haemophilus] ducreyi
type: Class
subclass of: Haemophilus
editor preferred label: [Haemophilus] ducreyi
alternative term: Haemophilus ducreyi
imported from: ncbitaxon.owl

Haemophilus sp.
type: Class
subclass of: Haemophilus
subclass of: Restriction
  on property: microbe susceptibly depleted in gut of human with disease
  some values from: rheumatoid arthritis
subclass of: Restriction
  on property: microbe susceptibly depleted in oral cavity of human with disease
  some values from: rheumatoid arthritis

Verrucomicrobia
type: Class
subclass of: PVC group
editor preferred label: Verrucomicrobia
imported from: ncbitaxon.owl

Collinsella aerofaciens
type: Class
subclass of: Collinsella
subclass of: Restriction
  on property: microbe susceptibly expanded in gut of human with disease
  some values from: rheumatoid arthritis
editor preferred label: Collinsella aerofaciens
imported from: ncbitaxon.owl

Escherichia coli NC101
type: Class
subclass of: Escherichia coli
subclass of: Restriction
  on property: microbe susceptibly expanded in gut of human with disease
  some values from: colorectal cancer
editor preferred label: Escherichia coli NC101
imported from: ncbitaxon.owl

Escherichia coli EPEC 32/73
type: Class
subclass of: Escherichia coli
subclass of: Restriction
  on property: microbe susceptibly expanded in gut of human with disease
  some values from: gout
subclass of: Restriction
  on property: participates in
  some values from: expansion of Escherichia coli EPEC 32/73 in gout human gut
editor preferred label: Escherichia coli EPEC 32/73
alternative term: Escherichia coli str. EPEC 32/73
alternative term: Escherichia coli strain EPEC 32/73
imported from: ncbitaxon.owl

Malassezia restricta
type: Class
subclass of: Malassezia
editor preferred label: Malassezia restricta
imported from: ncbitaxon.owl

Malassezia sympodialis
type: Class
subclass of: Malassezia
editor preferred label: Malassezia sympodialis
imported from: ncbitaxon.owl

Fusobacterium nucleatum subsp. nucleatum
type: Class
subclass of: Fusobacterium nucleatum
editor preferred label: Fusobacterium nucleatum subsp. nucleatum
alternative term: Fusibacterium nucleatum subsp. nucleatum
imported from: ncbitaxon.owl

Fusobacterium nucleatum subsp. polymorphum
type: Class
subclass of: Fusobacterium nucleatum
editor preferred label: Fusobacterium nucleatum subsp. polymorphum
alternative term: Fusibacterium nucleatum subsp. polymorphum
imported from: ncbitaxon.owl

Fusobacterium nucleatum subsp. animalis
type: Class
subclass of: Fusobacterium nucleatum
editor preferred label: Fusobacterium nucleatum subsp. animalis
alternative term: Fusibacterium nucleatum subsp. animalis
imported from: ncbitaxon.owl

Malassezia pachydermatis
type: Class
subclass of: Malassezia
editor preferred label: Malassezia pachydermatis
imported from: ncbitaxon.owl

Vertebrata <Metazoa>
type: Class
subclass of: Bilateria
editor preferred label: Vertebrata <Metazoa>
alternative term: Vertebrata
alternative term: vertebrates
imported from: ncbitaxon.owl

Danio rerio
type: Class
subclass of: Euteleostomi
editor preferred label: Danio rerio
alternative term: leopard danio
alternative term: zebra danio
alternative term: zebra fish
alternative term: zebrafish
imported from: ncbitaxon.owl

Burkholderiales
type: Class
subclass of: Betaproteobacteria
editor preferred label: Burkholderiales
imported from: ncbitaxon.owl

Chlamydia
type: Class
subclass of: PVC group
editor preferred label: Chlamydia
imported from: ncbitaxon.owl

Chlamydia trachomatis
type: Class
subclass of: Chlamydia

Bacteroidaceae
type: Class
subclass of: Bacteroidales
editor preferred label: Bacteroidaceae
imported from: ncbitaxon.owl

Bacteroides
type: Class
subclass of: Bacteroidaceae
subclass of: Restriction
  on property: microbe susceptibly depleted in gut of human with disease
  some values from: rheumatoid arthritis
subclass of: Restriction
  on property: microbe susceptibly depleted (compared to fibromyalgia patients) in gut of human with disease
  some values from: rheumatoid arthritis
editor preferred label: Bacteroides
imported from: ncbitaxon.owl

Bacteroides fragilis
type: Class
subclass of: Bacteroides
subclass of: Restriction
  on property: microbe susceptibly expanded in gut of human with disease
  some values from: rheumatoid arthritis
subclass of: Restriction
  on property: microbe susceptibly depleted (compared to fibromyalgia patients) in gut of human with disease
  some values from: rheumatoid arthritis
editor preferred label: Bacteroides fragilis
imported from: ncbitaxon.owl

Enterococcaceae
type: Class
subclass of: Lactobacillales
editor preferred label: Enterococcaceae
imported from: ncbitaxon.owl

Bacteroides uniformis
type: Class
subclass of: Bacteroides
editor preferred label: Bacteroides uniformis
imported from: ncbitaxon.owl

Bacteroides vulgatus
type: Class
subclass of: Bacteroides
editor preferred label: Bacteroides vulgatus
imported from: ncbitaxon.owl

Anura
type: Class
subclass of: Tetrapoda
editor preferred label: Anura
alternative term: anurans
alternative term: frogs
alternative term: frogs and toads
imported from: ncbitaxon.owl

Xenopus <genus>
type: Class
subclass of: Anura
editor preferred label: Xenopus <genus>
alternative term: Xenopus
imported from: ncbitaxon.owl

Porphyromonas
type: Class
subclass of: Porphyromonadaceae
subclass of: Restriction
  on property: microbe susceptibly depleted in gut of human with disease
  some values from: rheumatoid arthritis
subclass of: Restriction
  on property: microbe susceptibly depleted in respiratory airway of human with disease
  some values from: rheumatoid arthritis
editor preferred label: Porphyromonas
imported from: ncbitaxon.owl

Porphyromonas gingivalis
type: Class
subclass of: Porphyromonas
subclass of: Restriction
  on property: microbe susceptibly expanded in gut of human with disease
  some values from: rheumatoid arthritis
subclass of: Restriction
  on property: microbe susceptibly expanded in oral cavity of human with disease
  some values from: rheumatoid arthritis
editor preferred label: Porphyromonas gingivalis
imported from: ncbitaxon.owl

Prevotella
type: Class
subclass of: Prevotellaceae
subclass of: Restriction
  on property: microbe susceptibly expanded in gut of human with disease
  some values from: systemic lupus erythematosus
subclass of: Restriction
  on property: microbe susceptibly expanded in gut of human with disease
  some values from: colorectal cancer
subclass of: Restriction
  on property: microbe susceptibly expanded in gut of human with disease
  some values from: enthesitis-related juvenile idiopathic arthritis
subclass of: Restriction
  on property: microbe susceptibly depleted in gut of human with disease
  some values from: diarrhea
subclass of: Restriction
  on property: microbe susceptibly depleted in gut of human with disease
  some values from: rheumatoid arthritis
subclass of: Restriction
  on property: microbe susceptibly expanded in gut of rat with disease
  some values from: ankylosing spondylitis
subclass of: Restriction
  on property: microbe susceptibly depleted in respiratory airway of human with disease
  some values from: rheumatoid arthritis
subclass of: Restriction
  on property: microbe susceptibly expanded in oral cavity of human with disease
  some values from: rheumatoid arthritis
subclass of: Restriction
  on property: microbe susceptibly expanded in oral cavity of human with disease
  some values from: systemic lupus erythematosus
editor preferred label: Prevotella
imported from: ncbitaxon.owl

Roseburia
type: Class
subclass of: Lachnospiraceae
editor preferred label: Roseburia
alternative term: Roseburya
alternative term: Roseburyella
imported from: ncbitaxon.owl

Coriobacteriaceae
type: Class
subclass of: Coriobacteriales
editor preferred label: Coriobacteriaceae
imported from: ncbitaxon.owl

Slackia
type: Class
subclass of: Eggerthellaceae
editor preferred label: Slackia
imported from: ncbitaxon.owl

Eggerthella
type: Class
subclass of: Eggerthellaceae
subclass of: Restriction
  on property: microbe susceptibly expanded in gut of human with disease
  some values from: rheumatoid arthritis

Eggerthella lenta
type: Class
subclass of: Eggerthellaceae
subclass of: Restriction
  on property: microbe susceptibly expanded in gut of human with disease
  some values from: rheumatoid arthritis
editor preferred label: Eggerthella lenta
imported from: ncbitaxon.owl

Cryptobacterium curtum
type: Class
subclass of: Eggerthellaceae
subclass of: Restriction
  on property: microbe susceptibly depleted in oral cavity of human with disease
  some values from: rheumatoid arthritis
editor preferred label: Cryptobacterium curtum
imported from: ncbitaxon.owl

Dolosicoccus paucivorans
type: Class
subclass of: Lactobacillales
editor preferred label: Dolosicoccus paucivorans
imported from: ncbitaxon.owl

Fusobacterium
type: Class
subclass of: Fusobacteriaceae
editor preferred label: Fusobacterium
alternative term: Fusibacterium
imported from: ncbitaxon.owl

Coriobacteriia
type: Class
subclass of: Actinobacteria <phylum>
editor preferred label: Coriobacteriia
imported from: ncbitaxon.owl

Coriobacteriales
type: Class
subclass of: Coriobacteriia
editor preferred label: Coriobacteriales
imported from: ncbitaxon.owl

Bifidobacteriales
type: Class
subclass of: Actinobacteria <class>
editor preferred label: Bifidobacteriales
imported from: ncbitaxon.owl

Micrococcales
type: Class
subclass of: Actinobacteria <class>
editor preferred label: Micrococcales
imported from: ncbitaxon.owl

Corynebacteriales
type: Class
subclass of: Actinobacteria <class>
editor preferred label: Corynebacteriales
imported from: ncbitaxon.owl

Nocardiaceae
type: Class
subclass of: Corynebacteriales
editor preferred label: Nocardiaceae
imported from: ncbitaxon.owl

Fusobacterium nucleatum
type: Class
subclass of: Fusobacterium
editor preferred label: Fusobacterium nucleatum
alternative term: Fusibacterium nucleatum
imported from: ncbitaxon.owl

Faecalibacterium prausnitzii
type: Class
subclass of: Faecalibacterium
editor preferred label: Faecalibacterium prausnitzii
alternative term: [Fusobacterium] prausnitzii
imported from: ncbitaxon.owl

Mogibacterium
type: Class
subclass of: Clostridiales Family XIII. Incertae Sedis
editor preferred label: Mogibacterium
imported from: ncbitaxon.owl

Magnolia globosa
type: Class
subclass of: Mesangiospermae
editor preferred label: Magnolia globosa
imported from: ncbitaxon.owl

Umbilicariaceae
type: Class
subclass of: leotiomyceta
editor preferred label: Umbilicariaceae
imported from: ncbitaxon.owl

[Clostridium] hiranonis
type: Class
subclass of: Peptostreptococcaceae
editor preferred label: [Clostridium] hiranonis
alternative term: Clostridium hiranonis
imported from: ncbitaxon.owl

[Clostridium] hylemonae
type: Class
subclass of: Lachnoclostridium
editor preferred label: [Clostridium] hylemonae
alternative term: Clostridium hylemonae
imported from: ncbitaxon.owl

Gallus gallus
type: Class
subclass of: Amniota
editor preferred label: Gallus gallus
alternative term: bantam
alternative term: chicken
alternative term: chickens
imported from: ncbitaxon.owl

Salmonella enterica subsp. enterica serovar Typhi
type: Class
subclass of: Salmonella enterica subsp. enterica
editor preferred label: Salmonella enterica subsp. enterica serovar Typhi
imported from: ncbitaxon.owl

Salmonella enterica subsp. enterica serovar Typhimurium
type: Class
subclass of: Salmonella enterica subsp. enterica
editor preferred label: Salmonella enterica subsp. enterica serovar Typhimurium
imported from: ncbitaxon.owl

Selenomonadales
type: Class
subclass of: Negativicutes

Negativicutes
type: Class
subclass of: Firmicutes
editor preferred label: Negativicutes
imported from: ncbitaxon.owl

Bacilli
type: Class
subclass of: Firmicutes
editor preferred label: Bacilli
imported from: ncbitaxon.owl

Enterobacterales
type: Class
subclass of: Gammaproteobacteria
editor preferred label: Enterobacterales
imported from: ncbitaxon.owl

Flavonifractor
type: Class
subclass of: unclassified Clostridiales

Homo sapiens
type: Class
subclass of: Euarchontoglires
editor preferred label: Homo sapiens
alternative term: human
alternative term: man
imported from: ncbitaxon.owl

Selenomonas
type: Class
subclass of: Selenomonadaceae
editor preferred label: Selenomonas
imported from: ncbitaxon.owl

Bacteroidetes
type: Class
subclass of: Bacteria
editor preferred label: Bacteroidetes
imported from: ncbitaxon.owl

Rodentia
type: Class
subclass of: Euarchontoglires
editor preferred label: Rodentia
alternative term: rodent
imported from: ncbitaxon.owl

Porphyromonas macacae
type: Class
subclass of: Porphyromonas
imported from: ncbitaxon.owl

planned process
type: Class
equivalent class: Restriction
  on property: realizes
  some values from: Restriction
    on property: concretizes
    some values from: plan specification
subclass of: process
editor preferred label: planned process
example of usage: Injecting mice with a vaccine in order to test its efficacy
has curation status: IAO_0000122
textual definition: A processual entity that realizes a plan which is the concretization of a plan specification.
editor note: 'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.)
editor note: We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some objectives is a planned process.
definition editor: Bjoern Peters
definition source: branch derived
curator notes: 6/11/9: Edited at workshop. Used to include: is initiated by an agent
curator notes: This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call)
imported from: obi.owl

biological feature identification objective
type: Class
subclass of: objective specification
editor preferred label: biological feature identification objective
has curation status: IAO_0000123
textual definition: Biological_feature_identification_objective is an objective role carried out by the proposition defining the aim of a study designed to examine or characterize a particular biological feature.
definition editor: Jennifer Fostel
imported from: obi.owl

processed material
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: material processing
subclass of: material entity
editor preferred label: processed material
example of usage: Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples
has curation status: IAO_0000122
textual definition: Is a material entity that is created or changed during material processing.
definition editor: PERSON: Alan Ruttenberg
imported from: obi.owl

evaluant role
type: Class
subclass of: role
subclass of: Restriction
  on property: inheres in
  some values from: material entity
subclass of: Restriction
  on property: realized in
  all values from: assay
editor preferred label: evaluant role
example of usage: When a specimen of blood is assayed for glucose concentration, the blood has the evaluant role. When measuring the mass of a mouse, the evaluant is the mouse. When measuring the time of DNA replication, the evaluant is the DNA. When measuring the intensity of light on a surface, the evaluant is the light source.
has curation status: IAO_0000122
textual definition: a role that inheres in a material entity that is realized in an assay in which data is generated about the bearer of the evaluant role
editor note: Role call - 17nov-08: JF and MC think an evaluant role is always specified input of a process. Even in the case where we have an assay taking blood as evaluant and outputting blood, the blood is not the specified output at the end of the assay (the concentration of glucose in the blood is)
editor note: examples of features that could be described in an evaluant: quality.... e.g. "contains 10 pg/ml IL2", or "no glucose detected")
definition editor: GROUP: Role Branch
definition source: OBI
curator notes: Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term.
imported from: obi.owl

assay
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: assay objective
subclass of: planned process
subclass of: Restriction
  on property: realizes
  some values from: evaluant role
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    intersection of: material entity
    intersection of: Restriction
      on property: has role
      some values from: evaluant role
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: is about
      some values from: Class
        intersection of: material entity
        intersection of: Restriction
editor preferred label: assay
example of usage: Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house.
has curation status: IAO_0000122
textual definition: A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies.
editor note: 12/3/12: BP: the reference to the 'physical examination' is included to point out that a prediction is not an assay, as that does not require physical examiniation.
definition editor: PlanAndPlannedProcess Branch
alternative term: measuring
alternative term: scientific observation
definition source: OBI branch derived
imported from: obi.owl
ISA alternative term: study assay
IEDB alternative term: any method

sample preparation for assay
type: Class
subclass of: material processing
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material transformation objective
editor preferred label: sample preparation for assay
has curation status: IAO_0000125
textual definition: A sample_preparation_for_assay is a protocol_application including material_enrollments and biomaterial_transformations. definition_source: OBI.
definition editor: PlanAndPlannedProcess Branch
alternative term: study
definition source: OBI branch derived
imported from: obi.owl

culture medium
type: Class
subclass of: processed material
editor preferred label: culture medium
example of usage: A growth medium or culture medium is a substance in which microorganisms or cells can grow. Wikipedia, growth medium, Feb 29, 2008
has curation status: IAO_0000122
textual definition: a processed material that provides the needed nourishment for microorganisms or cells grown in vitro.
editor note: changed from a role to a processed material based on on Aug 22, 2011 dev call. Details see the tracker item: http://sourceforge.net/tracker/?func=detail&aid=3325270&group_id=177891&atid=886178 Modification made by JZ.
definition editor: Person: Jennifer Fostel, Jie Zheng
definition source: OBI
imported from: obi.owl

reagent role
type: Class
subclass of: role
editor preferred label: reagent role
example of usage: Buffer, dye, a catalyst, a solvating agent.
has curation status: IAO_0000120
textual definition: A role inhering in a biological or chemical entity that is intended to be applied in a scientific technique to participate (or have molecular components that participate) in a chemical reaction that facilitates the generation of data about some entity distinct from the bearer, or the generation of some specified material output distinct from the bearer.
definition editor: PERSON:Matthew Brush
alternative term: reagent
definition source: PERSON:Matthew Brush
curator notes: Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. May 28 2013. Updated definition taken from ReO based on discussions initiated in Philly 2011 workshop. Former defnition described a narrower view of reagents in chemistry that restricts bearers of the role to be chemical entities ("a role played by a molecular entity used to produce a chemical reaction to detect, measure, or produce other substances"). Updated definition allows for broader view of reagents in the domain of biomedical research to include larger materials that have parts that participate chemically in a molecular reaction or interaction.
imported from: obi.owl
comment: (copied from ReO) Reagents are distinguished from instruments or devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in or have parts that participate in some chemical interaction or reaction during their intended participation in some technique. By contrast, instruments do not participate in a chemical reaction/interaction during the technique. Reagents are distinguished from study subjects/evaluants in that study subjects and evaluants are that about which conclusions are drawn and knowledge is sought in an investigation - while reagents, by definition, are not. It should be noted, however, that reagent and study subject/evaluant roles can be borne by instances of the same type of material entity - but a given instance will realize only one of these roles in the execution of a given assay or technique. For example, taq polymerase can bear a reagent role or an evaluant role. In a DNA sequencing assay aimed at generating sequence data about some plasmid, the reagent role of the taq polymerase is realized. In an assay to evaluate the quality of the taq polymerase itself, the evaluant/study subject role of the taq is realized, but not the reagent role since the taq is the subject about which data is generated. In regard to the statement that reagents are 'distinct' from the specified outputs of a technique, note that a reagent may be incorporated into a material output of a technique, as long as the IDENTITY of this output is distinct from that of the bearer of the reagent role. For example, dNTPs input into a PCR are reagents that become part of the material output of this technique, but this output has a new identity (ie that of a 'nucleic acid molecule') that is distinct from the identity of the dNTPs that comprise it. Similarly, a biotin molecule input into a cell labeling technique are reagents that become part of the specified output, but the identity of the output is t…

material processing
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: material transformation objective
subclass of: planned process
subclass of: Restriction
  on property: has_specified_input
  some values from: material entity
subclass of: Restriction
  on property: has_specified_output
  some values from: processed material
subclass of: Restriction
  on property: has_specified_input
  all values from: material entity
subclass of: Restriction
  on property: has_specified_output
  all values from: material entity
editor preferred label: material processing
example of usage: A cell lysis, production of a cloning vector, creating a buffer.
has curation status: IAO_0000122
textual definition: A planned process which results in physical changes in a specified input material
definition editor: PERSON: Bjoern Peters
definition editor: PERSON: Frank Gibson
definition editor: PERSON: Jennifer Fostel
definition editor: PERSON: Melanie Courtot
definition editor: PERSON: Philippe Rocca Serra
alternative term: material transformation
definition source: OBI branch derived
imported from: obi.owl

specimen role
type: Class
subclass of: role
subclass of: Restriction
  on property: inheres in
  some values from: Class
    intersection of: material entity
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: specimen collection process
editor preferred label: specimen role
example of usage: liver section; a portion of a culture of cells; a nemotode or other animal once no longer a subject (generally killed); portion of blood from a patient.
has curation status: IAO_0000122
textual definition: a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation
editor note: 22Jun09. The definition includes whole organisms, and can include a human. The link between specimen role and study subject role has been removed. A specimen taken as part of a case study is not considered to be a population representative, while a specimen taken as representing a population, e.g. person taken from a cohort, blood specimen taken from an animal) would be considered a population representative and would also bear material sample role.
editor note: Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation.
editor note: blood taken from animal: animal continues in study, whereas blood has role specimen. something taken from study subject, leaves the study and becomes the specimen.
editor note: parasite example - when parasite in people we study people, people are subjects and parasites are specimen - when parasite extracted, they become subject in the following study specimen can later be subject.
definition editor: GROUP: Role Branch
definition source: OBI
imported from: obi.owl

molecular feature identification objective
type: Class
subclass of: biological feature identification objective
editor preferred label: molecular feature identification objective
has curation status: IAO_0000123
textual definition: Molecular_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize molecular features of a biological system, e.g. expression profiling, copy number of molecular components, epigenetic modifications.
definition editor: Jennifer Fostel
imported from: obi.owl

DNA extraction
type: Class
subclass of: nucleic acid extraction
subclass of: Restriction
  on property: has_specified_output
  some values from: deoxyribonucleic acid
editor preferred label: DNA extraction
has curation status: IAO_0000123
textual definition: A DNA extraction is a nucleic acid extraction where the desired output material is DNA.
definition editor: PlanAndPlannedProcess Branch
definition source: OBI branch derived
imported from: obi.owl

analyte role
type: Class
subclass of: measurand role
subclass of: Restriction
  on property: role of
  some values from: Class
    union of: molecular entity
    union of: atom
editor preferred label: analyte role
example of usage: Glucose in blood (measured in an assay to determine the concentration of glucose).
has curation status: IAO_0000122
textual definition: A measurand role borne by a molecular entity or an atom and realized in an analyte assay which achieves the objective to measure the magnitude/concentration/amount of the analyte in the entity bearing evaluant role.
editor note: interestingly, an analyte is still an analyte even if it is not detected. for this reason it does not bear a specified input role
editor note: pH (technically the inverse log of [H+]) may be considered a quality; this remains to be tested.
editor note: qualities such as weight, color are not assayed but measured, so they do not fall into this category.
definition editor: GROUP: Role Branch
definition source: OBI
curator notes: Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term.
imported from: obi.owl

extract
type: Class
subclass of: processed material
subclass of: Restriction
  on property: is_specified_output_of
  some values from: extraction
editor preferred label: extract
example of usage: Up-regulation of inflammatory signalings by areca nut extract and role of cyclooxygenase-2 -1195G>a polymorphism reveal risk of oral cancer. Cancer Res. 2008 Oct 15;68(20):8489-98. PMID: 18922923
has curation status: IAO_0000120
textual definition: an extract is a material entity which results from an extraction process
definition editor: PERSON: Philippe Rocca-Serra
alternative term: extracted material
definition source: GROUP: OBI Biomatrial Branch
imported from: obi.owl

transcription profiling assay
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Class
    intersection of: Restriction
      on property: realizes
      some values from: Class
        intersection of: evaluant role
        intersection of: Restriction
    intersection of: Restriction
      on property: has_specified_input
      some values from: Class
        intersection of: RNA extract
        intersection of: Restriction
  intersection of: Class
    intersection of: Restriction
      on property: realizes
      some values from: Class
        intersection of: analyte role
        intersection of: Restriction
    intersection of: Restriction
      on property: has_specified_input
      some values from: ribonucleic acid
  intersection of: Restriction
    on property: has_specified_input
    some values from: Class
      intersection of: specimen
      intersection of: Restriction
        on property: has part
        some values from: ribonucleic acid
  intersection of: Restriction
    on property: has_specified_output
    some values from: measurement datum
  intersection of: Restriction
    on property: has_specified_output
    some values from: Restriction
      on property: is about
      some values from: gene expression
  intersection of: Restriction
    on property: achieves_planned_objective
    some values from: transcription profiling identification objective
subclass of: assay
editor preferred label: transcription profiling assay
example of usage: Whole genome transcription profiling of Anaplasma phagocytophilum in human and tick host cells by tiling array analysis. BMC Genomics. 2008 Jul 31;9:364. PMID: 18671858
has curation status: IAO_0000120
textual definition: An assay that determines gene expression and transcription activity using ribonucleic acids collected from a material entity.
editor note: This term should encompass transcription and post-transcription, but before translation into protein. So 'gene expression' itself is too broad, and we use 'transcription profiling identification objective' to constrain the scope of this term.
definition editor: Philippe Rocca-Serra
alternative term: gene expression profiling
alternative term: transcription profiling
definition source: OBI
imported from: obi.owl

assay objective
type: Class
subclass of: objective specification
editor preferred label: assay objective
example of usage: the objective to determine the weight of a mouse.
has curation status: IAO_0000122
textual definition: an objective specification to determine a specified type of information about an evaluated entity (the material entity bearing evaluant role)
definition editor: PPPB branch
definition source: PPPB branch
imported from: obi.owl

measure function
type: Class
subclass of: function
subclass of: Restriction
  on property: function of
  some values from: processed material
subclass of: Restriction
  on property: realized in
  all values from: Restriction
    on property: has_specified_output
    some values from: measurement datum
editor preferred label: measure function
example of usage: A glucometer measures blood glucose concentration, the glucometer has a measure function.
has curation status: IAO_0000122
textual definition: Measure function is a function that is borne by a processed material and realized in a process in which information about some entity is expressed relative to some reference.
definition editor: PERSON: Daniel Schober
definition editor: PERSON: Helen Parkinson
definition editor: PERSON: Melanie Courtot
definition editor: PERSON:Frank Gibson
imported from: obi.owl

material transformation objective
type: Class
subclass of: objective specification
editor preferred label: material transformation objective
example of usage: The objective to create a mouse infected with LCM virus. The objective to create a defined solution of PBS.
has curation status: IAO_0000122
textual definition: an objective specifiction that creates an specific output object from input materials.
definition editor: PERSON: Bjoern Peters
definition editor: PERSON: Frank Gibson
definition editor: PERSON: Jennifer Fostel
definition editor: PERSON: Melanie Courtot
definition editor: PERSON: Philippe Rocca-Serra
alternative term: artifact creation objective
definition source: GROUP: OBI PlanAndPlannedProcess Branch
imported from: obi.owl

DNA sequencing assay
type: Class
equivalent class: Class
  intersection of: sequencing assay
  intersection of: Class
    intersection of: Restriction
      on property: realizes
      some values from: Class
        intersection of: function
        intersection of: Restriction
    intersection of: Restriction
      on property: has_specified_input
      some values from: DNA sequencer
  intersection of: Class
    intersection of: Restriction
      on property: realizes
      some values from: Class
        intersection of: evaluant role
        intersection of: Restriction
    intersection of: Restriction
      on property: has_specified_input
      some values from: Class
        intersection of: DNA extract
        intersection of: Restriction
  intersection of: Restriction
    on property: has_specified_output
    some values from: DNA sequence data
subclass of: sequencing assay
editor preferred label: DNA sequencing assay
example of usage: Illumina (Solexa) sequencing is an example of DNA sequencing
has curation status: IAO_0000123
textual definition: A sequencing assay which determines information on the sequence of a DNA molecule.
definition editor: Philippe Rocca-Serra
alternative term: nucleotide sequencing
definition source: url:https://en.wikipedia.org/wiki/DNA_sequencing
imported from: obi.owl

material separation objective
type: Class
equivalent class: Class
  union of: portioning objective
  union of: separation into different composition objective
subclass of: material transformation objective
editor preferred label: material separation objective
example of usage: The objective to obtain multiple aliquots of an enzyme preparation. The objective to obtain cells contained in a sample of blood.
has curation status: IAO_0000122
textual definition: is an objective to transform a material entity into spatially separated components.
definition editor: PPPB branch
definition source: PPPB branch
imported from: obi.owl

specimen collection process
type: Class
equivalent class: Class
  intersection of: planned process
  intersection of: Restriction
    on property: achieves_planned_objective
    some values from: specimen collection objective
subclass of: planned process
subclass of: Restriction
  on property: has_specified_input
  some values from: material entity
subclass of: Restriction
  on property: has_specified_output
  some values from: specimen
editor preferred label: specimen collection process
example of usage: drawing blood from a patient for analysis, collecting a piece of a plant for depositing in a herbarium, buying meat from a butcher in order to measure its protein content in an investigation
has curation status: IAO_0000122
textual definition: A planned process with the objective of collecting a specimen.
editor note: Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation.
editor note: Philly2013: A specimen collection can have as part a material entity acquisition, such as ordering from a bank. The distinction is that specimen collection necessarily involves the creation of a specimen role. However ordering cell lines cells from ATCC for use in an investigation is NOT a specimen collection, because the cell lines already have a specimen role.
editor note: Philly2013: The specimen_role for the specimen is created during the specimen collection process.
editor note: label changed to 'specimen collection process' on 10/27/2014, details see tracker: http://sourceforge.net/p/obi/obi-terms/716/
definition editor: Bjoern Peters
alternative term: specimen collection
curator notes: 5/31/2012: This process is not necessarily an acquisition, as specimens may be collected from materials already in posession
curator notes: 6/9/09: used at workshop
imported from: obi.owl

sample from organism
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: collecting specimen from organism
  intersection of: Restriction
    on property: has role
    some values from: material sample role
subclass of: material sample
subclass of: specimen from organism
subclass of: Restriction
  on property: derives from
  some values from: UBERON_0000465
editor preferred label: sample from organism
has curation status: IAO_0000002
textual definition: a material obtained from an organism in order to be a representative of the whole
editor note: 5/29: This is a helper class for now
editor note: we need to work on this: Is taking a urine sample a material separation process? If not, we will need to specify what 'taking a sample from organism' entails. We can argue that the objective to obtain a urine sample from a patient is enough to call it a material separation process, but it could dilute what material separation was supposed to be about.
imported from: obi.owl

portioning objective
type: Class
subclass of: material separation objective
editor preferred label: portioning objective
example of usage: The objective to obtain multiple aliquots of an enzyme preparation.
has curation status: IAO_0000123
textual definition: A material separation objective aiming to separate material into multiple portions, each of which contains a similar composition of the input material.
imported from: obi.owl

separation into different composition objective
type: Class
subclass of: material separation objective
editor preferred label: separation into different composition objective
example of usage: The objective to obtain cells contained in a sample of blood.
has curation status: IAO_0000120
textual definition: A material separation objective aiming to separate a material entity that has parts of different types, and end with at least one output that is a material with parts of fewer types (modulo impurities).
editor note: We should be using has the grain relations or concentrations to distinguish the portioning and other sub-objectives
imported from: obi.owl

specimen collection objective
type: Class
subclass of: objective specification
editor preferred label: specimen collection objective
example of usage: The objective to collect bits of excrement in the rainforest. The objective to obtain a blood sample from a patient.
has curation status: IAO_0000122
textual definition: A objective specification to obtain a material entity for potential use as an input during an investigation.
definition editor: Bjoern Peters
definition source: Bjoern Peters
imported from: obi.owl

host role
type: Class
subclass of: role
subclass of: Restriction
  on property: inheres in
  some values from: organism
editor preferred label: host role
example of usage: In biology, a host is an organism that harbors a virus or parasite, or a mutual or commensal symbiont, typically providing nourishment and shelter. http://en.wikipedia.org/wiki/Host_(biology) 30 March 09
has curation status: IAO_0000120
textual definition: host role is a role played by an organism and realized by providing nourishment, shelter or a means of reproduction to another organism within the organism playing the host role
editor note: 30Mar09 virus reproducing inside a cell; bacteria causing a disease, host can be harmed or not. we want to avoid a cat sitting on my lap and an animal care technician; these are not examples or hosts; dental cares = on tooth, but part of outer layer of tooth, so covered by "within" in the definition
definition editor: GROUP: Role Branch
definition source: 30 Mar09 submitted by vaccine community
definition source: OBI
definition source: http://en.wikipedia.org/wiki/Host_(biology)
imported from: obi.owl

material sample role
type: Class
subclass of: specimen role
editor preferred label: material sample role
example of usage: a role borne by a portion of blood taken to represent all the blood in an organism; the role borne by a population of humans with HIV enrolled in a study taken to represent patients with HIV in general.
has curation status: IAO_0000125
textual definition: A material sample role is a specimen role borne by a material entity that is the output of a material sampling process.
editor note: 7/13/09: Note that this is a relational role: between the sample taken and the 'sampled' material of which the sample is thought to be representative off.
imported from: obi.owl

material sampling process
type: Class
equivalent class: Class
  intersection of: specimen collection process
  intersection of: Restriction
    on property: has_specified_input
    some values from: material entity
  intersection of: Restriction
    on property: has_specified_output
    some values from: material sample
subclass of: specimen collection process
editor preferred label: material sampling process
has curation status: IAO_0000123
textual definition: A specimen gathering process with the objective to obtain a specimen that is representative of the input material entity
imported from: obi.owl

material sample
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: has role
    some values from: material sample role
subclass of: specimen
editor preferred label: material sample
example of usage: blood drawn from patient to measure his systemic glucose level. A population of humans with HIV enrolled in a study taken to represent patients with HIV in general.
has curation status: IAO_0000123
textual definition: A material entity that has the material sample role
definition editor: OBI: workshop
alternative term: sample population
imported from: obi.owl
ISA alternative term: sample

material maintenance objective
type: Class
subclass of: objective specification
editor preferred label: material maintenance objective
has curation status: IAO_0000122
textual definition: An objective specification maintains some or all of the qualities of a material over time.
definition editor: PERSON: Bjoern Peters
definition source: PERSON: Bjoern Peters
imported from: obi.owl

primary structure of DNA macromolecule
type: Class
equivalent class: Restriction
  on property: is concretized as
  some values from: Restriction
    on property: inheres in
    some values from: deoxyribonucleic acid
subclass of: SO_0000001
editor preferred label: primary structure of DNA macromolecule
has curation status: IAO_0000123
textual definition: a quality of a DNA molecule that inheres in its bearer due to the order of its DNA nucleotide residues.
editor note: placeholder for SO
definition editor: BP et al
imported from: obi.owl

measurement device
type: Class
equivalent class: Class
  intersection of: device
  intersection of: Restriction
    on property: has function
    some values from: measure function
subclass of: device
editor preferred label: measurement device
example of usage: A ruler, a microarray scanner, a Geiger counter.
has curation status: IAO_0000122
textual definition: A device in which a measure function inheres.
definition editor: GROUP:OBI Philly workshop
definition source: OBI
imported from: obi.owl

material maintenance
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: material maintenance objective
subclass of: planned process
editor preferred label: material maintenance
has curation status: IAO_0000123
textual definition: a process with that achieves the objective to maintain some or all of the characteristics of an input material over time
imported from: obi.owl

RNA extract
type: Class
subclass of: nucleic acid extract
subclass of: Restriction
  on property: is_specified_output_of
  some values from: RNA extraction
subclass of: Restriction
  on property: has grain
  some values from: ribonucleic acid
editor preferred label: RNA extract
has curation status: IAO_0000120
textual definition: an extract which is the output of an extraction process in which RNA molecules are isolated from a specimen.
definition editor: PERSON: Chris Stoeckert
definition editor: PERSON: Jie Zheng
definition source: Group: UPenn Group
imported from: obi.owl

processed specimen
type: Class
equivalent class: Class
  intersection of: processed material
  intersection of: specimen
subclass of: processed material
subclass of: specimen
editor preferred label: processed specimen
example of usage: A tissue sample that has been sliced and stained for a histology study. A blood specimen that has been centrifuged to obtain the white blood cells.
has curation status: IAO_0000122
textual definition: A specimen that has been intentionally physically modified.
definition editor: Bjoern Peters
definition source: Bjoern Peters
imported from: obi.owl
comment: A tissue sample that has been sliced and stained for a histology study.

device
type: Class
subclass of: processed material
subclass of: Restriction
  on property: is_specified_output_of
  some values from: material processing
subclass of: Restriction
  on property: has function
  some values from: function
editor preferred label: device
example of usage: A voltmeter is a measurement device which is intended to perform some measure function.
example of usage: An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure.
has curation status: IAO_0000122
textual definition: A material entity that is designed to perform a function in a scientific investigation, but is not a reagent.
editor note: 2012-12-17 JAO: In common lab usage, there is a distinction made between devices and reagents that is difficult to model. Therefore we have chosen to specifically exclude reagents from the definition of "device", and are enumerating the types of roles that a reagent can perform. 2013-6-5 MHB: The following clarifications are outcomes of the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For example: (1) An HPLC machine is considered a device, but has a column that holds a stationary phase resin as an operational component. This resin qualifies as a device if it participates purely in size exclusion, but bears a reagent role that is realized in the running of a column if it interacts electrostatically or chemically with the evaluant. The container the resin is in (“the column”) considered alone is a device. So the entire column as well as the entire HPLC machine are devices that have a reagent as an operating part. (2) A pH meter is a device, but its electrode component bears a reagent role in virtue of its interacting directly with the evaluant in execution of an assay. (3) A gel running box is a device that has a metallic lead as a component that participates in a chemical reaction with the running buffer when a charge is passed through it. This metallic lead is considered to have a reagent role as a component of this device realized in the running of a gel. In the examples above, a reagent is an operational component of a device, but the device itself does not realize a reagent role (as bearing a reagent…
definition editor: PERSON: Helen Parkinson
alternative term: instrument
definition source: OBI development call 2012-12-17.
imported from: obi.owl

sequence data
type: Class
subclass of: measurement datum
subclass of: Class
  intersection of: measurement datum
  intersection of: Restriction
    on property: is about
    some values from: SO_0000001
editor preferred label: sequence data
example of usage: example of usage: the representation of a nucleotide sequence in FASTA format used for a sequence similarity search.
has curation status: IAO_0000120
textual definition: A measurement datum that representing the primary structure of a macromolecule(it's sequence) sometimes associated with an indicator of confidence of that measurement.
definition editor: Person:Chris Stoeckert
definition source: GROUP: OBI
imported from: obi.owl

nucleic acid extract
type: Class
subclass of: extract
subclass of: processed specimen
subclass of: Class
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: nucleic acid extraction
  intersection of: Restriction
    on property: has role
    some values from: specimen role
subclass of: Restriction
  on property: has grain
  some values from: nucleic acid
editor preferred label: nucleic acid extract
has curation status: IAO_0000120
textual definition: An extract that is the output of an extraction process in which nucleic acid molecules are isolated from a specimen.
definition editor: PERSON: Jie Zheng
definition source: UPenn Group
imported from: obi.owl

DNA extract
type: Class
subclass of: nucleic acid extract
subclass of: Restriction
  on property: is_specified_output_of
  some values from: DNA extraction
subclass of: Restriction
  on property: has grain
  some values from: deoxyribonucleic acid
editor preferred label: DNA extract
has curation status: IAO_0000120
textual definition: The output of an extraction process in which DNA molecules are purified in order to exclude DNA from organellas.
definition editor: Person: Jie Zheng
definition source: Group: UPenn group
imported from: obi.owl

nucleic acid sequencer
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: measure function
editor preferred label: nucleic acid sequencer
has curation status: IAO_0000120
textual definition: An device that is used to determine the order of nucleotides in nucleic acid sequences.
definition editor: PERSON: Erik Segerdell
definition source: PERSON: Erik Segerdell
imported from: obi.owl

protein sequencer
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: measure function
editor preferred label: protein sequencer
has curation status: IAO_0000120
textual definition: An device that is used to determine the order of amino acids in protein sequences.
definition editor: PERSON: Erik Segerdell
definition source: PERSON: Erik Segerdell
imported from: obi.owl

RNA-seq assay
type: Class
subclass of: transcription profiling assay
subclass of: sequencing assay
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: function
      intersection of: Restriction
        on property: inheres in
        some values from: DNA sequencer
  intersection of: Restriction
    on property: has_specified_input
    some values from: DNA sequencer
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: analyte role
      intersection of: Restriction
        on property: inheres in
        some values from: ribonucleic acid
  intersection of: Restriction
    on property: has_specified_input
    some values from: ribonucleic acid
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    intersection of: specimen
    intersection of: Restriction
      on property: has part
      some values from: ribonucleic acid
subclass of: Restriction
  on property: has_specified_output
  some values from: sequence data
subclass of: Restriction
  on property: has_specified_output
  some values from: Restriction
    on property: is about
    some values from: gene expression
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: transcription profiling identification objective
editor preferred label: RNA-seq assay
has curation status: IAO_0000120
textual definition: An transcription profiling assay that determines an RNA sequence by analyzing the transcibed regions of the genome and or to quantitate transcript abundance.
definition editor: James Malone
alternative term: transcription profiling by high throughput sequencing
definition source: EFO:0002770
imported from: obi.owl

transcription profiling identification objective
type: Class
subclass of: molecular feature identification objective
editor preferred label: transcription profiling identification objective
has curation status: IAO_0000120
textual definition: A molecular feature identification objective that aims to characterize the abundance of transcripts
definition editor: Person: Chris Stoeckert, Jie Zheng
definition source: Group: Penn Group
imported from: obi.owl

specimen from organism
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: has role
    some values from: specimen role
  intersection of: Restriction
    on property: derives from
    some values from: Class
      union of: UBERON_0000465
      union of: UBERON_0000477
subclass of: specimen
editor preferred label: specimen from organism
has curation status: IAO_0000122
textual definition: A specimen that derives from an anatomical part or substance arising from an organism. Examples of tissue specimen include tissue, organ, physiological system, blood, or body location (arm).
definition editor: PERSON: Chris Stoeckert, Jie Zheng
alternative term: tissue specimen
definition source: MO_954 organism_part
imported from: obi.owl

sampling time measurement datum
type: Class
subclass of: time measurement datum
editor preferred label: sampling time measurement datum
has curation status: IAO_0000120
textual definition: A time measurement datum when an observation is made or a sample is taken from a material as measured from some reference point.
definition editor: Person: Chris Stoeckert
alternative term: time point
definition source: MO_738 timepoint
imported from: obi.owl

DNA sequence data
type: Class
subclass of: sequence data
subclass of: Restriction
  on property: is about
  some values from: primary structure of DNA macromolecule
editor preferred label: DNA sequence data
example of usage: The part of a FASTA file that contains the letters ACTGGGAA
has curation status: IAO_0000120
textual definition: A sequence data item that is about the primary structure of DNA
definition editor: OBI call; Bjoern Peters
definition source: OBI call; Melanie Courtout
curator notes: 8/29/11 call: This is added after a request from Melanie and Yu. They should review it further. This should be a child of 'sequence data', and as of the current definition will infer there.
imported from: obi.owl

specimen collection time measurement datum
type: Class
subclass of: time measurement datum
subclass of: Restriction
  on property: is about
  some values from: Class
    intersection of: process boundary
    intersection of: Restriction
      on property: starts
      some values from: specimen collection process
editor preferred label: specimen collection time measurement datum
has curation status: IAO_0000120
textual definition: A time measurement datum that is the measure of the time when the specimens are collected.
definition editor: Person: Chris Stoeckert, Jie Zheng
alternative term: collection date
definition source: NIAID GSCID-BRC metadata working group
imported from: obi.owl
NIAID GSCID-BRC alternative term: Specimen Collection Date
Source: NIAID GSCID-BRC

sample preparation for sequencing assay
type: Class
equivalent class: Class
  intersection of: sample preparation for assay
  intersection of: Restriction
    on property: has_specified_input
    some values from: Class
      intersection of: specimen
      intersection of: Restriction
        on property: has grain
        some values from: nucleic acid
  intersection of: Restriction
    on property: has_specified_output
    some values from: Class
      intersection of: specimen
      intersection of: Restriction
        on property: is_specified_input_of
        some values from: sequencing assay
subclass of: sample preparation for assay
editor preferred label: sample preparation for sequencing assay
has curation status: IAO_0000120
textual definition: A sample preparation for assay that preparation of nucleic acids for a sequencing assay
definition editor: PERSON: Chris Stoeckert, Jie Zheng
definition source: NIAID GSCID-BRC metadata working group
imported from: obi.owl
NIAID GSCID-BRC alternative term: Nucleic Acid Preparation Method
Source: NIAID GSCID-BRC

cell freezing medium
type: Class
subclass of: processed material
editor preferred label: cell freezing medium
has curation status: IAO_0000120
textual definition: A processed material that serves as a liquid vehicle for freezing cells for long term quiescent stroage, which contains chemicls needed to sustain cell viability across freeze-thaw cycles.
definition editor: PERSON: Matthew Brush
imported from: obi.owl

scalar value specification
type: Class
subclass of: value specification
subclass of: Restriction
  on property: has measurement unit label
  min cardinality: 1
subclass of: Restriction
  on property: has specified numeric value
  min cardinality: 1
editor preferred label: scalar value specification
has curation status: IAO_0000123
textual definition: A value specification that consists of two parts: a numeral and a unit label
definition editor: PERSON:Bjoern Peters
imported from: obi.owl

value specification
type: Class
subclass of: information content entity
editor preferred label: value specification
example of usage: The value of 'positive' in a classification scheme of "positive or negative"; the value of '20g' on the quantitative scale of mass.
has curation status: IAO_0000122
textual definition: An information content entity that specifies a value within a classification scheme or on a quantitative scale.
editor note: This term is currently a descendant of 'information content entity', which requires that it 'is about' something. A value specification of '20g' for a measurement data item of the mass of a particular mouse 'is about' the mass of that mouse. However there are cases where a value specification is not clearly about any particular. In the future we may change 'value specification' to remove the 'is about' requirement.
definition editor: PERSON:Bjoern Peters
imported from: obi.owl

whole genome sequencing assay
type: Class
subclass of: DNA sequencing assay
editor preferred label: whole genome sequencing assay
example of usage: WGS permits comprehensive sequencing of introns and exons, whereas whole exome sequencing (WES) allows deeper sequencing of exonic regions at a lower cost. Due to the large number of genetic variants found in each genome, it is necessary to use filtering approaches to distinguish deleterious from benign variants. WES has been used successfully to identify novel genetic causes of primary immunodeficiency. Complex structural variations and non-Mendelian disorders remain challenges for WGS.
has curation status: IAO_0000120
textual definition: A DNA sequencing assay that intends to provide information about the sequence of an entire genome of an organism.
editor note: Genotyping assays should ideally identify which part of the genome the information is about. We do not currently have a good way to do this. That information should be added later.
definition editor: ImmPort
alternative term: WGS
definition source: PMID:23095910
definition source: PMID:25827230
imported from: obi.owl

measurand role
type: Class
subclass of: role
subclass of: Restriction
  on property: role of
  some values from: material entity
editor preferred label: measurand role
has curation status: IAO_0000120
textual definition: A role borne by a material entity and realized in an assay which achieves the objective to measure the magnitude/concentration/amount of the measurand in the entity bearing evaluant role.
definition editor: Person: Alan Ruttenberg, Jie Zheng
definition source: https://en.wiktionary.org/wiki/measurand
term tracker item: https://github.com/obi-ontology/obi/issues/778
imported from: obi.owl

organism
type: Class
equivalent class: Class
  union of: Viruses
  union of: Bacteria
  union of: Archaea
  union of: Eukaryota
subclass of: material entity
editor preferred label: organism
example of usage: animal
example of usage: fungus
example of usage: plant
example of usage: virus
has curation status: IAO_0000122
textual definition: A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs.
editor note: 10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms')
editor note: 13-02-2009: OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. This issue is outside the scope of OBI.
definition editor: GROUP: OBI Biomaterial Branch
definition source: WEB: http://en.wikipedia.org/wiki/Organism
imported from: obi.owl

specimen
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: has role
    some values from: specimen role
subclass of: material entity
editor preferred label: specimen
example of usage: Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen.
has curation status: IAO_0000122
textual definition: A material entity that has the specimen role.
editor note: Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation.
definition editor: PERSON: James Malone
definition editor: PERSON: Philippe Rocca-Serra
definition source: GROUP: OBI Biomaterial Branch
imported from: obi.owl

cultured cell population
type: Class
subclass of: processed material
subclass of: Restriction
  on property: is_specified_output_of
  some values from: maintaining cell culture
subclass of: Restriction
  on property: has grain
  some values from: cultured cell
subclass of: Restriction
  on property: has grain
  all values from: cultured cell
editor preferred label: cultured cell population
example of usage: A cultured cell population applied in an experiment: "293 cells expressing TrkA were serum-starved for 18 hours and then neurotrophins were added for 10 min before cell harvest." (Lee, Ramee, et al. "Regulation of cell survival by secreted proneurotrophins." Science 294.5548 (2001): 1945-1948). A cultured cell population maintained in vitro: "Rat cortical neurons from 15 day embryos are grown in dissociated cell culture and maintained in vitro for 8–12 weeks" (Dichter, Marc A. "Rat cortical neurons in cell culture: culture methods, cell morphology, electrophysiology, and synapse formation." Brain Research 149.2 (1978): 279-293).
has curation status: IAO_0000120
textual definition: A processed material comprised of a collection of cultured cells that has been continuously maintained together in culture and shares a common propagation history.
editor note: 2013-6-5 MHB: This OBI class was formerly called 'cell culture', but label changed and definition updated following CLO alignment efforts in spring 2013, during which the intent of this class was clarified to refer to portions of a culture or line rather than a complete cell culture or line.
definition editor: PERSON:Matthew Brush
alternative term: cell culture sample
definition source: PERSON:Matthew Brush
imported from: obi.owl
comment: The extent of a 'cultured cell population' is restricted only in that all cell members must share a propagation history (ie be derived through a common lineage of passages from an initial culture). In being defined in this way, this class can be used to refer to the populations that researchers actually use in the practice of science - ie are the inputs to culturing, experimentation, and sharing. The cells in such populations will be a relatively uniform population as they have experienced similar selective pressures due to their continuous co-propagation. And this population will also have a single passage number, again owing to their common passaging history. Cultured cell populations represent only a collection of cells (ie do not include media, culture dishes, etc), and include populations of cultured unicellular organisms or cultured multicellular organism cells. They can exist under active culture, stored in a quiescent state for future use, or applied experimentally.

extraction
type: Class
subclass of: material component separation
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: separation into different composition objective
editor preferred label: extraction
example of usage: nucleic acid extraction using phenol chloroform
has curation status: IAO_0000123
textual definition: A material separation in which a desired component of an input material is separated from the remainder
editor note: Current the output of material processing defined as the molecular entity, main component in the output material entity, rather than the material entity that have grain molecular entity. 'nucleic acid extract' is the output of 'nucleic acid extraction' and has grain 'nucleic acid'. However, the output of 'nucleic acid extraction' is 'nucleic acid' rather than 'nucleic acid extract'. We are aware of this issue and will work it out in the future.
definition editor: Person:Bjoern Peters
definition editor: Philippe Rocca-Serra
imported from: obi.owl

DNA sequencer
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: measure function
editor preferred label: DNA sequencer
example of usage: ABI 377 DNA Sequencer, ABI 310 DNA Sequencer
has curation status: IAO_0000122
textual definition: A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences.
definition editor: Trish Whetzel
definition source: MO
imported from: obi.owl

collecting specimen from organism
type: Class
subclass of: specimen collection process
subclass of: Restriction
  on property: has_specified_input
  some values from: organism
subclass of: Restriction
  on property: has_specified_output
  some values from: specimen
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: specimen collection objective
editor preferred label: collecting specimen from organism
example of usage: taking a sputum sample from a cancer patient, taking the spleen from a killed mouse, collecting a urine sample from a patient
has curation status: IAO_0000122
textual definition: a process with the objective to obtain a material entity that was part of an organism for potential future use in an investigation
definition editor: PERSON:Bjoern Peters
definition source: IEDB
imported from: obi.owl

environmental material collection process
type: Class
subclass of: specimen collection process
subclass of: Restriction
  on property: has_specified_input
  some values from: environmental material
subclass of: Restriction
  on property: has_specified_output
  some values from: specimen
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: specimen collection objective
editor preferred label: environmental material collection
example of usage: Taking 1 liter of surface ocean water from the San Diego Mission Bay Jetty. Capturing mice living in rural Arkansas
has curation status: IAO_0000123
textual definition: environmental_material_collection is an acquisition where an object is taken from an environment and put into a storage container. Roles include, environment, thing collected, container, acquirer.
editor note: relabel the term and add axiom connecting to EnVO:'environmental material' discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/obi-terms/779/
definition editor: Bjoern Peters, Alan Ruttenberg
definition source: IEDB
curator notes: the researcher is very interested in the location
imported from: obi.owl

material component separation
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: material separation objective
subclass of: material processing
subclass of: Restriction
  on property: has_specified_input
  some values from: material entity
subclass of: Restriction
  on property: has_specified_output
  some values from: material entity
editor preferred label: material component separation
example of usage: Using a cell sorter to separate a mixture of T cells into two fractions; one with surface receptor CD8 and the other lacking the receptor, or purification
has curation status: IAO_0000122
textual definition: a material processing in which components of an input material become segregated in space
definition editor: Bjoern Peters
definition source: IEDB
imported from: obi.owl

maintaining cell culture
type: Class
subclass of: material maintenance
subclass of: Restriction
  on property: has_specified_input
  some values from: cultured cell population
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    union of: culture medium
    union of: cell freezing medium
subclass of: Restriction
  on property: has_specified_output
  some values from: cultured cell population
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material maintenance objective
editor preferred label: maintaining cell culture
example of usage: When harvesting blood from a human, isolating T cells, and then limited dilution cloning of the cells, the maintaining_cell_culture step comprises all steps after the initial dilution and plating of the cells into culture, e.g. placing the culture into an incubator, changing or adding media, and splitting a cell culture
has curation status: IAO_0000125
textual definition: a protocol application in which cells are kept alive in a defined environment outside of an organism. part of cell_culturing
definition editor: PlanAndPlannedProcess Branch
definition source: OBI branch derived
imported from: obi.owl

establishing cell culture
type: Class
subclass of: material processing
subclass of: Restriction
  on property: has_specified_input
  some values from: cell
subclass of: Restriction
  on property: has_specified_input
  some values from: culture medium
subclass of: Restriction
  on property: has_specified_output
  some values from: cultured cell population
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material transformation objective
editor preferred label: 'establishing cell culture'
has curation status: IAO_0000120
textual definition: a process through which a new type of cell culture or cell line is created, either through the isolation and culture of one or more cells from a fresh source, or the deliberate experimental modification of an existing cell culture (e.g passaging a primary culture to become a secondary culture or line, or the immortalization or stable genetic modification of an existing culture or line).
definition editor: PERSON:Matthew Brush
definition source: PERSON:Matthew Brush
imported from: obi.owl
comment: A 'cell culture' as used here referes to a new lineage of cells in culture deriving from a single biological source.. New cultures are established through the initial isolation and culturing of cells from an organismal source, or through changes in an existing cell culture or line that result in a new culture with unique characteristics. This can occur through the passaging/selection of a primary culture into a secondary culture or line, or experimental modifications of an existing cell culture or line such as an immortalization process or other stable genetic modification. This class covers establishment of cultures of either multicellular organism cells or unicellular organisms.

sequencing assay
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Class
    intersection of: Restriction
      on property: realizes
      some values from: Class
        intersection of: function
        intersection of: Restriction
    intersection of: Restriction
      on property: has_specified_input
      some values from: Class
        union of: nucleic acid sequencer
        union of: protein sequencer
        union of: DNA sequencer
  intersection of: Class
    intersection of: Restriction
      on property: realizes
      some values from: Class
        intersection of: evaluant role
        intersection of: Restriction
    intersection of: Restriction
      on property: has_specified_input
      some values from: Class
        intersection of: Class
        intersection of: Restriction
  intersection of: Restriction
    on property: has_specified_output
    some values from: sequence data
  intersection of: Restriction
    on property: has_specified_output
    some values from: Restriction
      on property: is about
      some values from: SO_0000001
subclass of: assay
editor preferred label: sequencing assay
example of usage: The use of the Sanger method of DNA sequencing to determine the order of the nucleotides in a DNA template
has curation status: IAO_0000125
textual definition: An assay the uses chemical or biochemical means to infer the sequence of a biomaterial
definition editor: PlanAndPlannedProcess Branch
definition source: OBI branch derived
imported from: obi.owl

RNA extraction
type: Class
subclass of: nucleic acid extraction
subclass of: Restriction
  on property: has_specified_output
  some values from: ribonucleic acid
editor preferred label: RNA extraction
has curation status: IAO_0000125
textual definition: A RNA extraction is a nucleic acid extraction where the desired output material is RNA
definition editor: PlanAndPlannedProcess Branch
definition source: OBI branch derived
curator notes: requested by Helen Parkinson for MO
imported from: obi.owl

nucleic acid extraction
type: Class
subclass of: extraction
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    union of: sample from organism
    union of: organism
    union of: cultured cell population
subclass of: Restriction
  on property: has_specified_output
  some values from: nucleic acid
editor preferred label: nucleic acid extraction
example of usage: Phenol / chlorophorm extraction disolvation of protein content folllowed by ethanol precipitation of the nucleic acid fraction over night in the fridge followed by centrifugation to obtain a nucleic acid pellet.
has curation status: IAO_0000125
textual definition: a material separation to recover the nucleic acid fraction of an input material
definition editor: PlanAndPlannedProcess Branch
definition source: OBI branch derived
curator notes: requested by Helen Parkinson for MO. Could be defined class
imported from: obi.owl

infection process
type: Class
subclass of: pathologic process
subclass of: Restriction
  on property: realizes
  some values from: disposition to infect an organism
subclass of: Restriction
  on property: has participant
  some values from: infection
editor preferred label: infection process
has curation status: IAO_0000120
textual definition: the detrimental process in which an infectious agent colonizes or replicates in a host environment
definition editor: IEDB
definition source: IEDB
imported from: obi.owl

disposition to infect an organism
type: Class
subclass of: disposition
subclass of: Restriction
  on property: realized in
  all values from: infection process
editor preferred label: disposition to infect an organism
has curation status: IAO_0000123
textual definition: Is a role borne by an agent, and realized when in contact with or inside another organism in which it is capable of replicating and causing disease
definition editor: IEDB
definition source: IEDB
imported from: obi.owl

pathologic process
type: Class
subclass of: biological_process
editor preferred label: pathologic process
has curation status: IAO_0000123
textual definition: abnormal, harmful processes caused by or associated with a disease
definition editor: IEDB
definition source: IEDB
imported from: obi.owl

genome
type: Class
subclass of: material entity
textual definition: A genome is a material entity that represents the entirety of an organism's hereditary information. The genome includes both the genes and the non-coding sequences of the DNA and RNA.
definition editor: Oliver He
definition source: Book: Eugene Nester, Denise Anderson, C. Evans Roberts, Jr., Microbiology (Companion Site): A Human Perspective, 7th Edition. Mcgraw Hill, October 18, 2011. ISBN-13: 978-0073375311
definition source: WEB: http://en.wikipedia.org/wiki/Genome
imported from: ogg.owl

gene
type: Class
subclass of: material entity
textual definition: A gene is a material entity that represents the entire DNA sequence required for synthesis of a functional protein or RNA molecule.
definition editor: Oliver He
definition source: WEB: http://www.ncbi.nlm.nih.gov/books/NBK21640/
imported from: ogg.owl

host-microbiome interaction
type: Class
equivalent class: Class
  intersection of: interaction
  intersection of: Restriction
    on property: has participant
    some values from: microbiome
  intersection of: Restriction
    on property: has participant
    some values from: OHMI_0000485
subclass of: interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0001062
subclass of: Restriction
  on property: has participant
  some values from: microbiome
subclass of: Restriction
  on property: has participant
  some values from: OHMI_0000485
textual definition: A biological interaction between a microbiome and its host
definition editor: Oliver He, Jie Zheng, Jihad Obeid, Anna Maria Masci
alternative term: microbiome-host interaction
definition source: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1669-4
definition source: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4644880/

human microbiome
type: Class
subclass of: microbiome
subclass of: Restriction
  on property: located in
  some values from: Homo sapiens
textual definition: A microbiome located in a human body
definition editor: JZ, YH
definition source: https://www.ncbi.nlm.nih.gov/pubmed/3418802/

microbiome
type: Class
subclass of: biome
subclass of: Restriction
  on property: has part
  some values from: OHMI_0000463
textual definition: A biome that consists of a collection of microorganisms (i.e., microbiota) and the surrounding environment where the microorganisms reside.
definition editor: Oliver He, Jie Zheng, Jihad Obeid, Anna Maria Masci
definition source: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4520061/

mouse microbiome
type: Class
subclass of: microbiome
subclass of: Restriction
  on property: located in
  some values from: Mus musculus
textual definition: A microbiome located in a mouse body
definition editor: JZ, YH

bacterial microbiome
type: Class
subclass of: microbiome
textual definition: A microbiome that includes a collective population of bacterial organisms.
definition editor: YH, JZ, JO, AA

fungal microbiome
type: Class
subclass of: microbiome
textual definition: A microbiome that includes a collective population of fungal microorganisms.
definition editor: YH, JZ, JO, AA
definition source: https://www.ncbi.nlm.nih.gov/pubmed/3708484/

viral microbiome
type: Class
subclass of: microbiome
textual definition: A microbiome that includes a collective population of virus

fungal microbiome of skin
type: Class
subclass of: fungal microbiome
textual definition: A fungal microbiome that is located in the skin of a host organism
definition editor: YH, JZ, JO, AA
definition source: https://www.ncbi.nlm.nih.gov/pubmed/3708484/

fungal microbiome of mucosal site
type: Class
subclass of: fungal microbiome
textual definition: A fungal microbiome that is located in a mucosal site of a host organism (e.g., urogenital tract, oral cavity, and gastrointestinal tract)
definition editor: YH, JZ, JO, AA
definition source: https://www.ncbi.nlm.nih.gov/pubmed/3708484/

fungal microbiome of lung
type: Class
subclass of: fungal microbiome
textual definition: A fungal microbiome that is located in a lung of a host organism
definition editor: YH, JZ, JO, AA
definition source: https://www.ncbi.nlm.nih.gov/pubmed/3708484/

interaction between microbiome and host immune system
type: Class
subclass of: host-microbiome interaction
textual definition: A host-microbiome interaction where the microbiome interacts with the host immune system
definition editor: YH, JZ, JO, AA

interaction between microbiome and adaptive immune system
type: Class
subclass of: interaction between microbiome and host immune system
textual definition: A interaction between microbiome and host immune system where the immune system is the host adaptive immune system
definition editor: YH, JZ, JO, AA
definition source: https://www.ncbi.nlm.nih.gov/pubmed/27366226

microbiome in human lung
type: Class
subclass of: microbiome in human respiratory system
textual definition: a human microbiome that is located in a human respiratory system
definition editor: JO, AA, YH

microbiome in human respiratory system
type: Class
subclass of: human microbiome
textual definition: a human microbiome that is located in a human lung
definition editor: JO, AA, YH

microbiome in human oral
type: Class
subclass of: human microbiome
textual definition: a human microbiome that is located in a human oral system
definition editor: JO, AA, YH

microbiome in human gastrointestinal system
type: Class
subclass of: human microbiome
textual definition: a human microbiome that is located in a human gastrointestinal system
definition editor: JO, AA, YH

microbiome in human cutaneous system
type: Class
subclass of: human microbiome
textual definition: a human microbiome that is located in a human cutaneous system
definition editor: JO, AA, YH

microbiome in human urogenital system
type: Class
subclass of: human microbiome
textual definition: a human microbiome that is located in a human urogenital system
definition editor: JO, AA, YH

human-microbiome interaction
type: Class
subclass of: host-microbiome interaction
subclass of: Restriction
  on property: has participant
  some values from: Class
    intersection of: Homo sapiens
    intersection of: Restriction
      on property: has role
      some values from: host role
textual definition: A host-microbiome interaction where the host is human
definition editor: YH, HW

human gut microbiome
type: Class
subclass of: microbiome in human gastrointestinal system
textual definition: A microbiome located in a human gut.
definition editor: YH
alternative term: human gut microbiota
comment: A human being's gut microbiota contains tens of trillions of microorganisms, including at least 1000 different species of known bacteria with more than 3 million genes (150 times more than human genes). Microbiota can, in total, weigh up to 2 kg. One third of our gut microbiota is common to most people, while two thirds are specific to each one of us. In other words, the microbiota in your intestine is like an individual identity card. URL: http://www.gutmicrobiotaforhealth.com/en/about-gut-microbiota-info/

human-gut microbiome interaction
type: Class
subclass of: human-microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: Class
    intersection of: UBERON_0004907
    intersection of: Restriction
      on property: part of
      some values from: Homo sapiens
subclass of: Restriction
  on property: has participant
  some values from: Class
    intersection of: microbiome
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
textual definition: An interaction between human and gut microbiome.
definition editor: YH

human gut microbiome interaction in bowel syndrome
type: Class
subclass of: human-gut microbiome interaction
textual definition: A human-gut microbiome interaction that is associated with bowel syndrome.
definition editor: YH
definition source: https://www.ncbi.nlm.nih.gov/pubmed/25864640

human gut microbiome interaction in Crohn's disease
type: Class
subclass of: human-gut microbiome interaction
textual definition: A human-gut microbiome interaction that is associated with Crohn's disease.
definition editor: YH
definition source: https://www.ncbi.nlm.nih.gov/pubmed/25864640

colon cancer human-gut microbiome interaction
type: Class
subclass of: human-gut microbiome interaction
subclass of: Restriction
  on property: has participant
  some values from: Class
    intersection of: Homo sapiens
    intersection of: Restriction
      on property: has disease
      some values from: colon cancer
textual definition: A human-gut microbiome interaction that is associated with colon cancer.
definition editor: YH
definition source: https://www.ncbi.nlm.nih.gov/pubmed/25864640

human gut microbiome and Clostridium difficile interaction
type: Class
subclass of: human-gut microbiome interaction
textual definition: A human-gut microbiome interaction that involves in Clostridium difficile
definition editor: YH
definition source: https://www.ncbi.nlm.nih.gov/pubmed/4892173/

antibiotics reducing colonization resistance against C. difficile in human gut
type: Class
subclass of: human gut microbiome and Clostridium difficile interaction
textual definition: A human-gut microbiome interaction where antibiotics have significant and long-lasting effects on the intestinal microbiota and consequently reduce colonization resistance against Clostridium difficile.
definition editor: YH
definition source: https://www.ncbi.nlm.nih.gov/pubmed/4892173/

restoring human gut microbiome resistance to C. difficile infection by fecal microbiota transplantation
type: Class
subclass of: human gut microbiome and Clostridium difficile interaction
textual definition: A human-gut microbiome interaction where a fecal microbiota transplantation is used to restore a human gut microbiome to a state resistant to Clostridium difficile infection.
definition editor: YH
alternative term: restoring human gut microbiome resistance to CDI by FMT
definition source: https://www.ncbi.nlm.nih.gov/pubmed/4328137/

Clostridioides difficile infection
type: Class
subclass of: infection process
textual definition: An infection process that is caused by Clostridioides difficile.
definition editor: YH
alternative term: CDI

RA human-gut microbiome interaction
type: Class
subclass of: human-gut microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has participant
  some values from: Class
    intersection of: Homo sapiens
    intersection of: Restriction
      on property: has disease
      some values from: rheumatoid arthritis
textual definition: A human gut-microbiome interaction that is associated with rheumatoid arthritis (RA).
definition editor: YH
definition source: https://www.ncbi.nlm.nih.gov/pubmed/4840970/

patient with RA having decreased gut microbial diversity
type: Class
subclass of: RA human-gut microbiome interaction
subclass of: Restriction
  on property: has participant
  some values from: Class
    intersection of: OHMI_0000460
    intersection of: Restriction
      on property: has quality
      some values from: descreased microbiome organism diversity
textual definition: An association of human gut microbiota with rheumatoid arthritis (RA) that shows a patient with RV exhibits decreased gut microbial diversity
definition editor: YH
definition source: https://www.ncbi.nlm.nih.gov/pubmed/4840970/

increased organism quantity compared with healthy control
type: Class
subclass of: quality
textual definition: A quality with an increased quantity of a type of organism (e.g., bacteria inside human gut) compared with control.
definition editor: YH, HW, HY

descreased microbiome organism diversity
type: Class
subclass of: quality
textual definition: A quality with an decreased microbiome organism dirversity in a host microbiome environment (e.g., gut).
definition editor: YH, HW, HY

depletion of Klebsiella pneumoniae in RA human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Klebsiella pneumoniae
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: RA human-gut microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Klebsiella pneumoniae
textual definition: a RA human-gut microbiome interaction that shows an decrease of Klebsiella pneumoniae in patients with RA compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/

decreased organism quantity compared with healthy controls
type: Class
subclass of: quality
textual definition: A quality with a depleted quantity of a type of organism (e.g., bacteria inside human gut) compared with control.
definition editor: YH, HW, HY

human oral cavity microbiome interaction
type: Class
subclass of: human-microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: Class
    intersection of: UBERON_0000167
    intersection of: Restriction
      on property: part of
      some values from: Homo sapiens
textual definition: An interaction between human and oral microbiome.
definition editor: YH WH YH

expansion of Gordonibacter pamelaeae in RA human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Gordonibacter pamelaeae
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: expansion of Actinobacteria<phylum> in RA human gut
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Gordonibacter pamelaeae
textual definition: a RA human-gut microbiome interaction that shows an expansion of Gordonibacter pamelaeae in patients with RA compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/26214836/

expansion of Prevotellaceae in RA human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Prevotellaceae
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: RA human-gut microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Prevotellaceae
textual definition: a RA human-gut microbiome interaction that shows an expansion of Prevotellaceae in patients with chronic RA compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pmc/articles/PMID:24192039/

depletion of Bifidobacterium bifidum in RA human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Bifidobacterium bifidum
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: RA human-gut microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Bifidobacterium bifidum
textual definition: a RA human-gut microbiome interaction that shows an decrease of Bifidobacterium bifidum in patients with RA compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/

depletion of Veillonella in RA human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Veillonella
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: RA human-gut microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Veillonella
textual definition: a RA human-gut microbiome interaction that shows an decrease of Veillonellain in patients with RA compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/

depletion of Sutterella wadsworthensis in RA human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Sutterella wadsworthensis
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: RA human-gut microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Sutterella wadsworthensis
textual definition: RA human-gut microbiome interaction that shows an decrease of Sutterella wadsworthensis in patients with RA compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/

depletion of Megamonas hypermegale in RA human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Megamonas hypermegale
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: RA human-gut microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Megamonas hypermegale
textual definition: a RA human-gut microbiome interaction that shows an decrease of Megamonas hypermegale in patients with RA compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/

expansion of [Clostridium] asparagiforme in RA human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: [Clostridium] asparagiforme
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: expansion of Clostridia in RA human gut
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: [Clostridium] asparagiforme
textual definition: a RA human-gut microbiome interaction that shows an expansion of [Clostridium] asparagiforme in patients with RA compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
evidence publication: https://www.ncbi.nlm.nih.gov/pubmed/26214836/

expansion of B. fragilis in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Bacteroides fragilis
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: expansion of Bacteroides in colorectal cancer human gut
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Bacteroides fragilis
textual definition: A colorectal cancer human-gut microbiome interaction where B. fragilis is increased.
definition editor: YH, HW
evidence publication: https://www.ncbi.nlm.nih.gov/pubmed/24967088
evidence publication: https://www.ncbi.nlm.nih.gov/pubmed/27810411

expansion of Eggerthella lenta in RA human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Eggerthella lenta
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: expansion of Actinobacteria<phylum> in RA human gut
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Eggerthella lenta
textual definition: a RA human-gut microbiome interaction that shows an expansion of Eggerthella lenta in patients with RA compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/26214836/

decreased organism quantity in acute disease patient compared with chronic disease control
type: Class
subclass of: quality
textual definition: A quality with a depleted quantity of a type of organism (e.g., bacteria inside human gut) in a patient with an acute disease compared with a patient control with the same disease but at a chronic stage.
definition editor: YH, HW, HY

rat-microbiome interaction
type: Class
subclass of: host-microbiome interaction
subclass of: Restriction
  on property: has participant
  some values from: Class
    intersection of: Rattus
    intersection of: Restriction
      on property: has role
      some values from: host role
textual definition: A host-microbiome interaction where the host is rattus.
definition editor: YH, HW

expansion of Bifidobacterium dentium in RA human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Bifidobacterium dentium
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: expansion of Actinobacteria<phylum> in RA human gut
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Bifidobacterium dentium
textual definition: a RA human-gut microbiome interaction that shows an expansion of Bifidobacterium dentium in patients with RA compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/26214836/

expansion of Lactobacillus sp in RA human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Lactobacillus sp.
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: RA human-gut microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Lactobacillus sp.
textual definition: a RA human-gut microbiome interaction that shows an expansion of Lactobacillus sp in patients with RA compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/26214836/

expansion of Ruminococcus lactaris in RA human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Ruminococcus lactaris
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: expansion of Clostridia in RA human gut
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Ruminococcus lactaris
textual definition: a RA human-gut microbiome interaction that shows an expansion of Ruminococcus lactaris in patients with chronic RA compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/26214836/

segregation of Prevotella or Bacteroides dominance in RA human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Class
      union of: Bacteroides sp.
      union of: Prevotella
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: RA human-gut microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Class
    union of: Bacteroides sp.
    union of: Prevotella
textual definition: a RA human-gut microbiome interaction that shows high Prevotella or high Bacteroides relative abundance, but rarely a high relative abundance of both.
definition editor: Haihe Wang, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/24192039

decreased organism quantity compared with fibromyalgia patients
type: Class
subclass of: quality
textual definition: A quality with a depleted quantity of a type of organism (e.g., bacteria inside human gut) compared with a patient control with the fibromyalgia (FM) disease.
definition editor: YH, HW, HY

SLE human-gut microbiome interaction
type: Class
subclass of: human-gut microbiome interaction
subclass of: Restriction
  on property: has participant
  some values from: Class
    intersection of: Homo sapiens
    intersection of: Restriction
      on property: has disposition
      some values from: systemic lupus erythematosus
textual definition: A human gut-microbiome interaction that is associated with systemic lupus erythematosus (SLE).
definition editor: Haihe Wang, Hong Yu, Yongqun He

colorectal cancer human-gut microbiome interaction
type: Class
subclass of: human-gut microbiome interaction
subclass of: Restriction
  on property: has participant
  some values from: Class
    intersection of: Homo sapiens
    intersection of: Restriction
      on property: has disease
      some values from: colorectal cancer
textual definition: A human-gut microbiome interaction that is associated with colorectal cancer.
definition editor: YH, HW

expansion of Fusobacterium sp. in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Fusobacterium sp.
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: expansion of Fusobacterium in colorectal cancer human gut
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Fusobacterium sp.
textual definition: A colorectal cancer human-gut microbiome interaction where Fusobacterium sp. is increased.
definition editor: YH, HW
evidence publication: https://www.ncbi.nlm.nih.gov/pubmed/23733170
evidence publication: https://www.ncbi.nlm.nih.gov/pubmed/23954159
evidence publication: https://www.ncbi.nlm.nih.gov/pubmed/25104642

depletion of Citrobacter in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Citrobacter
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: colorectal cancer human-gut microbiome interaction
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Citrobacter
textual definition: A colorectal cancer human-gut microbiome interaction where Citrobacter is decreased.
definition editor: YH, HW
evidence publication: https://www.ncbi.nlm.nih.gov/pubmed/21647227

expansion of Porphyromonas gingivalis in RA human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Porphyromonas gingivalis
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: RA human-gut microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Porphyromonas gingivalis
textual definition: a RA human-gut microbiome interaction that shows an expansion of Porphyromonas gingivalis in patients with RA compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/20436074 /
definition source: https://www.ncbi.nlm.nih.gov/pubmed/24873878/

depletion of Shigella in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Shigella
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: colorectal cancer human-gut microbiome interaction
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Shigella
textual definition: A colorectal cancer human-gut microbiome interaction where Shigella is decreased.
definition editor: YH, HW
evidence publication: https://www.ncbi.nlm.nih.gov/pubmed/21647227

expansion of Prevotella intermedia in RA human oral cavity
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Prevotella intermedia
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0000167
        intersection of: Restriction
subclass of: expansion of Prevotella in RA human oral cavity
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0000167
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Prevotella intermedia
textual definition: a RA human oral cavity microbiome interaction that shows an expansion of rare taxa,Prevotella intermedia in patients with RA compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/22576262
definition source: https://www.ncbi.nlm.nih.gov/pubmed/27789760

expansion of Porphyromonas gingivalis in RA human oral cavity
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Porphyromonas gingivalis
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0000167
        intersection of: Restriction
subclass of: RA human oral cavity microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0000167
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Porphyromonas gingivalis
textual definition: a RA human oral cavity microbiome interaction that shows an expansion of Porphyromonas gingivalis in patients with RA compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/19554393
definition source: https://www.ncbi.nlm.nih.gov/pubmed/23902301
definition source: https://www.ncbi.nlm.nih.gov/pubmed/27641915
definition source: https://www.ncbi.nlm.nih.gov/pubmed/27789760

expansion of Proteus mirabilis in RA human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Proteus mirabilis
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: RA human-gut microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Proteus mirabilis
textual definition: a RA human-gut microbiome interaction that shows an expansion of Proteus mirabilis in patients with RA compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/19895906/
definition source: https://www.ncbi.nlm.nih.gov/pubmed/24873878/

expansion of Collinsella aerofaciens in RA human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Collinsella aerofaciens
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: expansion of Actinobacteria<phylum> in RA human gut
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Collinsella aerofaciens
textual definition: a RA human-gut microbiome interaction that shows an expansion of Collinsella aerofaciens in patients with RA compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/27102666/

diarrheal patient-gut microbiome interaction
type: Class
subclass of: human-gut microbiome interaction
subclass of: Restriction
  on property: has participant
  some values from: Class
    intersection of: Homo sapiens
    intersection of: Restriction
      on property: has disease
      some values from: diarrhea
textual definition: A human gut-microbiome interaction that is associated with the diarrhea disease
definition editor: YH

expansion of Klebsiella in SLE human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Klebsiella
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: SLE human-gut microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Klebsiella
textual definition: a SLE human-gut microbiome interaction that shows an expansion of Klebsiella in patients with SLE compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/27980687/

expansion of Lactobacillus salivarius in RA human oral cavity
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Lactobacillus salivarius
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0000167
        intersection of: Restriction
subclass of: RA human oral cavity microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0000167
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Lactobacillus salivarius
textual definition: a RA human oral cavity microbiome interaction that shows an expansion of Lactobacillus salivarius in patients with RA compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/26214836
definition source: https://www.ncbi.nlm.nih.gov/pubmed/27789760
evidence publication: https://www.ncbi.nlm.nih.gov/pubmed/26214836

expansion of Clostridia in RA human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Clostridia
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: RA human-gut microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Clostridia
textual definition: a RA human-gut microbiome interaction that shows an expansion of Clostridia in patients with RA compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/26385261/
definition source: https://www.ncbi.nlm.nih.gov/pubmed/2889500/

expansion of Clostridium perfringens in RA human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Clostridium perfringens
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: expansion of Clostridia in RA human gut
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Clostridium perfringens
textual definition: a RA human-gut microbiome interaction that shows an expansion of Clostridium perfringens in patients with RA compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/2889500

expansion of Prevotella in SLE human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Prevotella
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: expansion of Bacteroidales in SLE human gut
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Prevotella
textual definition: a SLE human-gut microbiome interaction that shows an expansion of Prevotella in patients with SLE compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/27980687/

depletion of Dialister in SLE human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Dialister
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: SLE human-gut microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Dialister
textual definition: a SLE human-gut microbiome interaction that shows a depletion of Dialister in patients with SLE compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/27980687/

depletion of Bacteroides in RA human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Bacteroides
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: RA human-gut microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Bacteroides
textual definition: a RA human-gut microbiome interaction that shows an decrease of Bacteroides in patients with RA compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
evidence publication: https://www.ncbi.nlm.nih.gov/pubmed/

depletion of Porphyromonas in RA human gut compared to fibromyalgia patients
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Porphyromonas
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with fibromyalgia patients
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: RA human-gut microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Porphyromonas
textual definition: a RA human-gut microbiome interaction that shows an decrease of Porphyromonas in patients with RA compared to fibromyalgia patients
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/18528968
definition source: https://www.ncbi.nlm.nih.gov/pubmed/

depletion of Prevotella in RA human gut compared to fibromyalgia patients
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Prevotella
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with fibromyalgia patients
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: RA human-gut microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Prevotella
textual definition: a RA human-gut microbiome interaction that shows an decrease of Prevotella in patients with RA compared to fibromyalgia patients
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/

human respiratory airway microbiome interaction
type: Class
subclass of: human-microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: Class
    intersection of: UBERON_0001005
    intersection of: Restriction
      on property: part of
      some values from: Homo sapiens
textual definition: An interaction between human and respiratory airway microbiome.
definition editor: Haihe Wang, Hong Yu, Yongqun He

RA human respiratory airway microbiome interaction
type: Class
subclass of: human respiratory airway microbiome interaction
subclass of: Restriction
  on property: has participant
  some values from: Class
    intersection of: Homo sapiens
    intersection of: Restriction
      on property: has disposition
      some values from: rheumatoid arthritis
textual definition: A human respiratory airway microbiome interaction that is associated with rheumatoid arthritis (RA).
definition editor: Haihe Wang, Hong Yu, Yongqun He

depletion of Porphyromonas in RA human respiratory airway
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Porphyromonas
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0001005
        intersection of: Restriction
subclass of: RA human respiratory airway microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0001005
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Porphyromonas
textual definition: RA human respiratory airway microbiome interaction that shows an decrease of Porphyromonas in patients with RA compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/

depletion of Prevotella in RA human respiratory airway
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Prevotella
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0001005
        intersection of: Restriction
subclass of: RA human respiratory airway microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0001005
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Prevotella
textual definition: RA human respiratory airway microbiome interaction that shows an decrease of Prevotella in patients with RA compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/

depletion of Pseudobutyrivibrio in SLE human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Pseudobutyrivibrio
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: SLE human-gut microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Pseudobutyrivibrio
textual definition: a SLE human-gut microbiome interaction that shows a depletion of Pseudobutyrivibrio in patients with SLE compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/27980687/

SLE human oral cavity microbiome interaction
type: Class
subclass of: human oral cavity microbiome interaction
subclass of: Restriction
  on property: has participant
  some values from: Class
    intersection of: Homo sapiens
    intersection of: Restriction
      on property: has disposition
      some values from: systemic lupus erythematosus
textual definition: A human oral cavity microbiome interaction that is associated with systemic lupus erythematosus (SLE).
definition editor: YH

RA human oral cavity microbiome interaction
type: Class
subclass of: human oral cavity microbiome interaction
subclass of: Restriction
  on property: has participant
  some values from: Class
    intersection of: Homo sapiens
    intersection of: Restriction
      on property: has disposition
      some values from: rheumatoid arthritis
textual definition: A human oral cavity microbiome interaction that is associated with rheumatoid arthritis (RA).
definition editor: YH

depletion of Haemophilus in RA human oral cavity
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Haemophilus
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0000167
        intersection of: Restriction
subclass of: RA human oral cavity microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0000167
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Haemophilus
textual definition: a RA human oral cavity microbiome interaction that shows an decrease of Haemophilus in patients with RA compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/

expansion of Actinobacteria<phylum> in RA human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Actinobacteria <phylum>
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: RA human-gut microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Actinobacteria <phylum>
textual definition: a RA human-gut microbiome interaction that shows an expansion of Actinobacteria<phylum> in patients with RA compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/28376066/

depletion of Cardiobacterium in RA human oral cavity
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Cardiobacterium
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0000167
        intersection of: Restriction
subclass of: RA human oral cavity microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0000167
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Cardiobacterium
textual definition: a RA human oral cavity microbiome interaction that shows an decrease of Cardiobacterium in patients with RA compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/

depletion of Eikenella in RA human oral cavity
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Eikenella
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0000167
        intersection of: Restriction
subclass of: RA human oral cavity microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0000167
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Eikenella
textual definition: a RA human oral cavity microbiome interaction that shows an decrease of Eikenella in patients with RA compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/

depletion of Kingella in RA human oral cavity
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Kingella
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0000167
        intersection of: Restriction
subclass of: RA human oral cavity microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0000167
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Kingella
textual definition: a RA human oral cavity microbiome interaction that shows an expansion of Kingella in patients with RA compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/

depletion of Rothia aeria in RA human oral cavity
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Rothia aeria
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0000167
        intersection of: Restriction
subclass of: RA human oral cavity microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0000167
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Rothia aeria
textual definition: a RA human oral cavity microbiome interaction that shows an expansion of Rothia aeria in patients with RA compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/

depletion of Prevotella in diarrheal patient gut
type: Class
equivalent class: Restriction
  on property: has microbe depleted in diseased host
  some values from: Class
    intersection of: Prevotella
    intersection of: Class
      intersection of: Restriction
        on property: part of
        some values from: Class
      intersection of: Restriction
        on property: located in
        some values from: UBERON_0004907
subclass of: diarrheal patient-gut microbiome interaction
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Prevotella
textual definition: a diarrheal patient-gut microbiome interaction that shows an decrease of Prevotella in patients in the gut of human diarrheal patient compared with healthy controls.
definition editor: YH
definition source: http://microbiomedb.org/mbio/app/

expansion of Prevotella copri in RA human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Prevotella copri
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: expansion of Prevotellaceae in RA human gut
subclass of: segregation of Prevotella or Bacteroides dominance in RA human gut
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Prevotella copri
textual definition: a RA human-gut microbiome interaction that shows an expansion of Prevotella copri in patients with RA compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/27333153

depletion of Haemophilus spp. in RA human oral cavity
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Haemophilus sp.
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0000167
        intersection of: Restriction
subclass of: depletion of Haemophilus in RA human oral cavity
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0000167
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Haemophilus sp.
textual definition: a RA human oral cavity microbiome interaction that shows an decrease of Haemophilus sp in patients with RA compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/

expansion of Cryptobacterium curtum in RA human oral cavity
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Cryptobacterium curtum
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0000167
        intersection of: Restriction
subclass of: RA human oral cavity microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0000167
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Cryptobacterium curtum
textual definition: a RA human oral cavity microbiome interaction that shows an increase of Cryptobacterium curtum in patients with RA compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/

expansion of Veillonella in RA human oral cavity
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Veillonella
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0000167
        intersection of: Restriction
subclass of: RA human oral cavity microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0000167
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Veillonella
textual definition: a RA human oral cavity microbiome interaction that shows an expansion of Veillonella in patients with RA compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/

rat gut microbiome interaction
type: Class
subclass of: rat-microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: Class
    intersection of: UBERON_0004907
    intersection of: Restriction
      on property: part of
      some values from: Rattus
textual definition: An interaction between rattus and gut microbiome.
definition editor: YH

expansion of Escherichia coli in RA human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Escherichia coli
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: RA human-gut microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Escherichia coli
textual definition: a RA human-gut microbiome interaction that shows an expansion of Escherichia coli in patients with RA compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/20360042/

depletion of Clostridiales in SLE human oral cavity
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Clostridiales
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0000167
        intersection of: Restriction
subclass of: SLE human oral cavity microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0000167
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Clostridiales
textual definition: a SLE human oral cavity microbiome interaction that shows an decrease of Clostridiales in patients with SLE compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/

depletion of Faecalibacterium in RA human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Faecalibacterium
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: RA human-gut microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Faecalibacterium
textual definition: a RA human-gut microbiome interaction that shows an decrease of Faecalibacterium in patients with RA compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/

AS human-gut microbiome interaction
type: Class
subclass of: human-gut microbiome interaction
subclass of: Restriction
  on property: has participant
  some values from: Class
    intersection of: Homo sapiens
    intersection of: Restriction
      on property: has disease
      some values from: ankylosing spondylitis
textual definition: A human gut-microbiome interaction that is associated with ankylosing spondylitis (AS).
definition editor: Haihe Wang, Hong Yu, Yongqun He

expansion of Ruminococcaceae in AS human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Ruminococcaceae
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: AS human-gut microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Ruminococcaceae
textual definition: an AS human-gut microbiome interaction that shows an expansion of Ruminococcaceae in patients with AS compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/25417597/
definition source: https://www.ncbi.nlm.nih.gov/pubmed/26362739/

expansion of Lachnospiraceae in AS human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Lachnospiraceae
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: AS human-gut microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Lachnospiraceae
textual definition: an AS human-gut microbiome interaction that shows an expansion of Lachnospiraceae in patients with AS compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/25417597/
definition source: https://www.ncbi.nlm.nih.gov/pubmed/25434931/
definition source: https://www.ncbi.nlm.nih.gov/pubmed/26331579/

expansion of Bacteroidaceae in AS human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Bacteroidaceae
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: AS human-gut microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Bacteroidaceae
textual definition: an AS human-gut microbiome interaction that shows an expansion of Bacteroidaceae in patients with AS compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/25417597/

expansion of Prevotellaceae in AS human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Prevotellaceae
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: AS human-gut microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Prevotellaceae
textual definition: an AS human-gut microbiome interaction that shows an expansion of Prevotellaceae in patients with AS compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/25417597/

expansion of Veillonellaceae in AS human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Veillonellaceae
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: AS human-gut microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Veillonellaceae
textual definition: an AS human-gut microbiome interaction that shows an expansion of rare taxa,Veillonellaceae in patients with AS compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/25417597/
definition source: https://www.ncbi.nlm.nih.gov/pubmed/25434931/
definition source: https://www.ncbi.nlm.nih.gov/pubmed/26331579/

expansion of Klebsiella pneumoniae in AS human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Klebsiella pneumoniae
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: AS human-gut microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Klebsiella pneumoniae
textual definition: an AS human-gut microbiome interaction that shows an expansion of Klebsiella pneumoniae in patients with AS compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/1001180/

AS human oral cavity microbiome interaction
type: Class
subclass of: human oral cavity microbiome interaction
subclass of: Restriction
  on property: has participant
  some values from: Class
    intersection of: Homo sapiens
    intersection of: Restriction
      on property: has disposition
      some values from: ankylosing spondylitis
textual definition: A human oral cavity microbiome interaction that is associated with ankylosing spondylitis (AS).
definition editor: YH

expansion of Klebsiella pneumoniae in AS human oral cavity
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Klebsiella pneumoniae
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0000167
        intersection of: Restriction
subclass of: AS human oral cavity microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0000167
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Klebsiella pneumoniae
textual definition: an AS human oral cavity microbiome interaction that shows an expansion of Klebsiella pneumoniae in patients with AS compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/17458395/

expansion of Prevotella intermedia in AS human oral cavity
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Prevotella intermedia
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0000167
        intersection of: Restriction
subclass of: AS human oral cavity microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0000167
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Prevotella intermedia
textual definition: an AS human oral cavity microbiome interaction that shows an expansion of Prevotella intermedia in patients with AS compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/26002454/

expansion of Tannerella forsythia in AS human oral cavity
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Tannerella forsythia
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0000167
        intersection of: Restriction
subclass of: AS human oral cavity microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0000167
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Tannerella forsythia
textual definition: an AS human oral cavity microbiome interaction that shows an expansion of rare taxa,Tannerella forsythia in patients with AS compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/26002454/

AS rat-gut microbiome interaction
type: Class
subclass of: rat gut microbiome interaction
subclass of: Restriction
  on property: has participant
  some values from: Class
    intersection of: Rattus
    intersection of: Restriction
      on property: has disposition
      some values from: ankylosing spondylitis
textual definition: A rattus gut-microbiome interaction that is associated with ankylosing spondylitis (AS).
definition editor: Haihe Wang, Hong Yu, Yongqun He
alternative term: association of rat gut microbiota with ankylosing spondylitis

expansion of Prevotella in SLE human oral cavity
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Prevotella
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0000167
        intersection of: Restriction
subclass of: SLE human oral cavity microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0000167
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Prevotella
textual definition: a SLE human oral cavity microbiome interaction that shows an expansion of Prevotella in patients with SLE compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/28320468/

depletion of Firmicutes in SLE human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Firmicutes
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: SLE human-gut microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Firmicutes
textual definition: a SLE human-gut microbiome interaction that shows an decrease of Firmicutes in patients with SLEcompared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/

expansion of Bacteroidetes in SLE human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Bacteroidetes
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: SLE human-gut microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Bacteroidetes
textual definition: a SLE human-gut microbiome interaction that shows an expansion of Bacteroidetes in patients with SLE compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/25271284/

gout human-gut microbiome interaction
type: Class
subclass of: human-gut microbiome interaction
subclass of: Restriction
  on property: has participant
  some values from: Class
    intersection of: Homo sapiens
    intersection of: Restriction
      on property: has disease
      some values from: gout
textual definition: A human gut-microbiome interaction that is associated with gout.
definition editor: Haihe Wang, Hong Yu, Yongqun He

expansion of Bacteroidetes in gout human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Bacteroidetes
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: gout human-gut microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Bacteroidetes
textual definition: a Gout human-gut microbiome interaction that shows an decrease of rare taxa,Bacteroidetes in patients with gout compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/28270806/

expansion of Bacteroides in gout human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Bacteroides
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: expansion of Bacteroidaceae in gout human gut
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Bacteroides
textual definition: a Gout human-gut microbiome interaction that shows an expansion of Bacteroides in patients with gout compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/28270806/

expansion of Bacteroidales in gout human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Bacteroidales
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: expansion of Bacteroidetes in gout human gut
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Bacteroidales
textual definition: a Gout human-gut microbiome interaction that shows an expansion of Bacteroidales in patients with gout compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/28270806/

expansion of Porphyromonadaceae in gout human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Porphyromonadaceae
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: expansion of Bacteroidales in gout human gut
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Porphyromonadaceae
textual definition: a Gout human-gut microbiome interaction that shows an expansion of Porphyromonadaceae in patients with gout compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/28270806/

expansion of Bacteroidaceae in gout human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Bacteroidaceae
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: expansion of Bacteroidales in gout human gut
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Bacteroidaceae
textual definition: a Gout human-gut microbiome interaction that shows an expansion of Bacteroidaceae in patients with gout compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/28270806/

expansion of Negativicutes in gout human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Negativicutes
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: gout human-gut microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Negativicutes
textual definition: a Gout human-gut microbiome interaction that shows an expansion of Negativicutes in patients with gout compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/28270806/

human skin microbiome interaction
type: Class
subclass of: human-microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: Class
    intersection of: UBERON_0000014
    intersection of: Restriction
      on property: part of
      some values from: Homo sapiens
textual definition: An interaction between human and zone of skin microbiome.
definition editor: YH

PsA human zone of skin microbiome interaction
type: Class
subclass of: human skin microbiome interaction
subclass of: Restriction
  on property: has participant
  some values from: Class
    intersection of: Homo sapiens
    intersection of: Restriction
      on property: has disposition
      some values from: psoriatic arthritis
textual definition: A human skin microbiome interaction that is associated with psoriatic arthritis (PsA).
definition editor: Haihe Wang, Hong Yu, Yongqun He

depletion of Vibrionaceae in gout human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Vibrionaceae
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: gout human-gut microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Vibrionaceae
textual definition: a Gout human-gut microbiome interaction that shows an decrease of Vibrionaceae in patients with gout compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/

depletion of Photobacterium in gout human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Photobacterium
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: depletion of Vibrionaceae in gout human gut
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Photobacterium
textual definition: a Gout human-gut microbiome interaction that shows an decrease of Photobacterium in patients with gout compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/

depletion of Vibrio in gout human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Vibrio
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: depletion of Vibrionaceae in gout human gut
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Vibrio
textual definition: a Gout human-gut microbiome interaction that shows an decrease of Vibrio in patients with gout compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/

depletion of Eubacterium ventriosum in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Eubacterium ventriosum
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: depletion of Eubacteriaceae in colorectal cancer human gut
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Eubacterium ventriosum
textual definition: A colorectal cancer human-gut microbiome interaction where Eubacterium ventriosum is decreased.
definition editor: YH, HW
evidence publication: https://www.ncbi.nlm.nih.gov/pubmed/26408641

depletion of Lachnospiraceae in gout human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Lachnospiraceae
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: gout human-gut microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Lachnospiraceae
textual definition: a Gout human-gut microbiome interaction that shows an decrease of Lachnospiraceae in patients with gout compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/

depletion of Ruminococcaceae in gout human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Ruminococcaceae
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: gout human-gut microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Ruminococcaceae
textual definition: a Gout human-gut microbiome interaction that shows an decrease of Ruminococcaceae in patients with gout compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/

expansion of Erysipelatoclostridium in gout human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Erysipelatoclostridium
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: gout human-gut microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Erysipelatoclostridium
textual definition: a Gout human-gut microbiome interaction that shows an expansion of Erysipelatoclostridium in patients with gout compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/28270806/

expansion of Escherichia coli EPEC 32/73 in gout human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Escherichia coli EPEC 32/73
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: gout human-gut microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Escherichia coli EPEC 32/73
textual definition: a Gout human-gut microbiome interaction that shows an expansion of Escherichia coli EPEC32/73 in patients with gout compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/23340314/
definition source: https://www.ncbi.nlm.nih.gov/pubmed/23811846/

expansion of E. coli ETEC TW03439 in gout human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Escherichia coli ETEC TW03439
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: gout human-gut microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Escherichia coli ETEC TW03439
textual definition: a Gout human-gut microbiome interaction that shows an expansion of Escherichia coli ETEC TW03439 in patients with gout compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/23340314/
definition source: https://www.ncbi.nlm.nih.gov/pubmed/23811846/

expansion of Barnesiella in gout human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Barnesiella
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: expansion of Bacteroidales in gout human gut
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Barnesiella
textual definition: a Gout human-gut microbiome interaction that shows an expansion of Barnesiella in patients with gout compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/26852926/
definition source: https://www.ncbi.nlm.nih.gov/pubmed/27941389/

expansion of Parasporobacterium in gout human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Parasporobacterium
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: gout human-gut microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Parasporobacterium
textual definition: a Gout human-gut microbiome interaction that shows an expansion of Parasporobacterium in patients with gout compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/26852926/
definition source: https://www.ncbi.nlm.nih.gov/pubmed/27941389/

expansion of Paraprevotella in gout human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Paraprevotella
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: expansion of Bacteroidales in gout human gut
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Paraprevotella
textual definition: a Gout human-gut microbiome interaction that shows an expansion of Paraprevotella in patients with gout compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/26852926/
definition source: https://www.ncbi.nlm.nih.gov/pubmed/27941389/

expansion of Anaerotruncus in gout human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Anaerotruncus
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: gout human-gut microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Anaerotruncus
textual definition: a Gout human-gut microbiome interaction that shows an expansion of Anaerotruncus in patients with gout compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/26852926/
definition source: https://www.ncbi.nlm.nih.gov/pubmed/27941389/

expansion of Pseudobutyrivibrio in gout human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Pseudobutyrivibrio
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: gout human-gut microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Pseudobutyrivibrio
textual definition: a Gout human-gut microbiome interaction that shows an expansion of Pseudobutyrivibrio in patients with gout compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/26852926/
definition source: https://www.ncbi.nlm.nih.gov/pubmed/27941389/

expansion of Bacteroides caccae in gout human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Bacteroides caccae
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: expansion of Bacteroides in gout human gut
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Bacteroides caccae
textual definition: a Gout human-gut microbiome interaction that shows an expansion of Bacteroides caccae in patients with gout compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/26852926/
definition source: https://www.ncbi.nlm.nih.gov/pubmed/27941389/

expansion of Bacteroides sp in gout human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Bacteroides sp.
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: expansion of Bacteroides in gout human gut
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Bacteroides sp.
textual definition: a Gout human-gut microbiome interaction that shows an expansion of Bacteroides sp in patients with gout compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/26852926/
definition source: https://www.ncbi.nlm.nih.gov/pubmed/27941389/

expansion of Bacteroides xylanisolvens XB1A in gout human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Bacteroides xylanisolvens XB1A
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: expansion of Bacteroides in gout human gut
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Bacteroides xylanisolvens XB1A
textual definition: a Gout human-gut microbiome interaction that shows an expansion of Bacteroides xylanisolvens XB1A in patients with gout compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/26852926/
definition source: https://www.ncbi.nlm.nih.gov/pubmed/27941389/

expansion of Holdemania in gout human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Holdemania
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: gout human-gut microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Holdemania
textual definition: a Gout human-gut microbiome interaction that shows an expansion of Holdemania in patients with gout compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/26852926/
definition source: https://www.ncbi.nlm.nih.gov/pubmed/27941389/

expansion of Acetanaerobacterium in gout human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Acetanaerobacterium
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: gout human-gut microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Acetanaerobacterium
textual definition: a Gout human-gut microbiome interaction that shows an expansion of rare taxa,Acetanaerobacterium in patients with gout compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/26852926/
definition source: https://www.ncbi.nlm.nih.gov/pubmed/27941389/

depletion of Coprococcus catus in gout human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Coprococcus catus
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: depletion of Lachnospiraceae in gout human gut
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Coprococcus catus
textual definition: a Gout human-gut microbiome interaction that shows an decrease of Coprococcus catus in patients with gout compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/

depletion of Faecalibacterium prausnitzii in gout human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Faecalibacterium prausnitzii
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: depletion of Ruminococcaceae in gout human gut
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Faecalibacterium prausnitzii
textual definition: a Gout human-gut microbiome interaction that shows an decrease of Faecalibacterium prausnitzii in patients with gout compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/

depletion of Oscillibacter in gout human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Oscillibacter
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: gout human-gut microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Oscillibacter
textual definition: a Gout human-gut microbiome interaction that shows an decrease of Oscillibacter in patients with gout compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/

depletion of Ruminococcus sp. in gout human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Ruminococcus sp.
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: depletion of Ruminococcaceae in gout human gut
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Ruminococcus sp.
textual definition: a Gout human-gut microbiome interaction that shows an decrease of Ruminococcus sp. in patients with gout compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/

depletion of Odoribacter in gout human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Odoribacter
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: gout human-gut microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Odoribacter
textual definition: a Gout human-gut microbiome interaction that shows an decrease of Odoribacter in patients with gout compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/

depletion of Subdoligranulum in gout human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Subdoligranulum
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: depletion of Ruminococcaceae in gout human gut
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Subdoligranulum
textual definition: a Gout human-gut microbiome interaction that shows an decrease of Subdoligranulum in patients with gout compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/

depletion of Robinsoniella in gout human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Robinsoniella
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: depletion of Lachnospiraceae in gout human gut
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Robinsoniella
textual definition: a Gout human-gut microbiome interaction that shows an decrease of Robinsoniella in patients with gout compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/

depletion of Dialister in gout human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Dialister
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: gout human-gut microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Dialister
textual definition: a Gout human-gut microbiome interaction that shows an decrease of Dialister in patients with gout compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/

depletion of Alistipes in gout human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Alistipes
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: gout human-gut microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Alistipes
textual definition: a Gout human-gut microbiome interaction that shows an decrease of Alistipes in patients with gout compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/

depletion of Propionibacterium acnes 17B in PsA human skin
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Cutibacterium acnes 17B
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0000014
        intersection of: Restriction
subclass of: depletion of Actinobacteria <phylum> in PsA human skin
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0000014
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Cutibacterium acnes 17B
textual definition: a PsA human skin microbiome interaction that shows an decrease of Propionibacterium acnes 17B in patients with PsA compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/

PsA human-gut microbiome interaction
type: Class
subclass of: human-gut microbiome interaction
subclass of: Restriction
  on property: has participant
  some values from: Class
    intersection of: Homo sapiens
    intersection of: Restriction
      on property: has disposition
      some values from: psoriatic arthritis
textual definition: A human gut-microbiome interaction that is associated with juvenile psoriatic arthritis(PsA).
definition editor: Haihe Wang, Hong Yu, Yongqun He

depletion of Akkermansia in PsA human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Akkermansia
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: depletion of Verrucomicrobia in PsA human gut
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Akkermansia
textual definition: a PsA human-gut microbiome interaction that shows an decrease of Akkermansia in patients with PsA compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/

depletion of Ruminococcus in PsA human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Ruminococcus
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: PsA human-gut microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Ruminococcus
textual definition: a PsA human-gut microbiome interaction that shows an decrease of Ruminococcus in patients with PsA compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/

depletion of Pseudobutyrivibrio in PsA human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Pseudobutyrivibrio
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: PsA human-gut microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Pseudobutyrivibrio
textual definition: a PsA human-gut microbiome interaction that shows an decrease of Pseudobutyrivibrio in patients with PsA compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/

depletion of Verrucomicrobia in PsA human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Verrucomicrobia
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: PsA human-gut microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Verrucomicrobia
textual definition: a PsA human-gut microbiome interaction that shows an decrease of Verrucomicrobia in patients with PsA compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/

depletion of Parabacteroides in PsA human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Parabacteroides
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: PsA human-gut microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Parabacteroides
textual definition: a PsA human-gut microbiome interaction that shows an decrease of Parabacteroides in patients with PsA compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/

depletion of Coprobacillus in PsA human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Coprobacillus
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: PsA human-gut microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Coprobacillus
textual definition: a PsA human-gut microbiome interaction that shows an decrease of Coprobacillus in patients with PsA compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/

expansion of Streptococcus in PsA human skin
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Streptococcus
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0000014
        intersection of: Restriction
subclass of: expansion of Firmicutes in PsA human skin
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0000014
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Streptococcus
textual definition: a PsA human skin microbiome interaction that shows an expansion of Streptococcus in patients with PsA compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/18648509/

depletion of Propionibacterium in PsA human skin
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Propionibacterium
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0000014
        intersection of: Restriction
subclass of: depletion of Actinobacteria <phylum> in PsA human skin
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0000014
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Propionibacterium
textual definition: a PsA human skin microbiome interaction that shows an decrease of Propionibacterium in patients with PsA compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/
comment: https://www.ncbi.nlm.nih.gov/pubmed/

depletion of Actinobacteria <phylum> in PsA human skin
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Actinobacteria <phylum>
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0000014
        intersection of: Restriction
subclass of: PsA human zone of skin microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0000014
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Actinobacteria <phylum>
textual definition: a PsA human skin microbiome interaction that shows an decrease of Actinobacteria <phylum> in patients with PsA compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/
comment: https://www.ncbi.nlm.nih.gov/pubmed/

depletion of Proteobacteria in PsA human skin
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Proteobacteria
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0000014
        intersection of: Restriction
subclass of: PsA human zone of skin microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0000014
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Proteobacteria
textual definition: a PsA human skin microbiome interaction that shows an decrease of Proteobacteria in patients with PsA compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/
comment: https://www.ncbi.nlm.nih.gov/pubmed/

expansion of Firmicutes in PsA human skin
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Firmicutes
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0000014
        intersection of: Restriction
subclass of: PsA human zone of skin microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0000014
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Firmicutes
textual definition: a PsA human skin microbiome interaction that shows an expansion of Firmicutes in patients with PsA compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/23750937/
comment: https://www.ncbi.nlm.nih.gov/pubmed/18648509/
comment: https://www.ncbi.nlm.nih.gov/pubmed/21407241 /

expansion of Bacteroidetes in PsA human skin
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Bacteroidetes
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0000014
        intersection of: Restriction
subclass of: PsA human zone of skin microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0000014
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Bacteroidetes
textual definition: a PsA human skin microbiome interaction that shows an expansion of Bacteroidetes in patients with PsA compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/23750937/
comment: https://www.ncbi.nlm.nih.gov/pubmed/18648509/
comment: https://www.ncbi.nlm.nih.gov/pubmed/21407241 /

expansion of Candida albicans in PsA human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Candida albicans
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: PsA human-gut microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Candida albicans
textual definition: a PsA human-gut microbiome interaction that shows an expansion of Candida albicans in patients with PsA compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/11413927/

PsA human oral cavity microbiome interaction
type: Class
subclass of: human oral cavity microbiome interaction
subclass of: Restriction
  on property: has participant
  some values from: Class
    intersection of: Homo sapiens
    intersection of: Restriction
      on property: has disposition
      some values from: psoriatic arthritis
textual definition: A human oral cavity microbiome interaction that is associated with psoriatic arthritis (PsA).
definition editor: YH

expansion of Candida albicans in PsA human oral cavity
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Candida albicans
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0000167
        intersection of: Restriction
subclass of: PsA human oral cavity microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0000167
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Candida albicans
textual definition: An association of human oral cavity microbiota with psoriatic arthritis(PsA) that shows an expansion of Candida albicans in patients with PsA compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/11413927/

depletion of Malassezia restricta in PsA human skin
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Malassezia restricta
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0000014
        intersection of: Restriction
subclass of: PsA human zone of skin microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0000014
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Malassezia restricta
textual definition: a PsA human skin microbiome interaction that shows an decrease of Malassezia restricta in patients with PsA compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
comment: https://www.ncbi.nlm.nih.gov/pubmed/?term= 18294199

depletion of Malassezia sympodialis in PsA human skin
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Malassezia sympodialis
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0000014
        intersection of: Restriction
subclass of: PsA human zone of skin microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0000014
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Malassezia sympodialis
textual definition: a PsA human skin microbiome interaction that shows an decrease of Malassezia sympodialis in patients with PsA compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
comment: https://www.ncbi.nlm.nih.gov/pubmed/?term= 116891514

depletion of Malassezia pachydermatis in PsA human skin
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Malassezia pachydermatis
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0000014
        intersection of: Restriction
subclass of: PsA human zone of skin microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0000014
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Malassezia pachydermatis
textual definition: a PsA human skin microbiome interaction that shows an decrease of Malassezia pachydermatis in patients with PsA compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
comment: https://www.ncbi.nlm.nih.gov/pubmed/?term= 116891514

expansion of Porphyromonas gingivalis in AS human oral cavity
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Porphyromonas gingivalis
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0000167
        intersection of: Restriction
subclass of: AS human oral cavity microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0000167
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Porphyromonas gingivalis
textual definition: an AS human oral cavity microbiome interaction that shows an expansion of Porphyromonas gingivalis in patients with AS compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/26002454/

depletion of Lactobacillus in SLE mouse gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Lactobacillus
    intersection of: Class
      intersection of: Restriction
        on property: part of
        some values from: Class
      intersection of: Restriction
        on property: located in
        some values from: UBERON_0004907
    intersection of: Restriction
      on property: has quality
      some values from: increased organism quantity compared with healthy control
subclass of: SLE mouse-gut microbiome interaction
subclass of: Restriction
  on property: has participant
  some values from: Class
    intersection of: Lactobacillus
    intersection of: Class
      intersection of: Restriction
        on property: part of
        some values from: Class
      intersection of: Restriction
        on property: located in
        some values from: UBERON_0004907
    intersection of: Restriction
      on property: has quality
      some values from: increased organism quantity compared with healthy control
textual definition: An association of musculus gut microbiota with system lupus erythematosus(SLE) that shows a depletion of Lactobacillus in musculus with SLE compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/25261516/

depletion of Aggregatibacter in RA human oral cavity
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Aggregatibacter
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0000167
        intersection of: Restriction
subclass of: RA human oral cavity microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0000167
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Aggregatibacter
textual definition: a RA human oral cavity microbiome interaction that shows an decrease of Aggregatibacter in patients with RA compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/

depletion of Neisseria sp. in RA human oral cavity
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Neisseria sp.
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0000167
        intersection of: Restriction
subclass of: RA human oral cavity microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0000167
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Neisseria sp.
textual definition: a RA human oral cavity microbiome interaction that shows an expansion of Neisseria sp. in patients with RA compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/

expansion of Paraprevotella in AS rat gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Paraprevotella
    intersection of: Class
      intersection of: Restriction
        on property: part of
        some values from: Class
      intersection of: Restriction
        on property: located in
        some values from: UBERON_0004907
    intersection of: Restriction
      on property: has quality
      some values from: increased organism quantity compared with healthy control
subclass of: AS rat-gut microbiome interaction
subclass of: Restriction
  on property: has participant
  some values from: Class
    intersection of: Paraprevotella
    intersection of: Class
      intersection of: Restriction
        on property: part of
        some values from: Class
      intersection of: Restriction
        on property: located in
        some values from: UBERON_0004907
    intersection of: Restriction
      on property: has quality
      some values from: increased organism quantity compared with healthy control
textual definition: An association of rattus gut microbiota with ankylosing spondylitis(AS) that shows an expansion of Paraprevotella in rattus with AS compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/25140823/

expansion of Prevotella in AS rat gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Prevotella
    intersection of: Class
      intersection of: Restriction
        on property: part of
        some values from: Class
      intersection of: Restriction
        on property: located in
        some values from: UBERON_0004907
    intersection of: Restriction
      on property: has quality
      some values from: increased organism quantity compared with healthy control
subclass of: AS rat-gut microbiome interaction
subclass of: Restriction
  on property: has participant
  some values from: Class
    intersection of: Prevotella
    intersection of: Class
      intersection of: Restriction
        on property: part of
        some values from: Class
      intersection of: Restriction
        on property: located in
        some values from: UBERON_0004907
    intersection of: Restriction
      on property: has quality
      some values from: increased organism quantity compared with healthy control
textual definition: An association of rattus gut microbiota with ankylosing spondylitis(AS) that shows an expansion of Prevotella in rattus with AS compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/25140823/

expansion of Actinomyces in RA human oral cavity
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Actinomyces
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0000167
        intersection of: Restriction
subclass of: RA human oral cavity microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0000167
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Actinomyces
textual definition: a RA human oral cavity microbiome interaction that shows an expansion of Actinomyces in patients with RA compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/26214836

expansion of Prevotella in RA human oral cavity
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Prevotella
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0000167
        intersection of: Restriction
subclass of: RA human oral cavity microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0000167
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Prevotella
textual definition: a RA human oral cavity microbiome interaction that shows an expansion of Prevotella in patients with RA compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/22576262

expansion of Leptotrichia sp. in RA human oral cavity
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Leptotrichia sp.
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0000167
        intersection of: Restriction
subclass of: RA human oral cavity microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0000167
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Leptotrichia sp.
textual definition: a RA human oral cavity microbiome interaction that shows an expansion of Leptotrichia sp. in patients with RA compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/22576262

expansion of Tannerella forsythia in RA human oral cavity
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Tannerella forsythia
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0000167
        intersection of: Restriction
subclass of: RA human oral cavity microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0000167
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Tannerella forsythia
textual definition: a RA human oral cavity microbiome interaction that shows an expansion of rare taxa,Tannerella forsythia in patients with RA compared with healthy controls
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/19554393
definition source: https://www.ncbi.nlm.nih.gov/pubmed/22576262
definition source: https://www.ncbi.nlm.nih.gov/pubmed/23902301

Akkermansia muciniphila depletion in AS rat gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Akkermansia muciniphila
    intersection of: Class
      intersection of: Restriction
        on property: part of
        some values from: Class
      intersection of: Restriction
        on property: located in
        some values from: UBERON_0004907
    intersection of: Restriction
      on property: has quality
      some values from: decreased organism quantity compared with healthy controls
subclass of: AS rat-gut microbiome interaction
subclass of: Restriction
  on property: has participant
  some values from: Class
    intersection of: Akkermansia muciniphila
    intersection of: Restriction
      on property: has quality
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: UBERON_0004907
textual definition: An association of rattus gut microbiota with ankylosing spondylitis(AS) that shows a depleted quantity of Akkermansia muciniphila in rattus with AS compared with healty controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/

expansion of Bacteroides vulgatus in AS rat gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Bacteroides vulgatus
    intersection of: Class
      intersection of: Restriction
        on property: part of
        some values from: Class
      intersection of: Restriction
        on property: located in
        some values from: UBERON_0004907
    intersection of: Restriction
      on property: has quality
      some values from: increased organism quantity compared with healthy control
subclass of: AS rat-gut microbiome interaction
subclass of: Restriction
  on property: has participant
  some values from: Class
    intersection of: Bacteroides vulgatus
    intersection of: Class
      intersection of: Restriction
        on property: part of
        some values from: Class
      intersection of: Restriction
        on property: located in
        some values from: UBERON_0004907
    intersection of: Restriction
      on property: has quality
      some values from: increased organism quantity compared with healthy control
textual definition: An association of rattus gut microbiota with ankylosing spondylitis(AS) that shows an expansion of Bacteroides vulgatus in rattus with AS compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/10338507
definition source: https://www.ncbi.nlm.nih.gov/pubmed/25140823/
definition source: https://www.ncbi.nlm.nih.gov/pubmed/8770866

arthritis rat-gut microbiome interaction
type: Class
subclass of: rat gut microbiome interaction
subclass of: Restriction
  on property: has participant
  some values from: Class
    intersection of: Rattus
    intersection of: Restriction
      on property: has disposition
      some values from: arthritis
textual definition: A rattus gut-microbiome interaction that is associated with arthritis.
definition editor: Haihe Wang, Hong Yu, Yongqun He
alternative term: association of rat gut microbiota with arthritis

expansion of Bifidobacterium in arthritis rat gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Bifidobacterium
    intersection of: Class
      intersection of: Restriction
        on property: part of
        some values from: Class
      intersection of: Restriction
        on property: located in
        some values from: UBERON_0004907
    intersection of: Restriction
      on property: has quality
      some values from: increased organism quantity compared with healthy control
subclass of: arthritis rat-gut microbiome interaction
subclass of: Restriction
  on property: has participant
  some values from: Class
    intersection of: Bifidobacterium
    intersection of: Class
      intersection of: Restriction
        on property: part of
        some values from: Class
      intersection of: Restriction
        on property: located in
        some values from: UBERON_0004907
    intersection of: Restriction
      on property: has quality
      some values from: increased organism quantity compared with healthy control
textual definition: An association of rattus gut microbiota with arthritis that shows an expansion of Bifidobacterium in rattus with arthritis compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/2931580/

expansion of Propionibacterium acnes 17B in arthritis rat gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Cutibacterium acnes 17B
    intersection of: Class
      intersection of: Restriction
        on property: part of
        some values from: Class
      intersection of: Restriction
        on property: located in
        some values from: UBERON_0004907
    intersection of: Restriction
      on property: has quality
      some values from: increased organism quantity compared with healthy control
subclass of: arthritis rat-gut microbiome interaction
subclass of: Restriction
  on property: has participant
  some values from: Class
    intersection of: Cutibacterium acnes 17B
    intersection of: Class
      intersection of: Restriction
        on property: part of
        some values from: Class
      intersection of: Restriction
        on property: located in
        some values from: UBERON_0004907
    intersection of: Restriction
      on property: has quality
      some values from: increased organism quantity compared with healthy control
textual definition: An association of rattus gut microbiota with arthritis that shows an expansion of Propionibacterium acnes 17B in rattus with arthritis compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/2931580/

expansion of Lactobacillus casei in arthritis rat gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Lactobacillus casei
    intersection of: Class
      intersection of: Restriction
        on property: part of
        some values from: Class
      intersection of: Restriction
        on property: located in
        some values from: UBERON_0004907
    intersection of: Restriction
      on property: has quality
      some values from: increased organism quantity compared with healthy control
subclass of: expansion of Lactobacillus in arthritis rat gut
subclass of: Restriction
  on property: has participant
  some values from: Class
    intersection of: Lactobacillus casei
    intersection of: Class
      intersection of: Restriction
        on property: part of
        some values from: Class
      intersection of: Restriction
        on property: located in
        some values from: UBERON_0004907
    intersection of: Restriction
      on property: has quality
      some values from: increased organism quantity compared with healthy control
textual definition: An association of rattus gut microbiota with arthritis that shows an expansion of Lactobacillus casei in rattus with arthritis compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/2931580/

expansion of Lactobacillus fermentum in arthritis rat gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Lactobacillus fermentum
    intersection of: Class
      intersection of: Restriction
        on property: part of
        some values from: Class
      intersection of: Restriction
        on property: located in
        some values from: UBERON_0004907
    intersection of: Restriction
      on property: has quality
      some values from: increased organism quantity compared with healthy control
subclass of: expansion of Lactobacillus in arthritis rat gut
subclass of: Restriction
  on property: has participant
  some values from: Class
    intersection of: Lactobacillus fermentum
    intersection of: Class
      intersection of: Restriction
        on property: part of
        some values from: Class
      intersection of: Restriction
        on property: located in
        some values from: UBERON_0004907
    intersection of: Restriction
      on property: has quality
      some values from: increased organism quantity compared with healthy control
textual definition: An association of rattus gut microbiota with arthritis that shows an expansion of Lactobacillus fermentum in rattus with arthritis compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/2931580/

expansion of Lactobacillus murinus in arthritis rat gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Lactobacillus murinus
    intersection of: Class
      intersection of: Restriction
        on property: part of
        some values from: Class
      intersection of: Restriction
        on property: located in
        some values from: UBERON_0004907
    intersection of: Restriction
      on property: has quality
      some values from: increased organism quantity compared with healthy control
subclass of: expansion of Lactobacillus in arthritis rat gut
subclass of: Restriction
  on property: has participant
  some values from: Class
    intersection of: Lactobacillus murinus
    intersection of: Class
      intersection of: Restriction
        on property: part of
        some values from: Class
      intersection of: Restriction
        on property: located in
        some values from: UBERON_0004907
    intersection of: Restriction
      on property: has quality
      some values from: increased organism quantity compared with healthy control
textual definition: An association of rattus gut microbiota with arthritis that shows an expansion of Lactobacillus murinus in rattus with arthritis compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/2931580/

expansion of Lactobacillus acidophilus in arthritis rat gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Lactobacillus acidophilus
    intersection of: Class
      intersection of: Restriction
        on property: part of
        some values from: Class
      intersection of: Restriction
        on property: located in
        some values from: UBERON_0004907
    intersection of: Restriction
      on property: has quality
      some values from: increased organism quantity compared with healthy control
subclass of: expansion of Lactobacillus in arthritis rat gut
subclass of: Restriction
  on property: has participant
  some values from: Class
    intersection of: Lactobacillus acidophilus
    intersection of: Class
      intersection of: Restriction
        on property: part of
        some values from: Class
      intersection of: Restriction
        on property: located in
        some values from: UBERON_0004907
    intersection of: Restriction
      on property: has quality
      some values from: increased organism quantity compared with healthy control
textual definition: An association of rattus gut microbiota with arthritis that shows an expansion of Lactobacillus acidophilus in rattus with arthritis compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/2931580/

expansion of E. coli in arthritis rat gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Escherichia coli
    intersection of: Class
      intersection of: Restriction
        on property: part of
        some values from: Class
      intersection of: Restriction
        on property: located in
        some values from: UBERON_0004907
    intersection of: Restriction
      on property: has quality
      some values from: increased organism quantity compared with healthy control
subclass of: arthritis rat-gut microbiome interaction
subclass of: Restriction
  on property: has participant
  some values from: Class
    intersection of: Escherichia coli
    intersection of: Class
      intersection of: Restriction
        on property: part of
        some values from: Class
      intersection of: Restriction
        on property: located in
        some values from: UBERON_0004907
    intersection of: Restriction
      on property: has quality
      some values from: increased organism quantity compared with healthy control
textual definition: An association of rattus gut microbiota with arthritis that shows an expansion of Escherichia coli in rattus with arthritis compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/2931580/
definition source: https://www.ncbi.nlm.nih.gov/pubmed/3518723/

expansion of Lactobacillus in arthritis rat gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Lactobacillus
    intersection of: Class
      intersection of: Restriction
        on property: part of
        some values from: Class
      intersection of: Restriction
        on property: located in
        some values from: UBERON_0004907
    intersection of: Restriction
      on property: has quality
      some values from: increased organism quantity compared with healthy control
subclass of: arthritis rat-gut microbiome interaction
subclass of: Restriction
  on property: has participant
  some values from: Class
    intersection of: Lactobacillus
    intersection of: Class
      intersection of: Restriction
        on property: part of
        some values from: Class
      intersection of: Restriction
        on property: located in
        some values from: UBERON_0004907
    intersection of: Restriction
      on property: has quality
      some values from: increased organism quantity compared with healthy control
textual definition: An association of rattus gut microbiota with arthritis that shows an expansion of Lactobacillus in rattus with arthritis compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/27481047/

expansion of Bacteroidaceae in arthritis rat gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Bacteroidaceae
    intersection of: Class
      intersection of: Restriction
        on property: part of
        some values from: Class
      intersection of: Restriction
        on property: located in
        some values from: UBERON_0004907
    intersection of: Restriction
      on property: has quality
      some values from: increased organism quantity compared with healthy control
subclass of: arthritis rat-gut microbiome interaction
subclass of: Restriction
  on property: has participant
  some values from: Class
    intersection of: Bacteroidaceae
    intersection of: Class
      intersection of: Restriction
        on property: part of
        some values from: Class
      intersection of: Restriction
        on property: located in
        some values from: UBERON_0004907
    intersection of: Restriction
      on property: has quality
      some values from: increased organism quantity compared with healthy control
textual definition: An association of rattus gut microbiota with arthritis that shows an expansion of Bacteroidaceae in rattus with arthritis compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/27481047/

Lachnospiraceae depletion in arthritis rat gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Lachnospiraceae
    intersection of: Class
      intersection of: Restriction
        on property: part of
        some values from: Class
      intersection of: Restriction
        on property: located in
        some values from: UBERON_0004907
    intersection of: Restriction
      on property: has quality
      some values from: decreased organism quantity compared with healthy controls
subclass of: arthritis rat-gut microbiome interaction
subclass of: Restriction
  on property: has participant
  some values from: Class
    intersection of: Lachnospiraceae
    intersection of: Restriction
      on property: has quality
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: UBERON_0004907
textual definition: An association of rattus gut microbiota with arthritis that shows a depleted quantity of Lachnospiraceae in rattus with arthritis compared with healty controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/

expansion of Bacteroides fragilis in arthritis rat gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Bacteroides fragilis
    intersection of: Class
      intersection of: Restriction
        on property: part of
        some values from: Class
      intersection of: Restriction
        on property: located in
        some values from: UBERON_0004907
    intersection of: Restriction
      on property: has quality
      some values from: increased organism quantity compared with healthy control
subclass of: expansion of Bacteroidaceae in arthritis rat gut
subclass of: Restriction
  on property: has participant
  some values from: Class
    intersection of: Bacteroides fragilis
    intersection of: Class
      intersection of: Restriction
        on property: part of
        some values from: Class
      intersection of: Restriction
        on property: located in
        some values from: UBERON_0004907
    intersection of: Restriction
      on property: has quality
      some values from: increased organism quantity compared with healthy control
textual definition: An association of rattus gut microbiota with arthritis that shows an expansion of Bacteroides fragilis in rattus with arthritis compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/2931580/

mouse-microbiome interaction
type: Class
subclass of: host-microbiome interaction
subclass of: Restriction
  on property: has participant
  some values from: Class
    intersection of: Mus musculus
    intersection of: Restriction
      on property: has role
      some values from: host role
textual definition: A host-microbiome interaction where the host is musculus.
definition editor: YH, HW

mouse gut microbiome interaction
type: Class
subclass of: mouse-microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: Class
    intersection of: UBERON_0004907
    intersection of: Restriction
      on property: part of
      some values from: Mus musculus
textual definition: An interaction between musculus and gut microbiome.
definition editor: YH

SLE mouse-gut microbiome interaction
type: Class
subclass of: mouse gut microbiome interaction
subclass of: Restriction
  on property: has participant
  some values from: Class
    intersection of: Mus musculus
    intersection of: Restriction
      on property: has disposition
      some values from: systemic lupus erythematosus
textual definition: A musculus gut-microbiome interaction that is associated with system lupus erythematosus(SLE).
definition editor: Haihe Wang, Hong Yu, Yongqun He
alternative term: association of mouse gut microbiota with system lupus erythematosus

expansion of Lachnospiraceae in SLE mouse gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Lachnospiraceae
    intersection of: Class
      intersection of: Restriction
        on property: part of
        some values from: Class
      intersection of: Restriction
        on property: located in
        some values from: UBERON_0004907
    intersection of: Restriction
      on property: has quality
      some values from: increased organism quantity compared with healthy control
subclass of: expansion of Clostridiales in SLE mouse gut
subclass of: Restriction
  on property: has participant
  some values from: Class
    intersection of: Lachnospiraceae
    intersection of: Class
      intersection of: Restriction
        on property: part of
        some values from: Class
      intersection of: Restriction
        on property: located in
        some values from: UBERON_0004907
    intersection of: Restriction
      on property: has quality
      some values from: increased organism quantity compared with healthy control
textual definition: An association of musculus gut microbiota with system lupus erythematosus(SLE) that shows an expansion of Lachnospiraceae in musculus with SLE compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/25261516/

expansion of Ruminococcaceae in SLE mouse gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Ruminococcaceae
    intersection of: Class
      intersection of: Restriction
        on property: part of
        some values from: Class
      intersection of: Restriction
        on property: located in
        some values from: UBERON_0004907
    intersection of: Restriction
      on property: has quality
      some values from: increased organism quantity compared with healthy control
subclass of: expansion of Clostridiales in SLE mouse gut
subclass of: Restriction
  on property: has participant
  some values from: Class
    intersection of: Ruminococcaceae
    intersection of: Class
      intersection of: Restriction
        on property: part of
        some values from: Class
      intersection of: Restriction
        on property: located in
        some values from: UBERON_0004907
    intersection of: Restriction
      on property: has quality
      some values from: increased organism quantity compared with healthy control
textual definition: An association of musculus gut microbiota with system lupus erythematosus(SLE) that shows an expansion of Ruminococcaceae in musculus with SLE compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/25261516/

expansion of Clostridiales in SLE mouse gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Clostridiales
    intersection of: Class
      intersection of: Restriction
        on property: part of
        some values from: Class
      intersection of: Restriction
        on property: located in
        some values from: UBERON_0004907
    intersection of: Restriction
      on property: has quality
      some values from: increased organism quantity compared with healthy control
subclass of: SLE mouse-gut microbiome interaction
subclass of: Restriction
  on property: has participant
  some values from: Class
    intersection of: Clostridiales
    intersection of: Class
      intersection of: Restriction
        on property: part of
        some values from: Class
      intersection of: Restriction
        on property: located in
        some values from: UBERON_0004907
    intersection of: Restriction
      on property: has quality
      some values from: increased organism quantity compared with healthy control
textual definition: An association of musculus gut microbiota with system lupus erythematosus(SLE) that shows an expansion of Clostridiales in musculus with SLE compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/25261516/

expansion of Streptococcaceae in SLE mouse gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Streptococcaceae
    intersection of: Class
      intersection of: Restriction
        on property: part of
        some values from: Class
      intersection of: Restriction
        on property: located in
        some values from: UBERON_0004907
    intersection of: Restriction
      on property: has quality
      some values from: increased organism quantity compared with healthy control
subclass of: SLE mouse-gut microbiome interaction
subclass of: Restriction
  on property: has participant
  some values from: Class
    intersection of: Streptococcaceae
    intersection of: Class
      intersection of: Restriction
        on property: part of
        some values from: Class
      intersection of: Restriction
        on property: located in
        some values from: UBERON_0004907
    intersection of: Restriction
      on property: has quality
      some values from: increased organism quantity compared with healthy control
textual definition: An association of musculus gut microbiota with system lupus erythematosus(SLE) that shows an expansion of Streptococcaceae in musculus with SLE compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/25261516/

expansion of Streptococcus pyogenes in arthritis rat gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Streptococcus pyogenes
    intersection of: Class
      intersection of: Restriction
        on property: part of
        some values from: Class
      intersection of: Restriction
        on property: located in
        some values from: UBERON_0004907
    intersection of: Restriction
      on property: has quality
      some values from: increased organism quantity compared with healthy control
subclass of: arthritis rat-gut microbiome interaction
subclass of: Restriction
  on property: has participant
  some values from: Class
    intersection of: Streptococcus pyogenes
    intersection of: Class
      intersection of: Restriction
        on property: part of
        some values from: Class
      intersection of: Restriction
        on property: located in
        some values from: UBERON_0004907
    intersection of: Restriction
      on property: has quality
      some values from: increased organism quantity compared with healthy control
textual definition: An association of rattus gut microbiota with arthritis that shows an expansion of Streptococcus pyogenes in rattus with arthritis compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/1572097/

arthritis mouse-gut microbiome interaction
type: Class
subclass of: mouse gut microbiome interaction
subclass of: Restriction
  on property: has participant
  some values from: Class
    intersection of: Mus musculus
    intersection of: Restriction
      on property: has disposition
      some values from: arthritis
textual definition: A musculus gut-microbiome interaction that is associated with arthritis
definition editor: Haihe Wang, Hong Yu, Yongqun He
alternative term: association of mouse gut microbiota with arthritis

expansion of Prevotella copri in arthritis mouse gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Prevotella copri
    intersection of: Class
      intersection of: Restriction
        on property: part of
        some values from: Class
      intersection of: Restriction
        on property: located in
        some values from: UBERON_0004907
    intersection of: Restriction
      on property: has quality
      some values from: increased organism quantity compared with healthy control
subclass of: arthritis mouse-gut microbiome interaction
subclass of: Restriction
  on property: has participant
  some values from: Class
    intersection of: Prevotella copri
    intersection of: Class
      intersection of: Restriction
        on property: part of
        some values from: Class
      intersection of: Restriction
        on property: located in
        some values from: UBERON_0004907
    intersection of: Restriction
      on property: has quality
      some values from: increased organism quantity compared with healthy control
textual definition: An association of musuculus gut microbiota with arthritis that shows an expansion of Prevotella copri in musuculus with arthritis compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/22553482/
definition source: https://www.ncbi.nlm.nih.gov/pubmed/27789760/

Actinobacteria<class> depletion in arthritis mouse gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Actinobacteria <class>
    intersection of: Class
      intersection of: Restriction
        on property: part of
        some values from: Class
      intersection of: Restriction
        on property: located in
        some values from: UBERON_0004907
    intersection of: Restriction
      on property: has quality
      some values from: decreased organism quantity compared with healthy controls
subclass of: arthritis mouse-gut microbiome interaction
subclass of: Restriction
  on property: has participant
  some values from: Class
    intersection of: Actinobacteria <class>
    intersection of: Restriction
      on property: has quality
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: UBERON_0004907
textual definition: An association of musculus gut microbiota with arthritis that shows a depleted quantity of Actinobacteria<class> in musculus with arthritis compared with healty controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/

Bacteroides depletion in arthritis mouse gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Bacteroides
    intersection of: Class
      intersection of: Restriction
        on property: part of
        some values from: Class
      intersection of: Restriction
        on property: located in
        some values from: UBERON_0004907
    intersection of: Restriction
      on property: has quality
      some values from: decreased organism quantity compared with healthy controls
subclass of: arthritis mouse-gut microbiome interaction
subclass of: Restriction
  on property: has participant
  some values from: Class
    intersection of: Bacteroides
    intersection of: Restriction
      on property: has quality
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: UBERON_0004907
textual definition: An association of musculus gut microbiota with arthritis that shows a depleted quantity of Bacteroides in musculus with arthritis compared with healty controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/

expansion of Dialister in AS human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Dialister
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: expansion of Veillonellaceae in AS human gut
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Dialister
textual definition: an AS human-gut microbiome interaction that shows an expansion of Dialister in patients with AS compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/27390077/

expansion of Alistipes in SLE mouse gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Alistipes
    intersection of: Class
      intersection of: Restriction
        on property: part of
        some values from: Class
      intersection of: Restriction
        on property: located in
        some values from: UBERON_0004907
    intersection of: Restriction
      on property: has quality
      some values from: increased organism quantity compared with healthy control
subclass of: SLE mouse-gut microbiome interaction
subclass of: Restriction
  on property: has participant
  some values from: Class
    intersection of: Alistipes
    intersection of: Class
      intersection of: Restriction
        on property: part of
        some values from: Class
      intersection of: Restriction
        on property: located in
        some values from: UBERON_0004907
    intersection of: Restriction
      on property: has quality
      some values from: increased organism quantity compared with healthy control
textual definition: An association of musculus gut microbiota with system lupus erythematosus(SLE) that shows an expansion of Alistipes in musculus with SLE compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/25261516/

expansion of Bacteroidia in SLE human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Bacteroidia
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: expansion of Bacteroidetes in SLE human gut
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Bacteroidia
textual definition: a SLE human-gut microbiome interaction that shows an expansion of Bacteroidia in patients with SLE compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/25271284/

expansion of Bacteroidales in SLE human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Bacteroidales
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: expansion of Bacteroidia in SLE human gut
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Bacteroidales
textual definition: a SLE human-gut microbiome interaction that shows an expansion of Bacteroidales in patients with SLE compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/25271284/

depletion of Clostridia in SLE human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Clostridia
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: depletion of Firmicutes in SLE human gut
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Clostridia
textual definition: a SLE human-gut microbiome interaction that shows an decrease of Vibrio in patients with SLEcompared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/

depletion of Clostridiales in SLE human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Clostridiales
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: depletion of Clostridia in SLE human gut
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Clostridiales
textual definition: a SLE human-gut microbiome interaction that shows an decrease of Clostridiales in patients with SLE compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/

depletion of Treponema in RA human respiratory airway
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Treponema
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0001005
        intersection of: Restriction
subclass of: RA human respiratory airway microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0001005
subclass of: Restriction
  on property: has participant
  some values from: Class
    intersection of: Treponema
    intersection of: Restriction
      on property: has quality
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: UBERON_0001005
textual definition: RA human respiratory airway microbiome interaction that shows an decrease of Treponema in patients with RA compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/

depletion of Burkholderia in RA human respiratory airway
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Burkholderia
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0001005
        intersection of: Restriction
subclass of: RA human respiratory airway microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0001005
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Burkholderia
textual definition: RA human respiratory airway microbiome interaction that shows an decrease of Burkholderia in patients with RA compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/

depletion of Actynomyces in RA human respiratory airway
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Actinomyces
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0001005
        intersection of: Restriction
subclass of: RA human respiratory airway microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0001005
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Actinomyces
textual definition: RA human respiratory airway microbiome interaction that shows an decrease of Actynomyces in patients with RA compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/

expansion of Pseudonocardia in RA human respiratory airway
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Pseudonocardia
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0001005
        intersection of: Restriction
subclass of: RA human respiratory airway microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0001005
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Pseudonocardia
textual definition: RA human respiratory airway microbiome interaction that shows an expansion of Pseudonocardia in patients with RA compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/27855721/

expansion of Micrococcus in RA human respiratory airway
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Micrococcus
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0001005
        intersection of: Restriction
subclass of: RA human respiratory airway microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0001005
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Micrococcus
textual definition: RA human respiratory airway microbiome interaction that shows an expansion of Micrococcus in patients with RA compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/27855721/

expansion of Methylobacterium in RA human respiratory airway
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Methylobacterium
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0001005
        intersection of: Restriction
subclass of: RA human respiratory airway microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0001005
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Methylobacterium
textual definition: RA human respiratory airway microbiome interaction that shows an expansion of Methylobacterium in patients with RA compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/27855721

expansion of Natronobacillus in diarrheal patient gut
type: Class
equivalent class: Restriction
  on property: has microbe expanded in diseased host
  some values from: Class
    intersection of: Natronobacillus
    intersection of: Class
      intersection of: Restriction
        on property: part of
        some values from: Class
      intersection of: Restriction
        on property: located in
        some values from: UBERON_0004907
subclass of: diarrheal patient-gut microbiome interaction
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Natronobacillus
textual definition: a diarrheal patient-gut microbiome interaction that shows an increase of Prevotella in patients in the gut of human diarrheal patient compared with healthy controls.
definition editor: YH
definition source: http://microbiomedb.org/mbio/app/

expansion of Eggerthella in RA human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Eggerthella
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: expansion of Actinobacteria<phylum> in RA human gut
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Eggerthella
textual definition: a RA human-gut microbiome interaction that shows an expansion of Eggerthella in patients with RA compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/28376066/

expansion of Treponema denticola in AS human oral cavity
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Treponema denticola
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0000167
        intersection of: Restriction
subclass of: AS human oral cavity microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0000167
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Treponema denticola
textual definition: an AS human oral cavity microbiome interaction that shows an expansion of rare taxa,Treponema denticola in patients with AS compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/26002454/

expansion of Rikenellaceae in AS human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Rikenellaceae
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: AS human-gut microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Rikenellaceae
textual definition: an AS human-gut microbiome interaction that shows an expansion of Rikenellaceae in patients with AS compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/25417597/
definition source: https://www.ncbi.nlm.nih.gov/pubmed/26362730/

expansion of Porphyromonas macacae in AS human gut
type: Class
equivalent class: Restriction
  on property: has microbe expanded in diseased host
  some values from: Class
    intersection of: Porphyromonas macacae
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: AS human-gut microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Porphyromonas macacae
textual definition: an AS human-gut microbiome interaction that shows an expansion of Porphyromonas macacae in patients with AS compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/25417597/

Rikenellaceae depletion in AS rat gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Rikenellaceae
    intersection of: Class
      intersection of: Restriction
        on property: part of
        some values from: Class
      intersection of: Restriction
        on property: located in
        some values from: UBERON_0004907
    intersection of: Restriction
      on property: has quality
      some values from: decreased organism quantity compared with healthy controls
subclass of: AS rat-gut microbiome interaction
subclass of: Restriction
  on property: has participant
  some values from: Class
    intersection of: Rikenellaceae
    intersection of: Restriction
      on property: has quality
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: UBERON_0004907
textual definition: An association of rattus gut microbiota with ankylosing spondylitis(AS) that shows a depleted quantity of Rikenellaceae in rattus with AS compared with healty controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/

expansion of Campylobacter in AS human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Campylobacter
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: AS human-gut microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Campylobacter
textual definition: an AS human-gut microbiome interaction that shows an expansion of Campylobacter in patients with AS compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/25417597/

expansion of Eubacterium in SLE human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Eubacterium
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: SLE human-gut microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Eubacterium
textual definition: a SLE human-gut microbiome interaction that shows an expansion of Eubacterium in patients with SLE compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/27980687/

expansion of Flavonifractor in SLE human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Flavonifractor
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: SLE human-gut microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Flavonifractor
textual definition: a SLE human-gut microbiome interaction that shows an expansion of Flavonifractor in patients with SLE compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/27980687/

expansion of Rhodococcus in SLE human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Rhodococcus
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: SLE human-gut microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Rhodococcus
textual definition: a SLE human-gut microbiome interaction that shows an expansion of Rhodococcus in patients with SLE compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/27980687/

expansion of Atopobium sp. in RA human oral cavity
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Atopobium sp.
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0000167
        intersection of: Restriction
subclass of: RA human oral cavity microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0000167
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Atopobium sp.
textual definition: a RA human oral cavity microbiome interaction that shows an expansion of rare taxa,Atopobium sp. in patients with RA compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/26214836

expansion of Eggerthella in SLE human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Eggerthella
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: SLE human-gut microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Eggerthella
textual definition: a SLE human-gut microbiome interaction that shows an expansion of Eggerthella in patients with SLE compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/27980687/

depletion of Prevotella pleuritidis in SLE human oral cavity
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Prevotella pleuritidis
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0000167
        intersection of: Restriction
subclass of: SLE human oral cavity microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0000167
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Prevotella pleuritidis
textual definition: a SLE human oral cavity microbiome interaction that shows an decrease of Prevotella pleuritidis in patients with SLE compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/

depletion of Pseudomonas sp. in SLE human oral cavity
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Pseudomonas sp.
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0000167
        intersection of: Restriction
subclass of: SLE human oral cavity microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0000167
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Pseudomonas sp.
textual definition: a SLE human oral cavity microbiome interaction that shows an decrease of Pseudomonas sp. in patients with SLE compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/

depletion of Treponema maltophilum in SLE human oral cavity
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Treponema maltophilum
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0000167
        intersection of: Restriction
subclass of: SLE human oral cavity microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0000167
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Treponema maltophilum
textual definition: a SLE human oral cavity microbiome interaction that shows an decrease of Treponema maltophilum in patients with SLE compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/

depletion of Capnocytophaga gingivalis in SLE human oral cavity
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Capnocytophaga gingivalis
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0000167
        intersection of: Restriction
subclass of: SLE human oral cavity microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0000167
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Capnocytophaga gingivalis
textual definition: a SLE human oral cavity microbiome interaction that shows an decrease of Capnocytophaga gingivalis in patients with SLE compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/

depletion of Streptococcus sanguinis in SLE human oral cavity
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Streptococcus sanguinis
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0000167
        intersection of: Restriction
subclass of: SLE human oral cavity microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0000167
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Streptococcus sanguinis
textual definition: a SLE human oral cavity microbiome interaction that shows an decrease of Streptococcus sanguinis in patients with SLE compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/

depletion of Haemophilus parainfluenzae in SLE human oral cavity
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Haemophilus parainfluenzae
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0000167
        intersection of: Restriction
subclass of: SLE human oral cavity microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0000167
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Haemophilus parainfluenzae
textual definition: a SLE human oral cavity microbiome interaction that shows a depletion of Haemophilus parainfluenzae in patients with SLE compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/

expansion of Prevotella oulorum in SLE human oral cavity
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Prevotella oulorum
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0000167
        intersection of: Restriction
subclass of: expansion of Prevotella in SLE human oral cavity
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0000167
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Prevotella oulorum
textual definition: a SLE human oral cavity microbiome interaction that shows an expansion of Prevotella oulorum in patients with SLE compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/28320468

expansion of Fretibacterium fastidiosum in SLE human oral cavity
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Fretibacterium fastidiosum
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0000167
        intersection of: Restriction
subclass of: SLE human oral cavity microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0000167
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Fretibacterium fastidiosum
textual definition: a SLE human oral cavity microbiome interaction that shows an expansion of Fretibacterium fastidiosum in patients with SLE compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/28320468/

expansion of Fusobacterium in SLE human oral cavity
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Fusobacterium
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0000167
        intersection of: Restriction
subclass of: SLE human oral cavity microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0000167
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Fusobacterium
textual definition: a SLE human oral cavity microbiome interaction that shows an expansion of Fusobacterium in patients with SLE compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/28320468

expansion of Selenomonas in SLE human oral cavity
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Selenomonas
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0000167
        intersection of: Restriction
subclass of: SLE human oral cavity microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0000167
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Selenomonas
textual definition: a SLE human oral cavity microbiome interaction that shows an expansion of Selenomonas in patients with SLE compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/28320468/

expansion of Treponema in SLE human oral cavity
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Treponema
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0000167
        intersection of: Restriction
subclass of: SLE human oral cavity microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0000167
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Treponema
textual definition: a SLE human oral cavity microbiome interaction that shows an expansion of Treponema in patients with SLE compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/28320468/

expansion of Chloroflexi in gout human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Chloroflexi
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: gout human-gut microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Chloroflexi
textual definition: a Gout human-gut microbiome interaction that shows an expansion of Chloroflexi in patients with gout compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/28270806/

expansion of Anaerolineae in gout human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Anaerolineae
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: expansion of Chloroflexi in gout human gut
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Anaerolineae
textual definition: a Gout human-gut microbiome interaction that shows an expansion of Anaerolineae in patients with gout compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/28270806/

expansion of Anaerolineales in gout human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Anaerolineales
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: gout human-gut microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Anaerolineales
textual definition: a Gout human-gut microbiome interaction that shows an expansion of Anaerolineales in patients with gout compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/28270806/

expansion of Anaerolineaceae in gout human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Anaerolineaceae
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: expansion of Anaerolineales in gout human gut
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Anaerolineaceae
textual definition: a Gout human-gut microbiome interaction that shows an expansion of Anaerolineaceae in patients with gout compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/28270806/

expansion of Corynebacteriales in gout human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Corynebacteriales
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: gout human-gut microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Corynebacteriales
textual definition: a Gout human-gut microbiome interaction that shows an expansion of Corynebacteriales in patients with gout compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/28270806/

expansion of Nocardiaceae in gout human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Nocardiaceae
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: expansion of Corynebacteriales in gout human gut
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Nocardiaceae
textual definition: a Gout human-gut microbiome interaction that shows an expansion of Nocardiaceae in patients with gout compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/28270806/

expansion of Rhodococcus in gout human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Rhodococcus
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: expansion of Nocardiaceae in gout human gut
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Rhodococcus
textual definition: a Gout human-gut microbiome interaction that shows an expansion of Rhodococcus in patients with gout compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/28270806/

expansion of Selenomonadales in gout human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Selenomonadales
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: expansion of Negativicutes in gout human gut
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Selenomonadales
textual definition: a Gout human-gut microbiome interaction that shows an expansion of Selenomonadales in patients with gout compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/28270806/

expansion of Desulfovibrionaceae in arthritis rat gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Desulfovibrionaceae
    intersection of: Class
      intersection of: Restriction
        on property: part of
        some values from: Class
      intersection of: Restriction
        on property: located in
        some values from: UBERON_0004907
    intersection of: Restriction
      on property: has quality
      some values from: increased organism quantity compared with healthy control
subclass of: arthritis rat-gut microbiome interaction
subclass of: Restriction
  on property: has participant
  some values from: Class
    intersection of: Desulfovibrionaceae
    intersection of: Class
      intersection of: Restriction
        on property: part of
        some values from: Class
      intersection of: Restriction
        on property: located in
        some values from: UBERON_0004907
    intersection of: Restriction
      on property: has quality
      some values from: increased organism quantity compared with healthy control
textual definition: An association of rattus gut microbiota with arthritis that shows an expansion of Desulfovibrionaceae in rattus with arthritis compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/27481047/

ERA human-gut microbiome interaction
type: Class
subclass of: human-gut microbiome interaction
subclass of: Restriction
  on property: has participant
  some values from: Class
    intersection of: Homo sapiens
    intersection of: Restriction
      on property: has disposition
      some values from: enthesitis-related juvenile idiopathic arthritis
textual definition: A human gut-microbiome interaction that is associated with juvenile rheumatoid arthritis (ERA).
definition editor: Haihe Wang, Hong Yu, Yongqun He

expansion of Bacteroidaceae in ERA human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Bacteroidaceae
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: ERA human-gut microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Bacteroidaceae
textual definition: an ERA human-gut microbiome interaction that shows an expansion of Bacteroidaceae in patients with ERA compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/27861762

expansion of Enterobacteriaceae in ERA human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Enterobacteriaceae
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: ERA human-gut microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Enterobacteriaceae
textual definition: an ERA human-gut microbiome interaction that shows an expansion of Enterobacteriaceae in patients with ERA compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/27861762

expansion of Enterococcaceae in ERA human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Enterococcaceae
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: ERA human-gut microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Enterococcaceae
textual definition: an ERA human-gut microbiome interaction that shows an expansion of Enterococcaceae in patients with ERA compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/27861762

expansion of Bacteroides in ERA human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Bacteroides
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: expansion of Bacteroidaceae in ERA human gut
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Bacteroides
textual definition: an ERA human-gut microbiome interaction that shows an expansion of Bacteroides in patients with ERA compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
evidence publication: https://www.ncbi.nlm.nih.gov/pubmed/

expansion of Enterococcus in ERA human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Enterococcus
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: expansion of Enterococcaceae in ERA human gut
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Enterococcus
textual definition: an ERA human-gut microbiome interaction that shows an expansion of Enterococcus in patients with ERA compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/27861762

expansion of Klebsiella in ERA human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Klebsiella
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: expansion of Enterobacteriaceae in ERA human gut
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Klebsiella
textual definition: an ERA human-gut microbiome interaction that shows an expansion of Klebsiella in patients with ERA compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/27861762

expansion of Prevotella in ERA human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Prevotella
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: expansion of Prevotellaceae in RA human gut
subclass of: segregation of Prevotella or Bacteroides dominance in RA human gut
subclass of: ERA human-gut microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Prevotella
textual definition: an ERA human-gut microbiome interaction that shows an expansion of Prevotella in patients with ERA compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/27861762

expansion of Badula fragilis in ERA human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Badula fragilis
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: ERA human-gut microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Badula fragilis
textual definition: an ERA human-gut microbiome interaction that shows an expansion of Badula fragilis in patients with ERA compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/27861762

expansion of Bacteroides plebeius in ERA human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Bacteroides plebeius
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: expansion of Bacteroides in ERA human gut
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Bacteroides plebeius
textual definition: an ERA human-gut microbiome interaction that shows an expansion of Bacteroides plebeius in patients with ERA compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/27861762

depletion of Prevotellaceae in ERA human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Prevotellaceae
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: ERA human-gut microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Prevotellaceae
textual definition: an ERA human-gut microbiome interaction that shows an decrease of Prevotellaceae in patients with ERA compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/

depletion of Prevotella copri in ERA human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Prevotella copri
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: depletion of Prevotellaceae in ERA human gut
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Prevotella copri
textual definition: an ERA human-gut microbiome interaction that shows an decrease of Prevotella copri in patients with ERA compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/

expansion of Salmonella in ERA human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Salmonella
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: expansion of Enterobacteriaceae in ERA human gut
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Salmonella
textual definition: an ERA human-gut microbiome interaction that shows an expansion of Salmonella in patients with ERA compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/21679096

depletion of Prevotella in ERA human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Prevotella stercorea
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: depletion of Prevotellaceae in ERA human gut
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Prevotella stercorea
textual definition: an ERA human-gut microbiome interaction that shows an decrease of Prevotella stercorea in patients with ERA compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/

depletion of Faecalibacterium prausnitzii in ERA human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Faecalibacterium prausnitzii
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: depletion of Faecalibacterium in RA human gut
subclass of: ERA human-gut microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Faecalibacterium prausnitzii
textual definition: an ERA human-gut microbiome interaction that shows an decrease of Faecalibacterium prausnitzii in patients with ERA compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/

depletion of Lachnospiraceae in ERA human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Lachnospiraceae
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: ERA human-gut microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Lachnospiraceae
textual definition: an ERA human-gut microbiome interaction that shows an decrease of Lachnospiraceae in patients with ERA compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/

depletion of [Clostridium] clostridioforme in ERA human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: [Clostridium] clostridioforme
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: depletion of Lachnospiraceae in ERA human gut
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: [Clostridium] clostridioforme
textual definition: an ERA human-gut microbiome interaction that shows an decrease of [Clostridium] clostridioforme in patients with ERA compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/

expansion of Bifidobacterium in ERA human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Bifidobacterium
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: expansion of Actinobacteria<phylum> in RA human gut
subclass of: ERA human-gut microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Bifidobacterium
textual definition: an ERA human-gut microbiome interaction that shows an expansion of Bifidobacterium in patients with ERA compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/25434931

expansion of Akkermansia muciniphila in ERA human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Akkermansia muciniphila
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: ERA human-gut microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Akkermansia muciniphila
textual definition: an ERA human-gut microbiome interaction that shows an expansion of Akkermansia muciniphila in patients with ERA compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/25434931

depletion of Coprococcus in PsA human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Coprococcus
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: PsA human-gut microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Coprococcus
textual definition: a PsA human-gut microbiome interaction that shows an decrease of Coprococcus in patients with PsA compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/

expansion of P. micra in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Parvimonas micra
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: expansion of Parvimonas in colorectal cancer human gut
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Parvimonas micra
textual definition: A colorectal cancer human-gut microbiome interaction where Parvimonas micra is increased.
definition editor: YH, HW
evidence publication: https://www.ncbi.nlm.nih.gov/pubmed/26408641
evidence publication: https://www.ncbi.nlm.nih.gov/pubmed/28912574

expansion of Diutina rugosa in PsA human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Diutina rugosa
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: PsA human-gut microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Diutina rugosa
textual definition: a PsA human-gut microbiome interaction that shows an expansion of Diutina rugosa in patients with PsA compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/11413927/

expansion of Malassezia furfur in PsA human skin
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Malassezia furfur
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0000014
        intersection of: Restriction
subclass of: PsA human zone of skin microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0000014
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Malassezia furfur
textual definition: a PsA human skin microbiome interaction that shows an expansion of Malassezia furfur in patients with PsA compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
comment: https://www.ncbi.nlm.nih.gov/pubmed/14675283/

expansion of Yersinia in ERA human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Yersinia
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: ERA human-gut microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Yersinia
textual definition: an ERA human-gut microbiome interaction that shows an expansion of Yersinia in patients with ERA compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/21679096

reactive arthritis rat-gut microbiome interaction
type: Class
subclass of: arthritis rat-gut microbiome interaction
subclass of: Restriction
  on property: has participant
  some values from: Class
    intersection of: Rattus
    intersection of: Restriction
      on property: has disposition
      some values from: reactive arthritis
textual definition: A rattus gut-microbiome interaction that is associated with reactive arthritis'.
definition editor: Haihe Wang, Hong Yu, Yongqun He

expansion of Yersinia in reactive arthritis rat gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Yersinia
    intersection of: Class
      intersection of: Restriction
        on property: part of
        some values from: Class
      intersection of: Restriction
        on property: located in
        some values from: UBERON_0004907
    intersection of: Restriction
      on property: has quality
      some values from: increased organism quantity compared with healthy control
subclass of: reactive arthritis rat-gut microbiome interaction
subclass of: Restriction
  on property: has participant
  some values from: Class
    intersection of: Yersinia
    intersection of: Class
      intersection of: Restriction
        on property: part of
        some values from: Class
      intersection of: Restriction
        on property: located in
        some values from: UBERON_0004907
    intersection of: Restriction
      on property: has quality
      some values from: increased organism quantity compared with healthy control
textual definition: An association of rattus gut microbiota with reactive arthritis that shows an expansion of Yersinia in rattus with juvenile rheumatoid arthritis compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/7768612/

expansion of Salmonella in reactive arthritis rat gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Salmonella
    intersection of: Class
      intersection of: Restriction
        on property: part of
        some values from: Class
      intersection of: Restriction
        on property: located in
        some values from: UBERON_0004907
    intersection of: Restriction
      on property: has quality
      some values from: increased organism quantity compared with healthy control
subclass of: reactive arthritis rat-gut microbiome interaction
subclass of: Restriction
  on property: has participant
  some values from: Class
    intersection of: Salmonella
    intersection of: Class
      intersection of: Restriction
        on property: part of
        some values from: Class
      intersection of: Restriction
        on property: located in
        some values from: UBERON_0004907
    intersection of: Restriction
      on property: has quality
      some values from: increased organism quantity compared with healthy control
textual definition: An association of rattus gut microbiota with reactive arthritis that shows an expansion of Salmonella in rattus with reactive arthritis compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/7768612/

expansion of S. moorei in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Solobacterium moorei
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: expansion of Solobacterium in colorectal cancer human gut
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Solobacterium moorei
textual definition: A colorectal cancer human-gut microbiome interaction where Solobacterium moorei is increased.
definition editor: YH, HW
evidence publication: https://www.ncbi.nlm.nih.gov/pubmed/26408641

expansion of Fusobacteria in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Fusobacteria
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: colorectal cancer human-gut microbiome interaction
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Fusobacteria
textual definition: A colorectal cancer human-gut microbiome interaction where Fusobacteria is increased.
definition editor: YH, HW
evidence publication: https://www.ncbi.nlm.nih.gov/pubmed/26408641
evidence publication: https://www.ncbi.nlm.nih.gov/pubmed/28483840
evidence publication: https://www.ncbi.nlm.nih.gov/pubmed/28827587
evidence publication: https://www.ncbi.nlm.nih.gov/pubmed/28912574

expansion of Basidiomycota in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Basidiomycota
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: colorectal cancer human-gut microbiome interaction
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Basidiomycota
textual definition: A colorectal cancer human-gut microbiome interaction where Basidiomycota is increased.
definition editor: YH, HW
evidence publication: https://www.ncbi.nlm.nih.gov/pubmed/26408641

expansion of Parvimonas in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Parvimonas
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: colorectal cancer human-gut microbiome interaction
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Parvimonas
textual definition: A colorectal cancer human-gut microbiome interaction where Parvimonas is increased.
definition editor: YH, HW
evidence publication: https://www.ncbi.nlm.nih.gov/pubmed/25758642
evidence publication: https://www.ncbi.nlm.nih.gov/pubmed/26408641

expansion of Peptostreptococcusi in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Peptostreptococcus
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: expansion of Peptostreptococcaceae in colorectal cancer human gut
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Peptostreptococcus
textual definition: A colorectal cancer human-gut microbiome interaction where Peptostreptococcus is increased.
definition editor: YH, HW
evidence publication: https://www.ncbi.nlm.nih.gov/pubmed/26408641

expansion of Fusobacterium in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Fusobacterium
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: expansion of Fusobacteriaceae in colorectal cancer human gut
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Fusobacterium
textual definition: A colorectal cancer human-gut microbiome interaction where Fusobacterium is increased.
definition editor: YH, HW
evidence publication: https://www.ncbi.nlm.nih.gov/pubmed/26170900
evidence publication: https://www.ncbi.nlm.nih.gov/pubmed/26408641
comment: https://www.ncbi.nlm.nih.gov/pubmed/18644884
comment: https://www.ncbi.nlm.nih.gov/pubmed/24316595
comment: https://www.ncbi.nlm.nih.gov/pubmed/25104642
comment: https://www.ncbi.nlm.nih.gov/pubmed/25439270
comment: https://www.ncbi.nlm.nih.gov/pubmed/25758642

expansion of Beggiatoa in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Beggiatoa
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: expansion of Proteobacteria in colorectal cancer human gut
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Beggiatoa
textual definition: A colorectal cancer human-gut microbiome interaction where Beggiatoa is increased.
definition editor: YH, HW
comment: https://www.ncbi.nlm.nih.gov/pubmed/26408641

expansion of Malassezia in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Malassezia
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: expansion of Basidiomycota in colorectal cancer human gut
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Malassezia
textual definition: A colorectal cancer human-gut microbiome interaction where Malassezia is increased.
definition editor: YH, HW
comment: https://www.ncbi.nlm.nih.gov/pubmed/26408641

expansion of Leptotrichia in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Leptotrichia
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: expansion of Fusobacteria in colorectal cancer human gut
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Leptotrichia
textual definition: A colorectal cancer human-gut microbiome interaction where Leptotrichia is increased.
definition editor: YH, HW
comment: https://www.ncbi.nlm.nih.gov/pubmed/26408641

expansion of Filifactor in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Filifactor
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: expansion of Peptostreptococcaceae in colorectal cancer human gut
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Filifactor
textual definition: A colorectal cancer human-gut microbiome interaction where Filifactor is increased.
definition editor: YH, HW
comment: https://www.ncbi.nlm.nih.gov/pubmed/26408641

expansion of Crenothrix in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Crenothrix
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: expansion of Proteobacteria in colorectal cancer human gut
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Crenothrix
textual definition: A colorectal cancer human-gut microbiome interaction where Crenothrix is increased.
definition editor: YH, HW
comment: https://www.ncbi.nlm.nih.gov/pubmed/26408641

expansion of Solobacterium in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Solobacterium
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: expansion of Erysipelotrichaceae in colorectal cancer human gut
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Solobacterium
textual definition: A colorectal cancer human-gut microbiome interaction where Solobacterium is increased.
definition editor: YH, HW
comment: https://www.ncbi.nlm.nih.gov/pubmed/26408641

expansion of Sulfurovum in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Sulfurovum
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: expansion of Proteobacteria in colorectal cancer human gut
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Sulfurovum
textual definition: A colorectal cancer human-gut microbiome interaction where Sulfurovum is increased.
definition editor: YH, HW
comment: https://www.ncbi.nlm.nih.gov/pubmed/26408641

expansion of Streptobacillus in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Streptobacillus
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: expansion of Fusobacteria in colorectal cancer human gut
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Streptobacillus
textual definition: A colorectal cancer human-gut microbiome interaction where Streptobacillus is increased.
definition editor: YH, HW
comment: https://www.ncbi.nlm.nih.gov/pubmed/26408641

expansion of Moniliophthora in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Moniliophthora
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: expansion of Basidiomycota in colorectal cancer human gut
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Moniliophthora
textual definition: A colorectal cancer human-gut microbiome interaction where Moniliophthora is increased.
definition editor: YH, HW
comment: https://www.ncbi.nlm.nih.gov/pubmed/26408641

expansion of Slackia in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Slackia
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: colorectal cancer human-gut microbiome interaction
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Slackia
textual definition: A colorectal cancer human-gut microbiome interaction where Slackia is increased.
definition editor: YH, HW
comment: https://www.ncbi.nlm.nih.gov/pubmed/ 21647227

expansion of Collinsella in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Collinsella
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: expansion of Coriobacteriaceae in colorectal cancer human gut
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Collinsella
textual definition: A colorectal cancer human-gut microbiome interaction where Collinsella is increased.
definition editor: YH, HW
comment: https://www.ncbi.nlm.nih.gov/pubmed/ 21647227

expansion of Clostridiaceae in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Clostridiaceae
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: expansion of Clostridia in colorectal cancer human gut
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Clostridiaceae
textual definition: A colorectal cancer human-gut microbiome interaction where Clostridiaceae is increased.
definition editor: YH, HW
comment: https://www.ncbi.nlm.nih.gov/pubmed/ 21647227

expansion of Bacteroidales in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Bacteroidales
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: expansion of Bacteroidetes in colorectal cancer human gut
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Bacteroidales
textual definition: A colorectal cancer human-gut microbiome interaction where Bacteroidales is increased.
definition editor: YH, HW
comment: https://www.ncbi.nlm.nih.gov/pubmed/ 21647227

depletion of Cronobacter in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Cronobacter
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: colorectal cancer human-gut microbiome interaction
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Cronobacter
textual definition: A colorectal cancer human-gut microbiome interaction where Cronobacter is decreased.
definition editor: YH, HW
evidence publication: https://www.ncbi.nlm.nih.gov/pubmed/21647227

depletion of Kluyvera in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Kluyvera
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: colorectal cancer human-gut microbiome interaction
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Kluyvera
textual definition: A colorectal cancer human-gut microbiome interaction where Kluyvera is decreased.
definition editor: YH, HW
evidence publication: https://www.ncbi.nlm.nih.gov/pubmed/21647227

depletion of Serratia in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Serratia
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: colorectal cancer human-gut microbiome interaction
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Serratia
textual definition: A colorectal cancer human-gut microbiome interaction where Serratia is decreased.
definition editor: YH, HW
evidence publication: https://www.ncbi.nlm.nih.gov/pubmed/21647227

depletion of Salmonella enterica subsp. enterica in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Salmonella enterica subsp. enterica
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: colorectal cancer human-gut microbiome interaction
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Salmonella enterica subsp. enterica
textual definition: A colorectal cancer human-gut microbiome interaction where Salmonella enterica subsp. enterica is decreased.
definition editor: YH, HW
evidence publication: https://www.ncbi.nlm.nih.gov/pubmed/21647227

depletion of Eubacteriaceae in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Eubacteriaceae
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: depletion of Clostridiales in colorectal cancer human gut
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Eubacteriaceae
textual definition: A colorectal cancer human-gut microbiome interaction where Eubacteriaceae is decreased.
definition editor: YH, HW
evidence publication: https://www.ncbi.nlm.nih.gov/pubmed/21647227

depletion of Anaerovorax in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Anaerovorax
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: depletion of Clostridiales in colorectal cancer human gut
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Anaerovorax
textual definition: A colorectal cancer human-gut microbiome interaction where Anaerovorax is decreased.
definition editor: YH, HW
evidence publication: https://www.ncbi.nlm.nih.gov/pubmed/21647227

depletion of Microbacterium in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Microbacterium
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: colorectal cancer human-gut microbiome interaction
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Microbacterium
textual definition: A colorectal cancer human-gut microbiome interaction where Microbacterium is decreased.
definition editor: YH, HW
evidence publication: https://www.ncbi.nlm.nih.gov/pubmed/21647227
comment: https://www.ncbi.nlm.nih.gov/pubmed/23497613

depletion of B. finegoldii in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Bacteroides finegoldii
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: 'depletion of Bacteroides in colorectal cancer human gut'
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Bacteroides finegoldii
textual definition: A colorectal cancer human-gut microbiome interaction where Bacteroides finegoldii is decreased.
definition editor: YH, HW
comment: https://www.ncbi.nlm.nih.gov/pubmed/23940645

depletion of B.intestinalis in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Bacteroides intestinalis
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: 'depletion of Bacteroides in colorectal cancer human gut'
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Bacteroides intestinalis
textual definition: A colorectal cancer human-gut microbiome interaction where Bacteroides intestinalis is decreased.
definition editor: YH, HW
comment: https://www.ncbi.nlm.nih.gov/pubmed/23940645

depletion of P.copri in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Prevotella copri
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: depletion of Prevotellaceae in colorectal cancer human gut
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Prevotella copri
textual definition: A colorectal cancer human-gut microbiome interaction where Prevotella copri is decreased.
definition editor: YH, HW
comment: https://www.ncbi.nlm.nih.gov/pubmed/23940645

depletion of P. oris in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Prevotella oris
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: depletion of Prevotellaceae in colorectal cancer human gut
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Prevotella oris
textual definition: A colorectal cancer human-gut microbiome interaction where Prevotella oris is decreased.
definition editor: YH, HW
comment: https://www.ncbi.nlm.nih.gov/pubmed/23940645

depletion of D.formicigenerans in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Dorea formicigenerans
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: depletion of Lachnospiraceae in colorectal cancer human gut
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Dorea formicigenerans
textual definition: A colorectal cancer human-gut microbiome interaction where Dorea formicigenerans is decreased.
definition editor: YH, HW
comment: https://www.ncbi.nlm.nih.gov/pubmed/23940645

depletion of L. bovis in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Lachnobacterium bovis
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: depletion of Lachnospiraceae in colorectal cancer human gut
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Lachnobacterium bovis
textual definition: A colorectal cancer human-gut microbiome interaction where Lachnobacterium bovis is decreased.
definition editor: YH, HW
comment: https://www.ncbi.nlm.nih.gov/pubmed/23940645

depletion of L.pectinoschiza in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Lachnospira pectinoschiza
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: depletion of Lachnospiraceae in colorectal cancer human gut
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Lachnospira pectinoschiza
textual definition: A colorectal cancer human-gut microbiome interaction where Lachnospira pectinoschiza is decreased.
definition editor: YH, HW
comment: https://www.ncbi.nlm.nih.gov/pubmed/23940645

depletion of P.ruminis in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Pseudobutyrivibrio ruminis
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: depletion of Lachnospiraceae in colorectal cancer human gut
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Pseudobutyrivibrio ruminis
textual definition: A colorectal cancer human-gut microbiome interaction where Pseudobutyrivibrio ruminis is decreased.
definition editor: YH, HW
comment: https://www.ncbi.nlm.nih.gov/pubmed/23940645

depletion of R.albus in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Ruminococcus albus
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: depletion of Ruminococcus in colorectal cancer human gut
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Ruminococcus albus
textual definition: A colorectal cancer human-gut microbiome interaction where Ruminococcus albus is decreased.
definition editor: YH, HW
comment: https://www.ncbi.nlm.nih.gov/pubmed/23940645

depletion of D. invisus in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Dialister invisus
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: depletion of Firmicutes in colorectal cancer human gut
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Dialister invisus
textual definition: A colorectal cancer human-gut microbiome interaction where Dialister invisus is decreased.
definition editor: YH, HW
comment: https://www.ncbi.nlm.nih.gov/pubmed/23940645

depletion of D. pneumosintes in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Dialister pneumosintes
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: depletion of Firmicutes in colorectal cancer human gut
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Dialister pneumosintes
textual definition: A colorectal cancer human-gut microbiome interaction where Dialister pneumosintes is decreased.
definition editor: YH, HW
comment: https://www.ncbi.nlm.nih.gov/pubmed/23940645

depletion of M. hypermegale in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Megamonas hypermegale
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: depletion of Firmicutes in colorectal cancer human gut
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Megamonas hypermegale
textual definition: A colorectal cancer human-gut microbiome interaction where Megamonas hypermegale is decreased.
definition editor: YH, HW
comment: https://www.ncbi.nlm.nih.gov/pubmed/23940645

expansion of Acidaminobacter in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Acidaminobacter
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: expansion of Clostridia in colorectal cancer human gut
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Acidaminobacter
textual definition: A colorectal cancer human-gut microbiome interaction where Acidaminobacter is increased.
definition editor: YH, HW
comment: https://www.ncbi.nlm.nih.gov/pubmed/ 23940645

expansion of Phascolarctobacterium in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Phascolarctobacterium
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: colorectal cancer human-gut microbiome interaction
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Phascolarctobacterium
textual definition: A colorectal cancer human-gut microbiome interaction where Phascolarctobacterium is increased.
definition editor: YH, HW
comment: https://www.ncbi.nlm.nih.gov/pubmed/ 23940645

expansion of C.farmeri in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Citrobacter farmeri
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: expansion of Enterobacteriaceae in colorectal cancer human gut
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Citrobacter farmeri
textual definition: A colorectal cancer human-gut microbiome interaction where Citrobacter farmeri is increased.
definition editor: YH, HW
comment: https://www.ncbi.nlm.nih.gov/pubmed/ 23940645

expansion of Bacteroides fragilis in RA human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Bacteroides fragilis
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: depletion of Bacteroides in RA human gut
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Bacteroides fragilis
textual definition: a RA human-gut microbiome interaction that shows an decrease of Bacteroides fragilis in patients with RA compared with healthy controls. Bacteroides fragilis is a rare cause of septic arthritis.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/9456020

expansion of Roseburia in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Roseburia
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: expansion of Clostridia in colorectal cancer human gut
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Roseburia
textual definition: A colorectal cancer human-gut microbiome interaction where Roseburia is increased.
definition editor: YH, HW
evidence publication: https://www.ncbi.nlm.nih.gov/pubmed/21647227
comment: https://www.ncbi.nlm.nih.gov/pubmed/23497613
comment: https://www.ncbi.nlm.nih.gov/pubmed/23733170

depletion of Anoxybacillus in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Anoxybacillus
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: depletion of Firmicutes in colorectal cancer human gut
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Anoxybacillus
textual definition: A colorectal cancer human-gut microbiome interaction where Anoxybacillus is decreased.
definition editor: YH, HW
comment: https://www.ncbi.nlm.nih.gov/pubmed/23497613

expansion of Bacteroides in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Bacteroides
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: expansion of Bacteroidaceae in colorectal cancer human gut
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Bacteroides
textual definition: A colorectal cancer human-gut microbiome interaction where Bacteroides is increased.
definition editor: YH, HW
comment: https://www.ncbi.nlm.nih.gov/pubmed/24194538
comment: https://www.ncbi.nlm.nih.gov/pubmed/24967088
comment: https://www.ncbi.nlm.nih.gov/pubmed/25439270
comment: https://www.ncbi.nlm.nih.gov/pubmed/25758642

expansion of Odoribacter in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Odoribacter
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: expansion of Bacteroidales in colorectal cancer human gut
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Odoribacter
textual definition: A colorectal cancer human-gut microbiome interaction where Odoribacter is increased.
definition editor: YH, HW
comment: https://www.ncbi.nlm.nih.gov/pubmed/24194538

expansion of A. muciniphila in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Akkermansia muciniphila
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: colorectal cancer human-gut microbiome interaction
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Akkermansia muciniphila
textual definition: A colorectal cancer human-gut microbiome interaction where Akkermansia muciniphila is increased.
definition editor: YH, HW
evidence publication: https://www.ncbi.nlm.nih.gov/pubmed/23940645
comment: https://www.ncbi.nlm.nih.gov/pubmed/24194538
comment: https://www.ncbi.nlm.nih.gov/pubmed/24967088

depletion of Prevotellaceae in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Prevotellaceae
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: depletion of Bacteroidales in colorectal cancer human gut
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Prevotellaceae
textual definition: A colorectal cancer human-gut microbiome interaction where Prevotellaceae is decreased.
definition editor: YH, HW
comment: https://www.ncbi.nlm.nih.gov/pubmed/24194538

depletion of Porphyromonadaceae in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Porphyromonadaceae
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: depletion of Bacteroidales in colorectal cancer human gut
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Porphyromonadaceae
textual definition: A colorectal cancer human-gut microbiome interaction where Porphyromonadaceae is decreased.
definition editor: YH, HW
comment: https://www.ncbi.nlm.nih.gov/pubmed/24194538

depletion of Clostridiaceae in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Clostridiaceae
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: depletion of Clostridiales in colorectal cancer human gut
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Clostridiaceae
textual definition: A colorectal cancer human-gut microbiome interaction where Clostridiaceae is decreased.
definition editor: YH, HW
comment: https://www.ncbi.nlm.nih.gov/pubmed/24316595

expansion of Parabacteroides in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Parabacteroides
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: expansion of Bacteroidales in colorectal cancer human gut
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Parabacteroides
textual definition: A colorectal cancer human-gut microbiome interaction where Parabacteroides is increased.
definition editor: YH, HW
comment: https://www.ncbi.nlm.nih.gov/pubmed/24967088
comment: https://www.ncbi.nlm.nih.gov/pubmed/25758642

expansion of Alistipes in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Alistipes
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: expansion of Bacteroidales in colorectal cancer human gut
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Alistipes
textual definition: A colorectal cancer human-gut microbiome interaction where ParaAlistipes is increased.
definition editor: YH, HW
comment: https://www.ncbi.nlm.nih.gov/pubmed/24967088

expansion of B. ovatus in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Bacteroides ovatus
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: expansion of Bacteroides in colorectal cancer human gut
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Bacteroides ovatus
textual definition: A colorectal cancer human-gut microbiome interaction where Bacteroides ovatus is increased.
definition editor: YH, HW
comment: https://www.ncbi.nlm.nih.gov/pubmed/24967088

expansion of B. xylanisolvens in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Bacteroides xylanisolvens
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: expansion of Bacteroides in colorectal cancer human gut
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Bacteroides xylanisolvens
textual definition: A colorectal cancer human-gut microbiome interaction where Bacteroides xylanisolvens is increased.
definition editor: YH, HW
comment: https://www.ncbi.nlm.nih.gov/pubmed/24967088

human-urine microbiome interaction
type: Class
subclass of: human-microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: Class
    intersection of: UBERON_0001088
    intersection of: Restriction
      on property: part of
      some values from: Homo sapiens
subclass of: Restriction
  on property: has participant
  some values from: Class
    intersection of: microbiome
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0001088
        intersection of: Restriction
textual definition: An interaction between human and urine microbiome.
definition editor: YH

RA human-urine microbiome interaction
type: Class
subclass of: human-urine microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0001088
subclass of: Restriction
  on property: has participant
  some values from: Class
    intersection of: Homo sapiens
    intersection of: Restriction
      on property: has disease
      some values from: rheumatoid arthritis
textual definition: A human urine-microbiome interaction that is associated with rheumatoid arthritis (RA).
definition editor: YH

depletion of Lachnospiraceae in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Lachnospiraceae
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: depletion of Clostridiales in colorectal cancer human gut
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Lachnospiraceae
textual definition: A colorectal cancer human-gut microbiome interaction where Lachnospiraceae is decreased.
definition editor: YH, HW
evidence publication: https://www.ncbi.nlm.nih.gov/pubmed/22761885
evidence publication: https://www.ncbi.nlm.nih.gov/pubmed/23397545
evidence publication: https://www.ncbi.nlm.nih.gov/pubmed/25439270
comment: https://www.ncbi.nlm.nih.gov/pubmed/24967088
comment: https://www.ncbi.nlm.nih.gov/pubmed/25104642
comment: https://www.ncbi.nlm.nih.gov/pubmed/26170900

expansion of Enterobacteriaceae in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Enterobacteriaceae
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: expansion of Proteobacteria in colorectal cancer human gut
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Enterobacteriaceae
textual definition: A colorectal cancer human-gut microbiome interaction where Enterobacteriaceae is increased.
definition editor: YH, HW
comment: https://www.ncbi.nlm.nih.gov/pubmed/25104642

depletion of L. acidophilus in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Lactobacillus acidophilus
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: depletion of Lactobacillaceae in colorectal cancer human gut
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Lactobacillus acidophilus
textual definition: A colorectal cancer human-gut microbiome interaction where Lactobacillus acidophilus is decreased.
definition editor: YH, HW
comment: https://www.ncbi.nlm.nih.gov/pubmed/25439270

'depletion of Bacteroides in colorectal cancer human gut'
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Bacteroides
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: depletion of Bacteroidales in colorectal cancer human gut
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Bacteroides
textual definition: A colorectal cancer human-gut microbiome interaction where Bacteroides is decreased.
definition editor: YH, HW
comment: https://www.ncbi.nlm.nih.gov/pubmed/25104642

depletion of Clostridiales in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Clostridiales
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: depletion of Firmicutes in colorectal cancer human gut
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Clostridiales
textual definition: A colorectal cancer human-gut microbiome interaction where Clostridiales is decreased.
definition editor: YH, HW
evidence publication: https://www.ncbi.nlm.nih.gov/pubmed/24967088
comment: https://www.ncbi.nlm.nih.gov/pubmed/25104642

expansion of unclassified Proteobacteria in diarrheal patient gut
type: Class
equivalent class: Restriction
  on property: has microbe expanded in diseased host
  some values from: Class
    intersection of: unclassified Proteobacteria
    intersection of: Class
      intersection of: Restriction
        on property: part of
        some values from: Class
      intersection of: Restriction
        on property: located in
        some values from: UBERON_0004907
subclass of: diarrheal patient-gut microbiome interaction
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: unclassified Proteobacteria
textual definition: a diarrheal patient-gut microbiome interaction that shows an increase of unclassified Proteobacteria in patients in the gut of human diarrheal patient compared with healthy controls.
definition editor: YH
definition source: http://microbiomedb.org/mbio/app/

depletion of Firmicutes in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Firmicutes
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: colorectal cancer human-gut microbiome interaction
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Firmicutes
textual definition: A colorectal cancer human-gut microbiome interaction where Firmicutes is decreased.
definition editor: YH, HW
comment: https://www.ncbi.nlm.nih.gov/pubmed/26170900
comment: https://www.ncbi.nlm.nih.gov/pubmed/28912574

depletion of Bacteroidetes in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Bacteroidetes
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: colorectal cancer human-gut microbiome interaction
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Bacteroidetes
textual definition: A colorectal cancer human-gut microbiome interaction where Bacteroidetes is decreased.
definition editor: YH, HW
comment: https://www.ncbi.nlm.nih.gov/pubmed/26170900

depletion of Bacteroidales in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Bacteroidales
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: depletion of Bacteroidetes in colorectal cancer human gut
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Bacteroidales
textual definition: A colorectal cancer human-gut microbiome interaction where Bacteroidales is decreased.
definition editor: YH, HW
comment: https://www.ncbi.nlm.nih.gov/pubmed/26170900

depletion of Rikenellaceae in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Rikenellaceae
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: depletion of Bacteroidales in colorectal cancer human gut
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Rikenellaceae
textual definition: A colorectal cancer human-gut microbiome interaction where Rikenellaceae is decreased.
definition editor: YH, HW
comment: https://www.ncbi.nlm.nih.gov/pubmed/26170900

depletion of B. uniformis in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Bacteroides uniformis
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: 'depletion of Bacteroides in colorectal cancer human gut'
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Bacteroides uniformis
textual definition: A colorectal cancer human-gut microbiome interaction where Bacteroides uniformis is decreased.
definition editor: YH, HW
comment: https://www.ncbi.nlm.nih.gov/pubmed/26170900

expansion of Providencia in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Providencia
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: expansion of Proteobacteria in colorectal cancer human gut
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Providencia
textual definition: A colorectal cancer human-gut microbiome interaction where Providencia is increased.
definition editor: YH, HW
comment: https://www.ncbi.nlm.nih.gov/pubmed/26170900

expansion of Bacteroidaceae in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Bacteroidaceae
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: expansion of Bacteroidales in colorectal cancer human gut
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Bacteroidaceae
textual definition: A colorectal cancer human-gut microbiome interaction where Bacteroidaceae is increased.
definition editor: YH, HW
comment: https://www.ncbi.nlm.nih.gov/pubmed/ 22761885
comment: https://www.ncbi.nlm.nih.gov/pubmed/ 23397545
comment: https://www.ncbi.nlm.nih.gov/pubmed/25439270

expansion of Streptococcaceae in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Streptococcaceae
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: colorectal cancer human-gut microbiome interaction
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Streptococcaceae
textual definition: A colorectal cancer human-gut microbiome interaction where Streptococcaceae is increased.
definition editor: YH, HW
comment: https://www.ncbi.nlm.nih.gov/pubmed/ 22761885
comment: https://www.ncbi.nlm.nih.gov/pubmed/ 23397545
comment: https://www.ncbi.nlm.nih.gov/pubmed/25439270

expansion of Fusobacteriaceae in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Fusobacteriaceae
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: expansion of Fusobacteria in colorectal cancer human gut
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Fusobacteriaceae
textual definition: A colorectal cancer human-gut microbiome interaction where Fusobacteriaceae is increased.
definition editor: YH, HW
comment: https://www.ncbi.nlm.nih.gov/pubmed/ 22761885
comment: https://www.ncbi.nlm.nih.gov/pubmed/ 23397545
comment: https://www.ncbi.nlm.nih.gov/pubmed/25439270

expansion of Peptostreptococcaceae in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Peptostreptococcaceae
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: expansion of Clostridia in colorectal cancer human gut
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Peptostreptococcaceae
textual definition: A colorectal cancer human-gut microbiome interaction where Peptostreptococcaceae is increased.
definition editor: YH, HW
evidence publication: https://www.ncbi.nlm.nih.gov/pubmed/21647227
comment: https://www.ncbi.nlm.nih.gov/pubmed/22761885
comment: https://www.ncbi.nlm.nih.gov/pubmed/23397545
comment: https://www.ncbi.nlm.nih.gov/pubmed/25439270

expansion of Veillonellaceae in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Veillonellaceae
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: colorectal cancer human-gut microbiome interaction
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Veillonellaceae
textual definition: A colorectal cancer human-gut microbiome interaction where Veillonellaceae is increased.
definition editor: YH, HW
comment: https://www.ncbi.nlm.nih.gov/pubmed/ 22761885
comment: https://www.ncbi.nlm.nih.gov/pubmed/ 23397545
comment: https://www.ncbi.nlm.nih.gov/pubmed/25439270

expansion of Pasteurellaceae in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Pasteurellaceae
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: expansion of Proteobacteria in colorectal cancer human gut
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Pasteurellaceae
textual definition: A colorectal cancer human-gut microbiome interaction where Pasteurellaceae is increased.
definition editor: YH, HW
comment: https://www.ncbi.nlm.nih.gov/pubmed/ 22761885
comment: https://www.ncbi.nlm.nih.gov/pubmed/ 23397545
comment: https://www.ncbi.nlm.nih.gov/pubmed/25439270

expansion of Porphyromonas in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Porphyromonas
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: expansion of Bacteroidales in colorectal cancer human gut
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Porphyromonas
textual definition: A colorectal cancer human-gut microbiome interaction where Porphyromonas is increased.
definition editor: YH, HW
evidence publication: https://www.ncbi.nlm.nih.gov/pubmed/24316595
evidence publication: https://www.ncbi.nlm.nih.gov/pubmed/25104642
comment: https://www.ncbi.nlm.nih.gov/pubmed/22761885
comment: https://www.ncbi.nlm.nih.gov/pubmed/23397545
comment: https://www.ncbi.nlm.nih.gov/pubmed/25439270

expansion of Mogibacterium in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Mogibacterium
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: expansion of Clostridia in colorectal cancer human gut
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Mogibacterium
textual definition: A colorectal cancer human-gut microbiome interaction where Mogibacterium is increased.
definition editor: YH, HW
comment: https://www.ncbi.nlm.nih.gov/pubmed/ 22761885
comment: https://www.ncbi.nlm.nih.gov/pubmed/ 23397545
comment: https://www.ncbi.nlm.nih.gov/pubmed/25439270

expansion of Erysipelotrichaceae in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Erysipelotrichaceae
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: colorectal cancer human-gut microbiome interaction
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Erysipelotrichaceae
textual definition: A colorectal cancer human-gut microbiome interaction where Erysipelotrichaceae is increased.
definition editor: YH, HW
evidence publication: https://www.ncbi.nlm.nih.gov/pubmed/21647227
comment: https://www.ncbi.nlm.nih.gov/pubmed/22761885
comment: https://www.ncbi.nlm.nih.gov/pubmed/23397545
comment: https://www.ncbi.nlm.nih.gov/pubmed/25439270

expansion of Prevotellaceae in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Prevotellaceae
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: expansion of Bacteroidales in colorectal cancer human gut
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Prevotellaceae
textual definition: A colorectal cancer human-gut microbiome interaction where Prevotellaceae is increased.
definition editor: YH, HW
comment: https://www.ncbi.nlm.nih.gov/pubmed/ 22761885
comment: https://www.ncbi.nlm.nih.gov/pubmed/ 23397545
comment: https://www.ncbi.nlm.nih.gov/pubmed/25439270

expansion of Coriobacteriaceae in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Coriobacteriaceae
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: colorectal cancer human-gut microbiome interaction
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Coriobacteriaceae
textual definition: A colorectal cancer human-gut microbiome interaction where Coriobacteriaceae is increased.
definition editor: YH, HW
comment: https://www.ncbi.nlm.nih.gov/pubmed/ 22761885
comment: https://www.ncbi.nlm.nih.gov/pubmed/ 23397545
comment: https://www.ncbi.nlm.nih.gov/pubmed/25439270

depletion of Ruminococcaceae in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Ruminococcaceae
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: depletion of Clostridiales in colorectal cancer human gut
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Ruminococcaceae
textual definition: A colorectal cancer human-gut microbiome interaction where Ruminococcaceae is decreased.
definition editor: YH, HW
evidence publication: https://www.ncbi.nlm.nih.gov/pubmed/26170900
comment: https://www.ncbi.nlm.nih.gov/pubmed/22761885
comment: https://www.ncbi.nlm.nih.gov/pubmed/23397545
comment: https://www.ncbi.nlm.nih.gov/pubmed/25439270

depletion of Lactobacillaceae in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Lactobacillaceae
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: depletion of Firmicutes in colorectal cancer human gut
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Lactobacillaceae
textual definition: A colorectal cancer human-gut microbiome interaction where Lactobacillaceae is decreased.
definition editor: YH, HW
comment: https://www.ncbi.nlm.nih.gov/pubmed/ 23397545
comment: https://www.ncbi.nlm.nih.gov/pubmed/22761885
comment: https://www.ncbi.nlm.nih.gov/pubmed/25439270

depletion of B. longum in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Bifidobacterium longum
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: depletion of Bifidobacterium in colorectal cancer human gut
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Bifidobacterium longum
textual definition: A colorectal cancer human-gut microbiome interaction where Bifidobacterium longum is decreased.
definition editor: YH, HW
comment: https://www.ncbi.nlm.nih.gov/pubmed/22761885
comment: https://www.ncbi.nlm.nih.gov/pubmed/23397545
comment: https://www.ncbi.nlm.nih.gov/pubmed/25439270

depletion of F. prausnitzii in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Faecalibacterium prausnitzii
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: depletion of Ruminococcaceae in colorectal cancer human gut
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Faecalibacterium prausnitzii
textual definition: A colorectal cancer human-gut microbiome interaction where Faecalibacterium prausnitzii is decreased.
definition editor: YH, HW
evidence publication: https://www.ncbi.nlm.nih.gov/pubmed/22009989
evidence publication: https://www.ncbi.nlm.nih.gov/pubmed/24021287
evidence publication: https://www.ncbi.nlm.nih.gov/pubmed/26170900
comment: https://www.ncbi.nlm.nih.gov/pubmed/22761885
comment: https://www.ncbi.nlm.nih.gov/pubmed/23397545
comment: https://www.ncbi.nlm.nih.gov/pubmed/25439270

depletion of Blautia in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Blautia
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: depletion of Lachnospiraceae in colorectal cancer human gut
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Blautia
textual definition: A colorectal cancer human-gut microbiome interaction where Blautia is decreased.
definition editor: YH, HW
comment: https://www.ncbi.nlm.nih.gov/pubmed/ 23397545
comment: https://www.ncbi.nlm.nih.gov/pubmed/22761885
comment: https://www.ncbi.nlm.nih.gov/pubmed/25439270

depletion of L. rhamnosus in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Lactobacillus rhamnosus
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: depletion of Lactobacillaceae in colorectal cancer human gut
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Lactobacillus rhamnosus
textual definition: A colorectal cancer human-gut microbiome interaction where Lactobacillus rhamnosus is decreased.
definition editor: YH, HW
comment: https://www.ncbi.nlm.nih.gov/pubmed/25439270

'depletion of L. reuteri in colorectal cancer human gut'
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Lactobacillus reuteri
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: depletion of Lactobacillaceae in colorectal cancer human gut
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Lactobacillus reuteri
textual definition: A colorectal cancer human-gut microbiome interaction where Lactobacillus reuteri is decreased.
definition editor: YH, HW
comment: https://www.ncbi.nlm.nih.gov/pubmed/25439270

expansion of Proteus mirabilis in RA human urine
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Proteus mirabilis
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0001088
        intersection of: Restriction
subclass of: RA human-urine microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0001088
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Proteus mirabilis
textual definition: a RA human-urine microbiome interaction that shows an expansion of Proteus mirabilis in patients with RA compared with healthy controls.
definition editor: Haihe Wang, Hong Yu, Yongqun He
definition source: https://www.ncbi.nlm.nih.gov/pubmed/9032817

expansion of A. putredinis in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Alistipes putredinis
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: expansion of Alistipes in colorectal cancer human gut
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Alistipes putredinis
textual definition: A colorectal cancer human-gut microbiome interaction where Alistipes putredinis is increased.
definition editor: YH, HW
comment: https://www.ncbi.nlm.nih.gov/pubmed/25758642

expansion of L. bacterium in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Lachnospiraceae bacterium
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: expansion of Clostridia in colorectal cancer human gut
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Lachnospiraceae bacterium
textual definition: A colorectal cancer human-gut microbiome interaction where Lachnospiraceae bacterium is increased.
definition editor: YH, HW
comment: https://www.ncbi.nlm.nih.gov/pubmed/25758642

expansion of E. coli NC101 in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Escherichia coli NC101
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: expansion of Escherichia in colorectal cancer human gut
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Escherichia coli NC101
textual definition: A colorectal cancer human-gut microbiome interaction where Escherichia coli NC101 is increased.
definition editor: YH, HW
evidence publication: https://www.ncbi.nlm.nih.gov/pubmed/22903521
comment: https://www.ncbi.nlm.nih.gov/pubmed/25758642

expansion of B. wadsworthia in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Bilophila wadsworthia
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: expansion of Bilophila in colorectal cancer human gut
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Bilophila wadsworthia
textual definition: A colorectal cancer human-gut microbiome interaction where Bilophila wadsworthia is increased.
definition editor: YH, HW
comment: https://www.ncbi.nlm.nih.gov/pubmed/22009989
comment: https://www.ncbi.nlm.nih.gov/pubmed/25758642
comment: https://www.ncbi.nlm.nih.gov/pubmed/26073561

depletion of B. animalis in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Bifidobacterium animalis
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: depletion of Bifidobacterium in colorectal cancer human gut
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Bifidobacterium animalis
textual definition: A colorectal cancer human-gut microbiome interaction where Bifidobacterium animalis is decreased.
definition editor: YH, HW
comment: https://www.ncbi.nlm.nih.gov/pubmed/25758642

depletion of S. thermophilus in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Streptococcus thermophilus
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: depletion of Streptococcus in colorectal cancer human gut
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Streptococcus thermophilus
textual definition: A colorectal cancer human-gut microbiome interaction where Streptococcus thermophilus is decreased.
definition editor: YH, HW
comment: https://www.ncbi.nlm.nih.gov/pubmed/25758642

depletion of Ruminococcus in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Ruminococcus
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: depletion of Ruminococcaceae in colorectal cancer human gut
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Ruminococcus
textual definition: A colorectal cancer human-gut microbiome interaction where Ruminococcus is decreased.
definition editor: YH, HW
comment: https://www.ncbi.nlm.nih.gov/pubmed/25758642

depletion of Bifidobacterium in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Bifidobacterium
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: colorectal cancer human-gut microbiome interaction
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Bifidobacterium
textual definition: A colorectal cancer human-gut microbiome interaction where Bifidobacterium is decreased.
definition editor: YH, HW
comment: https://www.ncbi.nlm.nih.gov/pubmed/25758642

depletion of Streptococcus in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Streptococcus
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: depletion of Firmicutes in colorectal cancer human gut
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Streptococcus
textual definition: A colorectal cancer human-gut microbiome interaction where Streptococcus is decreased.
definition editor: YH, HW
comment: https://www.ncbi.nlm.nih.gov/pubmed/25758642

expansion of Escherichia in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Escherichia
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: expansion of Enterobacteriaceae in colorectal cancer human gut
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Escherichia
textual definition: A colorectal cancer human-gut microbiome interaction where Escherichia is increased.
definition editor: YH, HW
comment: https://www.ncbi.nlm.nih.gov/pubmed/25758642

expansion of Bilophila in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Bilophila
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: expansion of Proteobacteria in colorectal cancer human gut
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Bilophila
textual definition: A colorectal cancer human-gut microbiome interaction where Bilophila is increased.
definition editor: YH, HW
comment: https://www.ncbi.nlm.nih.gov/pubmed/25758642

expansion of Bacteroidetes in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Bacteroidetes
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: colorectal cancer human-gut microbiome interaction
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Bacteroidetes
textual definition: A colorectal cancer human-gut microbiome interaction where Bacteroidetes is increased.
definition editor: YH, HW
comment: https://www.ncbi.nlm.nih.gov/pubmed/22009989
comment: https://www.ncbi.nlm.nih.gov/pubmed/26073561

expansion of S. equinus in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Streptococcus equinus
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: expansion of Streptococcaceae in colorectal cancer human gut
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Streptococcus equinus
textual definition: A colorectal cancer human-gut microbiome interaction where Streptococcus equinus is increased.
definition editor: YH, HW
evidence publication: https://www.ncbi.nlm.nih.gov/pubmed/25439270
comment: https://www.ncbi.nlm.nih.gov/pubmed/19226366
comment: https://www.ncbi.nlm.nih.gov/pubmed/26073561
comment: https://www.ncbi.nlm.nih.gov/pubmed/484953
comment: https://www.ncbi.nlm.nih.gov/pubmed/9282212

expansion of Enterococcaceae in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Enterococcaceae
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: colorectal cancer human-gut microbiome interaction
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Enterococcaceae
textual definition: A colorectal cancer human-gut microbiome interaction where Enterococcaceae is increased.
definition editor: YH, HW
comment: https://www.ncbi.nlm.nih.gov/pubmed/18644884
comment: https://www.ncbi.nlm.nih.gov/pubmed/22009989
comment: https://www.ncbi.nlm.nih.gov/pubmed/23954159
comment: https://www.ncbi.nlm.nih.gov/pubmed/9282212

expansion of Campylobacter in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Campylobacter
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: expansion of Proteobacteria in colorectal cancer human gut
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Campylobacter
textual definition: A colorectal cancer human-gut microbiome interaction where Campylobacter is increased.
definition editor: YH, HW
comment: https://www.ncbi.nlm.nih.gov/pubmed/18644884
comment: https://www.ncbi.nlm.nih.gov/pubmed/22009989
comment: https://www.ncbi.nlm.nih.gov/pubmed/23954159
comment: https://www.ncbi.nlm.nih.gov/pubmed/9282212

expansion of Salmonella in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Salmonella
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: expansion of Enterobacteriaceae in colorectal cancer human gut
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Salmonella
textual definition: A colorectal cancer human-gut microbiome interaction where Salmonella is increased.
definition editor: YH, HW
comment: https://www.ncbi.nlm.nih.gov/pubmed/22009989

expansion of Shigella in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Shigella
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: expansion of Enterobacteriaceae in colorectal cancer human gut
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Shigella
textual definition: A colorectal cancer human-gut microbiome interaction where Shigella is increased.
definition editor: YH, HW
comment: https://www.ncbi.nlm.nih.gov/pubmed/22009989

depletion of B. animalis subsp. lactis in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Bifidobacterium animalis subsp. lactis
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: depletion of B. animalis in colorectal cancer human gut
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Bifidobacterium animalis subsp. lactis
textual definition: A colorectal cancer human-gut microbiome interaction where Bifidobacterium animalis subsp. lactis is decreased.
definition editor: YH, HW
comment: https://www.ncbi.nlm.nih.gov/pubmed/15542102
comment: https://www.ncbi.nlm.nih.gov/pubmed/22009989

expansion of Chlamydia in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Chlamydia
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: colorectal cancer human-gut microbiome interaction
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Chlamydia
textual definition: A colorectal cancer human-gut microbiome interaction where Chlamydia is increased.
definition editor: YH, HW
comment: https://www.ncbi.nlm.nih.gov/pubmed/22009989
comment: https://www.ncbi.nlm.nih.gov/pubmed/22687960
comment: https://www.ncbi.nlm.nih.gov/pubmed/22687961

expansion of Mycobacterium in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Mycobacterium
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: colorectal cancer human-gut microbiome interaction
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Mycobacterium
textual definition: A colorectal cancer human-gut microbiome interaction where Mycobacterium is increased.
definition editor: YH, HW
comment: https://www.ncbi.nlm.nih.gov/pubmed/22009989
comment: https://www.ncbi.nlm.nih.gov/pubmed/22687960
comment: https://www.ncbi.nlm.nih.gov/pubmed/22687961

expansion of Clostridia in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Clostridia
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: colorectal cancer human-gut microbiome interaction
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Clostridia
textual definition: A colorectal cancer human-gut microbiome interaction where Clostridia is increased.
definition editor: YH, HW
evidence publication: https://www.ncbi.nlm.nih.gov/pubmed/25439270
comment: https://www.ncbi.nlm.nih.gov/pubmed/22009989
comment: https://www.ncbi.nlm.nih.gov/pubmed/22687960
comment: https://www.ncbi.nlm.nih.gov/pubmed/22687961

expansion of C. Portiera in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Candidatus Portiera
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: expansion of Proteobacteria in colorectal cancer human gut
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Candidatus Portiera
textual definition: A colorectal cancer human-gut microbiome interaction where Candidatus Portiera is increased.
definition editor: YH, HW
evidence publication: https://www.ncbi.nlm.nih.gov/pubmed/26170900
comment: https://www.ncbi.nlm.nih.gov/pubmed/22009989
comment: https://www.ncbi.nlm.nih.gov/pubmed/22687960
comment: https://www.ncbi.nlm.nih.gov/pubmed/22687961

expansion of P. mirabilis in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Proteus mirabilis
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: expansion of Proteobacteria in colorectal cancer human gut
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Proteus mirabilis
textual definition: A colorectal cancer human-gut microbiome interaction where Proteus mirabilis is increased.
definition editor: YH, HW
comment: https://www.ncbi.nlm.nih.gov/pubmed/22009989
comment: https://www.ncbi.nlm.nih.gov/pubmed/22687960
comment: https://www.ncbi.nlm.nih.gov/pubmed/22687961

expansion of K. pneumoniae in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Klebsiella pneumoniae
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: expansion of Enterobacteriaceae in colorectal cancer human gut
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Klebsiella pneumoniae
textual definition: A colorectal cancer human-gut microbiome interaction where Klebsiella pneumoniae is increased.
definition editor: YH, HW
comment: https://www.ncbi.nlm.nih.gov/pubmed/22009989
comment: https://www.ncbi.nlm.nih.gov/pubmed/22687960
comment: https://www.ncbi.nlm.nih.gov/pubmed/22687961

expansion of Proteobacteria in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Proteobacteria
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: colorectal cancer human-gut microbiome interaction
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Proteobacteria
textual definition: A colorectal cancer human-gut microbiome interaction whereProteobacteria is increased.
definition editor: YH, HW
evidence publication: https://www.ncbi.nlm.nih.gov/pubmed/25439270
evidence publication: https://www.ncbi.nlm.nih.gov/pubmed/26170900
evidence publication: https://www.ncbi.nlm.nih.gov/pubmed/28827587
comment: https://www.ncbi.nlm.nih.gov/pubmed/20740058
comment: https://www.ncbi.nlm.nih.gov/pubmed/22009989
comment: https://www.ncbi.nlm.nih.gov/pubmed/22687960
comment: https://www.ncbi.nlm.nih.gov/pubmed/22687961

expansion of Helicobacter in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Helicobacter
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: expansion of Proteobacteria in colorectal cancer human gut
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Helicobacter
textual definition: A colorectal cancer human-gut microbiome interaction where Helicobacter is increased.
definition editor: YH, HW
comment: https://www.ncbi.nlm.nih.gov/pubmed/22009989
comment: https://www.ncbi.nlm.nih.gov/pubmed/22687960
comment: https://www.ncbi.nlm.nih.gov/pubmed/22687961
comment: https://www.ncbi.nlm.nih.gov/pubmed/28982615

depletion of R. hominis in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Roseburia hominis
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with healthy controls
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: depletion of Lachnospiraceae in colorectal cancer human gut
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Roseburia hominis
textual definition: A colorectal cancer human-gut microbiome interaction where Roseburia hominis is decreased.
definition editor: YH, HW
comment: https://www.ncbi.nlm.nih.gov/pubmed/22009989
comment: https://www.ncbi.nlm.nih.gov/pubmed/24021287

depletion of Blautia coccoides in RA human gut compared to fibromyalgia patients
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Blautia coccoides
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with fibromyalgia patients
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: RA human-gut microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Blautia coccoides
textual definition: a RA human-gut microbiome interaction that shows an decrease of Blautia coccoides in patients with RA compared with fibromyalgia patients.
definition editor: Haihe Wang, Hong Yu, Yongqun He
evidence publication: https://www.ncbi.nlm.nih.gov/pubmed/18528968

expansion of H. pylori in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Helicobacter pylori
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: expansion of Helicobacter in colorectal cancer human gut
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Helicobacter pylori
textual definition: A colorectal cancer human-gut microbiome interaction where Helicobacter pylori is increased.
definition editor: YH, HW
comment: https://www.ncbi.nlm.nih.gov/pubmed/24164483
comment: https://www.ncbi.nlm.nih.gov/pubmed/25834331
comment: https://www.ncbi.nlm.nih.gov/pubmed/28982615

expansion of H. hepaticus in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Helicobacter hepaticus
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: expansion of Helicobacter in colorectal cancer human gut
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Helicobacter hepaticus
textual definition: A colorectal cancer human-gut microbiome interaction where Helicobacter hepaticus is increased.
definition editor: YH, HW
comment: https://www.ncbi.nlm.nih.gov/pubmed/20944559
comment: https://www.ncbi.nlm.nih.gov/pubmed/28982615

expansion of F. nucleatum in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Fusobacterium nucleatum
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: expansion of Fusobacterium in colorectal cancer human gut
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Fusobacterium nucleatum
textual definition: A colorectal cancer human-gut microbiome interaction where Fusobacterium nucleatum is increased.
definition editor: YH, HW
evidence publication: https://www.ncbi.nlm.nih.gov/pubmed/22009990
evidence publication: https://www.ncbi.nlm.nih.gov/pubmed/26408641
evidence publication: https://www.ncbi.nlm.nih.gov/pubmed/28465070
evidence publication: https://www.ncbi.nlm.nih.gov/pubmed/28483840
evidence publication: https://www.ncbi.nlm.nih.gov/pubmed/28912574
comment: https://www.ncbi.nlm.nih.gov/pubmed/23335968
comment: https://www.ncbi.nlm.nih.gov/pubmed/24385213
comment: https://www.ncbi.nlm.nih.gov/pubmed/25751261
comment: https://www.ncbi.nlm.nih.gov/pubmed/27130618
comment: https://www.ncbi.nlm.nih.gov/pubmed/28982615

expansion of P. anaerobius in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Peptostreptococcus anaerobius
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: expansion of Peptostreptococcusi in colorectal cancer human gut
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Peptostreptococcus anaerobius
textual definition: A colorectal cancer human-gut microbiome interaction where Peptostreptococcus anaerobius is increased.
definition editor: YH, HW
comment: https://www.ncbi.nlm.nih.gov/pubmed/28126350

depletion of Bacteroides in RA human gut compared to fibromyalgia patients
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Bacteroides
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with fibromyalgia patients
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: RA human-gut microbiome interaction
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Bacteroides
textual definition: a RA human-gut microbiome interaction that shows an decrease of Bacteroides in patients with RA compared with fibromyalgia patients.
definition editor: Haihe Wang, Hong Yu, Yongqun He
evidence publication: https://www.ncbi.nlm.nih.gov/pubmed/18528968

expansion of F. hwasookii in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Fusobacterium hwasookii
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: expansion of Fusobacterium in colorectal cancer human gut
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Fusobacterium hwasookii
textual definition: A colorectal cancer human-gut microbiome interaction where Fusobacterium hwasookii is increased.
definition editor: YH, HW
comment: https://www.ncbi.nlm.nih.gov/pubmed/28912574

expansion of P. gingivalis in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Porphyromonas gingivalis
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: expansion of Porphyromonas in colorectal cancer human gut
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Porphyromonas gingivalis
textual definition: A colorectal cancer human-gut microbiome interaction where Porphyromonas gingivalis is increased.
definition editor: YH, HW
comment: https://www.ncbi.nlm.nih.gov/pubmed/28912574

expansion of Selenomonas in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Selenomonas
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: colorectal cancer human-gut microbiome interaction
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Selenomonas
textual definition: A colorectal cancer human-gut microbiome interaction where Selenomonas is increased.
definition editor: YH, HW
comment: https://www.ncbi.nlm.nih.gov/pubmed/28912574

expansion of Prevotella in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Prevotella
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: expansion of Prevotellaceae in colorectal cancer human gut
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Prevotella
textual definition: A colorectal cancer human-gut microbiome interaction where Prevotella is increased.
definition editor: YH, HW
comment: https://www.ncbi.nlm.nih.gov/pubmed/28912574

expansion of P. stomatis in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Peptostreptococcus stomatis
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: expansion of Peptostreptococcusi in colorectal cancer human gut
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Peptostreptococcus stomatis
textual definition: A colorectal cancer human-gut microbiome interaction where Peptostreptococcus stomatis is increased.
definition editor: YH, HW
comment: https://www.ncbi.nlm.nih.gov/pubmed/28912574

depletion of Bacteroides fragilis in RA human gut compared to fibromyalgia patients
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Bacteroides fragilis
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: decreased organism quantity compared with fibromyalgia patients
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: depletion of Bacteroides in RA human gut compared to fibromyalgia patients
subclass of: Restriction
  on property: occurs in
  some values from: UBERON_0004907
subclass of: Restriction
  on property: has microbe depleted in diseased host
  some values from: Bacteroides fragilis
textual definition: a RA human-gut microbiome interaction that shows an decrease of Bacteroides fragilis in patients with RA compared with fibromyalgia patients.
definition editor: Haihe Wang, Hong Yu, Yongqun He
evidence publication: https://www.ncbi.nlm.nih.gov/pubmed/18528968

expansion of Solobacterium sp. S4-A19 in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Solobacterium sp. S4-A19
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: expansion of Solobacterium in colorectal cancer human gut
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Solobacterium sp. S4-A19
textual definition: A colorectal cancer human-gut microbiome interaction where Solobacterium sp. S4-A19 is increased.
definition editor: YH, HW
comment: https://www.ncbi.nlm.nih.gov/pubmed/28827587

expansion of D. paucivorans in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Dolosicoccus paucivorans
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: colorectal cancer human-gut microbiome interaction
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Dolosicoccus paucivorans
textual definition: A colorectal cancer human-gut microbiome interaction where Dolosicoccus paucivorans is increased.
definition editor: YH, HW
comment: https://www.ncbi.nlm.nih.gov/pubmed/28827587

expansion of Clostridium sp. cp01.19 in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Clostridium sp. cp01.19
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: expansion of Clostridiaceae in colorectal cancer human gut
subclass of: Restriction
  on property: has microbe expanded in diseased host
  some values from: Clostridium sp. cp01.19
textual definition: A colorectal cancer human-gut microbiome interaction where Clostridium sp. cp01.19 is increased.
definition editor: YH, HW
comment: https://www.ncbi.nlm.nih.gov/pubmed/28827587

expansion of Bacteroides sp. in colorectal cancer human gut
type: Class
equivalent class: Restriction
  on property: has participant
  some values from: Class
    intersection of: Bacteroides sp.
    intersection of: Restriction
      on property: microbial population phenotype in host
      some values from: increased organism quantity compared with healthy control
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: UBERON_0004907
        intersection of: Restriction
subclass of: expansion of Bacteroides in colorectal cancer human gut
textual definition: A colorectal cancer human-gut microbiome interaction where Bacteroides sp. is increased.
definition editor: YH, HW
comment: https://www.ncbi.nlm.nih.gov/pubmed/28827587