Barry Smith
Alexander Alekseyenko
Anna Maria Masci
Haihe Wang
Jianmin Wu
Jie Zheng
Jihad Obeid
Kaiyong Liu
Yongqun "Oliver" He (YH)
Yu Hong
OHMI is a biomedical ontology that represents the entities and relations in the domain of host-microbiome interactions.
OWL-DL
OHMI: A biomedical ontology in the domain of host-microbiome interactions.
OHMI: Ontology of Host-Microbiome Interactions
2019-09-17
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.
Really of interest to developers only
BFO OWL specification label
Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2
Person:Alan Ruttenberg
Really of interest to developers only
BFO CLIF specification label
editor preferred label
editor preferred label
editor preferred term
editor preferred term
editor preferred term~editor preferred label
The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
editor preferred label
editor preferred label
editor preferred term
editor preferred term
editor preferred term~editor preferred label
example
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
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.
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
example of usage
has curation status
PERSON:Alan Ruttenberg
PERSON:Bill Bug
PERSON:Melanie Courtot
OBI_0000281
has curation status
definition
definition
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.
The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
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.
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
definition
definition
textual definition
editor note
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.
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obfoundry.org/obo/obi>
IAO:0000116
uberon
editor_note
true
editor_note
editor note
editor note
term editor
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
20110707, MC: label update to term editor and definition modified accordingly. See http://code.google.com/p/information-artifact-ontology/issues/detail?id=115.
20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115.
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
definition editor
definition editor
term editor
term editor
alternative term
An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
alternative term
definition source
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
PERSON:Daniel Schober
Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
definition source
definition source
curator note
An administrative note of use for a curator but of no use for a user
PERSON:Alan Ruttenberg
IAO:0000232
uberon
curator_notes
true
curator_notes
curator note
curator notes
term tracker item
the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/
An IRI or similar locator for a request or discussion of an ontology term.
Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
The 'tracker item' can associate a tracker with a specific ontology term.
term tracker item
imported from
For external terms/classes, the ontology from which the term was imported
PERSON:Alan Ruttenberg
PERSON:Melanie Courtot
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
imported from
expand expression to
OBO foundry unique label
An alternative name for a class or property which is unique across the OBO Foundry.
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 .
PERSON:Alan Ruttenberg
PERSON:Bjoern Peters
PERSON:Chris Mungall
PERSON:Melanie Courtot
GROUP:OBO Foundry <http://obofoundry.org/>
OBO foundry unique label
elucidation
person:Alan Ruttenberg
Person:Barry Smith
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
elucidation
has associated axiom(nl)
Person:Alan Ruttenberg
Person:Alan Ruttenberg
An axiom associated with a term expressed using natural language
has associated axiom(nl)
has associated axiom(fol)
Person:Alan Ruttenberg
Person:Alan Ruttenberg
An axiom expressed in first order logic using CLIF syntax
has associated axiom(fol)
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.
Yongqun He
has literature mining keywords
ISA alternative term
An alternative term used by the ISA tools project (http://isa-tools.org).
Requested by Alejandra Gonzalez-Beltran
https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891&atid=886178
Person: Alejandra Gonzalez-Beltran
Person: Philippe Rocca-Serra
ISA tools project (http://isa-tools.org)
ISA alternative term
NIAID GSCID-BRC alternative term
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).
PERSON: Chris Stoeckert, Jie Zheng
NIAID GSCID-BRC metadata working group
NIAID GSCID-BRC alternative term
IEDB alternative term
An alternative term used by the IEDB.
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IEDB
IEDB alternative term
An annotation property that represents a publication that includes the evidence of the presence of a class type.
Jie Zheng, Jihad, Anna Maria, Haihe, Oliver
evidence publication
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.
temporal interpretation
https://github.com/oborel/obo-relations/wiki/ROAndTime
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
https://github.com/oborel/obo-relations/wiki/ShortcutRelations
A logical macro assertion whose domain is an IRI for a property
logical macro assertion on a property
Used to annotate object properties to describe a logical meta-property or characteristic of the object property.
logical macro assertion on an object property
logical macro assertion on an annotation property
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
The general property hierarchy is:
"directly P" SubPropertyOf "P"
Transitive(P)
Where we have an annotation assertion
"directly P" "is direct form of" "P"
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'
Chris Mungall
is direct form of
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
Chris Mungall
is indirect form of
Used to annotate object properties representing a causal relationship where the value indicates a direction. Should be "+", "-" or "0"
cjm
2018-03-13T23:59:29Z
is directional form of
cjm
2018-03-14T00:03:16Z
is positive form of
cjm
2018-03-14T00:03:24Z
is negative form of
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.
UBPROP:0000001
uberon
external_definition
true
external_definition
This annotation property may be replaced with an annotation property from an external ontology such as IAO
external_definition
Notes on the homology status of this class.
UBPROP:0000003
uberon
homology_notes
true
homology_notes
This annotation property may be replaced with an annotation property from an external ontology such as IAO
homology_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'.
UBPROP:0000007
uberon
has_relational_adjective
true
has_relational_adjective
has_relational_adjective
Notes on the how instances of this class vary across species.
UBPROP:0000008
uberon
taxon_notes
true
taxon_notes
taxon_notes
Notes on the ontogenic development of instances of this class.
This annotation property may be replaced with an annotation property from an external ontology such as IAO
UBPROP:0000011
uberon
development_notes
true
development_notes
development_notes
Notes on how similar or equivalent classes are represented in other ontologies.
This annotation property may be replaced with an annotation property from an external ontology such as IAO
UBPROP:0000012
uberon
external_ontology_notes
true
external_ontology_notes
external_ontology_notes
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.
An entity responsible for making contributions to the
content of the resource.
Contributor
Contributor
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.
An entity primarily responsible for making the content
of the resource.
Creator
Creator
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.
A date associated with an event in the life cycle of the
resource.
Date
Date
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.
An account of the content of the resource.
Description
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).
The physical or digital manifestation of the resource.
Format
Format
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.
A reference to a resource from which the present resource
is derived.
Source
Source
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.
The topic of the content of the resource.
Subject and Keywords
Subject and Keywords
Mark Miller
2018-05-11T13:47:29Z
created_by
creation_date
has_alternative_id
has_broad_synonym
database_cross_reference
has_exact_synonym
has_narrow_synonym
disease_ontology
has_obo_namespace
has_related_synonym
id
in_subset
shorthand
is defined by
label
label
label
http://www.w3.org/2000/01/rdf-schema#seeAlso
seeAlso
true
true
seeAlso
seeAlso
is part of
my brain is part of my body (continuant parthood, two material entities)
my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)
this day is part of this year (occurrent parthood)
a core relation that holds between a part and its whole
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.
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
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'.
part_of
part of
http://www.obofoundry.org/ro/#OBO_REL:part_of
has part
my body has part my brain (continuant parthood, two material entities)
my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)
this year has part this day (occurrent parthood)
a core relation that holds between a whole and its part
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.
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
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'.
has_part
has part
realized in
this disease is realized in this disease course
this fragility is realized in this shattering
this investigator role is realized in this investigation
is realized by
realized_in
[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])
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
realized in
realizes
this disease course realizes this disease
this investigation realizes this investigator role
this shattering realizes this fragility
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])
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
realizes
accidentally included in BFO 1.2 proposal
- should have been BFO_0000062
obsolete preceded by
true
preceded by
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.
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.
is preceded by
preceded_by
http://www.obofoundry.org/ro/#OBO_REL:preceded_by
preceded by
precedes
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.
precedes
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
occurs_in
unfolds in
unfolds_in
Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant
occurs in
site of
[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
Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant
contains process
has measurement unit label
This document is about information artifacts and their representations
is_about is a (currently) primitive relation that relates an information artifact to an entity.
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.
person:Alan Ruttenberg
Smith, Ceusters, Ruttenberg, 2000 years of philosophy
is about
relates a process to a time-measurement-datum that represents the duration of the process
Person:Alan Ruttenberg
is duration of
has_specified_input
has_specified_input
see is_input_of example_of_usage
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.
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.
PERSON: Alan Ruttenberg
PERSON: Bjoern Peters
PERSON: Larry Hunter
PERSON: Melanie Coutot
has_specified_input
is_specified_input_of
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
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.
Alan Ruttenberg
PERSON:Bjoern Peters
is_specified_input_of
has_specified_output
has_specified_output
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.
PERSON: Alan Ruttenberg
PERSON: Bjoern Peters
PERSON: Larry Hunter
PERSON: Melanie Courtot
has_specified_output
is_specified_output_of
is_specified_output_of
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.
Alan Ruttenberg
PERSON:Bjoern Peters
is_specified_output_of
achieves_planned_objective
A cell sorting process achieves the objective specification 'material separation objective'
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.
BP, AR, PPPB branch
PPPB branch derived
modified according to email thread from 1/23/09 in accordince with DT and PPPB branch
achieves_planned_objective
has grain
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.
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
PERSON: Alan Ruttenberg
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
has grain
objective_achieved_by
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.
OBI
OBI
objective_achieved_by
has value specification
A relation between an information content entity and a value specification that specifies its value.
PERSON: James A. Overton
OBI
has value specification
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.
Oliver He
microbe susceptibly expanded in host with disease
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.
Oliver He
microbe susceptibly expanded in human with disease
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.
Oliver He
microbe susceptibly expanded in gut of human with disease
has disease
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.
Oliver He
microbe susceptibly depleted in host with disease
this is a shortcut object property that represents the phenotype that exists in a microbial population inside a host.
Yongqun He, Haihe Wang, Jie Zheng
microbial population phenotype in host
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.
Oliver He
microbe susceptibly depleted in human with disease
has phenotype
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.
Oliver He
microbe susceptibly depleted in gut of human with disease
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.
Oliver He
microbe susceptibly depleted in rat with disease
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.
Oliver He
microbe susceptibly expanded in rat with disease
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.
Oliver He
microbe susceptibly depleted in gut of rat with disease
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.
Oliver He
microbe susceptibly expanded in gut of rat with disease
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.
Oliver He
disease in host with susceptibly expanded microbe
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.
Oliver He
microbe susceptibly changed in host with disease
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.
Oliver He
disease in host with susceptibly depleted microbe
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.
Oliver He
microbe susceptibly depleted in respiratory airway of human with disease
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.
Oliver He
microbe susceptibly expanded in respiratory airway of human with disease
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.
Oliver He
microbe susceptibly expanded in oral cavity of human with disease
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.
Oliver He
microbe susceptibly depleted in oral cavity of human with disease
microbe susceptibly expanded in mouse with disease
microbe susceptibly expanded in gut of mouse with disease
microbe susceptibly depleted in mouse with disease
microbe susceptibly depleted in gut of mouse with disease
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.
Oliver He
has microbe depleted in diseased host
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.
Oliver He
has microbe expanded in diseased host
microbe susceptibly depleted (compared to fibromyalgia patients) in gut of human with disease
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
YH
has microbe population size altered in diseased host
Oliver He
an object subproperty of 'has participant' in which the participant is a host organism.
has host
inheres in
this fragility inheres in this vase
this red color inheres in this apple
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
A dependent inheres in its bearer at all times for which the dependent exists.
inheres_in
inheres in
bearer of
this apple is bearer of this red color
this vase is bearer of this fragility
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
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.
bearer_of
is bearer of
bearer of
participates in
this blood clot participates in this blood coagulation
this input material (or this output material) participates in this process
this investigator participates in this investigation
a relation between a continuant and a process, in which the continuant is somehow involved in the process
participates_in
participates in
has participant
this blood coagulation has participant this blood clot
this investigation has participant this investigator
this process has participant this input material (or this output material)
a relation between a process and a continuant, in which the continuant is somehow involved in the process
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.
has_participant
http://www.obofoundry.org/ro/#OBO_REL:has_participant
has participant
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).
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).
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.
is concretized as
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).
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).
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.
concretizes
this catalysis function is a function of this enzyme
a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence
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.
function_of
is function of
function of
this investigator role is a role of this person
a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence
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.
is role of
role_of
role of
this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)
a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence
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.
has_function
has function
this apple has quality this red color
a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence
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.
has_quality
has quality
this person has role this investigator role (more colloquially: this person has this role of investigator)
a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence
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.
has_role
has role
a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence
has disposition
inverse of has disposition
disposition of
derives from
this cell derives from this parent cell (cell division)
this nucleus derives from this parent nucleus (nuclear division)
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
This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'.
derives_from
derives from
this parent cell derives into this cell (cell division)
this parent nucleus derives into this nucleus (nuclear division)
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
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'.
derives_into
derives into
located in
my brain is located in my head
this rat is located in this cage
a relation between two independent continuants, the target and the location, in which the target is entirely within the location
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
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
located_in
http://www.obofoundry.org/ro/#OBO_REL:located_in
located in
dos
2017-05-24T09:44:33Z
A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B.
has component activity
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.
dos
2017-05-24T09:49:21Z
has component process
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.
dos
2017-09-22T14:14:36Z
This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations.
has effector activity
David Osumi-Sutherland
<=
Primitive instance level timing relation between events
before or simultaneous with
David Osumi-Sutherland
t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2)
simultaneous with
David Osumi-Sutherland
t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2)
before
David Osumi-Sutherland
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.
during which ends
David Osumi-Sutherland
di
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.
encompasses
David Osumi-Sutherland
X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)
ends after
David Osumi-Sutherland
starts_at_end_of
X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)
immediately preceded by
David Osumi-Sutherland
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.
during which starts
David Osumi-Sutherland
starts before
David Osumi-Sutherland
ends_at_start_of
meets
X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)
immediately precedes
David Osumi-Sutherland
io
X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y))
starts during
David Osumi-Sutherland
d
during
X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y))
happens during
David Osumi-Sutherland
o
overlaps
X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y).
ends during
x overlaps y if and only if there exists some z such that x has part z and z part of y
http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)
overlaps
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.
The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity.
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.
has component
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.
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
Chris Mungall
David Hill
Tanya Berardini
GO
Regulation precludes parthood; the regulatory process may not be within the regulated process.
regulates (processual)
false
regulates
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.
Chris Mungall
negatively regulates (process to process)
negatively regulates
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.
Chris Mungall
positively regulates (process to process)
positively regulates
'human p53 protein' SubClassOf some ('has prototype' some ('participates in' some 'DNA repair'))
heart SubClassOf 'has prototype' some ('participates in' some 'blood circulation')
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.
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)
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.
Chris Mungall
has prototype
move to BFO?
Chris Mungall
Allen
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.
https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1
A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.
temporal relation
temporally related to
inverse of starts with
Chris Mungall
Allen
starts
Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor
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.
Chris Mungall
started by
starts with
inverse of ends with
Chris Mungall
ends
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.
Chris Mungall
finished by
ends with
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.
Chris Mungall
consumes
has input
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.
Chris Mungall
produces
has output
cjm
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, positive effect
cjm
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
causally upstream of, negative effect
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.
Because part_of is transitive, inheres in is a sub-relation of inheres in part of
Chris Mungall
inheres in part of
A mereological relationship or a topological relationship
Chris Mungall
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships
mereotopologically related to
A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities.
Chris Mungall
This is a grouping relation that collects relations used for the purpose of connecting structure and function
functionally related to
inverse of regulates
Chris Mungall
regulated by (processual)
regulated by
inverse of negatively regulates
Chris Mungall
negatively regulated by
inverse of positively regulates
Chris Mungall
positively regulated by
has member is a mereological relation between a collection and an item.
SIO
has member
inverse of has input
Chris Mungall
input of
inverse of has output
Chris Mungall
output of
'protein catabolic process' SubClassOf has_direct_input some protein
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.
Chris Mungall
directly consumes
This is likely to be obsoleted. A candidate replacement would be a new relation 'has bound input' or 'has substrate'
has direct input
translation SubClassOf has_direct_output some protein
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.
Chris Mungall
directly produces
obsolete has direct output
true
inverse of upstream of
Chris Mungall
causally downstream of
Chris Mungall
immediately causally downstream of
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
Chris Mungall
directly positively regulates
directly activates (process to process)
directly activates
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
Chris Mungall
indirectly positively regulates
indirectly activates
Chris Mungall
directly negatively regulates
directly inhibits (process to process)
directly inhibits
Chris Mungall
indirectly negatively regulates
indirectly inhibits
This relation groups causal relations between material entities and causal relations between processes
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 yield a cross-product of different relation types.
Chris Mungall
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
causally related to
p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain
Chris Mungall
causally upstream of
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.
Chris Mungall
immediately causally upstream of
p1 directly provides input for p2 iff there exists some c such that p1 has_output c and p2 has_input c
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
Chris Mungall
directly provides input for (process to process)
directly provides input for
transitive form of directly_provides_input_for
Chris Mungall
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')
transitively provides input for (process to process)
transitively provides input for
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.
We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2
Chris Mungall
influences (processual)
affects
causally upstream of or within
inverse of causally upstream of or within
Chris Mungall
causally downstream of or within
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.
Chris Mungall
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
causal relation between processes
Chris Mungall
depends on
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.
Chris Mungall
directly regulates (processual)
directly regulates
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.
directly positively regulates (process to process)
directly positively regulates
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.
directly negatively regulates (process to process)
directly negatively regulates
cjm
2018-03-13T23:55:05Z
causally upstream of or within, negative effect
cjm
2018-03-13T23:55:19Z
causally upstream of or within, positive effect
Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison.
ECO:0000041
SO:similar_to
sameness
similar to
correspondence
resemblance
in similarity relationship with
has measurement value
has specified numeric value
A relation between a value specification and a number that quantifies it.
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.
PERSON: James A. Overton
OBI
has specified numeric value
has specified value
A relation between a value specification and a literal.
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.
OBI
has specified value
entity
Entity
Julius Caesar
Verdi’s Requiem
the Second World War
your body mass index
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
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
An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])
entity
continuant
Continuant
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.
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
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
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])
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])
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])
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])
(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]
(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]
(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]
continuant
occurrent
Occurrent
An entity that has temporal parts and that happens, unfolds or develops through time.
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
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.
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.
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.
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])
Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])
b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])
(forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001]
(forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001]
occurrent
ic
IndependentContinuant
a chair
a heart
a leg
a molecule
a spatial region
an atom
an orchestra.
an organism
the bottom right portion of a human torso
the interior of your mouth
A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.
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])
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])
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])
(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]
(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]
(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]
independent continuant
spatial region
process
Process
a process of cell-division, \ a beating of the heart
a process of meiosis
a process of sleeping
the course of a disease
the flight of a bird
the life of an organism
your process of aging.
An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.
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])
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)
(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]
process
disposition
Disposition
an atom of element X has the disposition to decay to an atom of element Y
certain people have a predisposition to colon cancer
children are innately disposed to categorize objects in certain ways.
the cell wall is disposed to filter chemicals in endocytosis and exocytosis
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.
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])
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])
(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]
(forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002]
disposition
realizable
RealizableEntity
the disposition of this piece of metal to conduct electricity.
the disposition of your blood to coagulate
the function of your reproductive organs
the role of being a doctor
the role of this boundary to delineate where Utah and Colorado meet
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.
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])
All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])
(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]
(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]
realizable entity
quality
Quality
the ambient temperature of this portion of air
the color of a tomato
the length of the circumference of your waist
the mass of this piece of gold.
the shape of your nose
the shape of your nostril
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])
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])
(forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001]
(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]
quality
sdc
SpecificallyDependentContinuant
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
of one-sided specifically dependent continuants: the mass of this tomato
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.
the disposition of this fish to decay
the function of this heart: to pump blood
the mutual dependence of proton donors and acceptors in chemical reactions [79
the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction
the pink color of a medium rare piece of grilled filet mignon at its center
the role of being a doctor
the shape of this hole.
the smell of this portion of mozzarella
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.
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])
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])
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.
(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]
(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]
specifically dependent continuant
role
Role
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.
the priest role
the role of a boundary to demarcate two neighboring administrative territories
the role of a building in serving as a military target
the role of a stone in marking a property boundary
the role of subject in a clinical trial
the student role
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.
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.
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])
(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001]
role
gdc
GenericallyDependentContinuant
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.
the pdf file on your laptop, the pdf file that is a copy thereof on my laptop
the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule.
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.
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])
(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001]
generically dependent continuant
function
Function
the function of a hammer to drive in nails
the function of a heart pacemaker to regulate the beating of a heart through electricity
the function of amylase in saliva to break down starch into sugar
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.
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])
(forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001]
function
p-boundary
ProcessBoundary
the boundary between the 2nd and 3rd year of your life.
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])
Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002])
(forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002]
(iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001]
process boundary
material
MaterialEntity
a flame
a forest fire
a human being
a hurricane
a photon
a puff of smoke
a sea wave
a tornado
an aggregate of human beings.
an energy wave
an epidemic
the undetached arm of a human being
An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
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
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.
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.
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])
Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])
every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])
(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002]
(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]
(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]
material entity
immaterial entity
Material anatomical entity that is a member of an individual species or is a viral or viroid particle.
organism or virus
Melissa Haendel
9/18/11
organism or virus or viroid
peptide
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.
peptide
deoxyribonucleic acid
High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms.
deoxyribonucleic acid
molecular entity
Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.
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
molecular entity
atom
A chemical entity constituting the smallest component of an element having the chemical properties of the element.
atom
nucleic acid
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.
nucleic acid
ribonucleic acid
High molecular weight, linear polymers, composed of nucleotides containing ribose and linked by phosphodiester bonds; RNA is central to the synthesis of proteins.
ribonucleic acid
macromolecule
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.
polymer
macromolecule
cell
cell
PMID:18089833.Cancer Res. 2007 Dec 15;67(24):12018-25. "...Epithelial cells were harvested from histologically confirmed adenocarcinomas .."
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.
cell
cell
cultured cell
A cell in vitro that is or has been maintained or propagated as part of a cell culture.
cultured cell
experimentally modified cell in vitro
A cell in vitro that has undergone physical changes as a consequence of a deliberate and specific experimental procedure.
experimentally modified cell in vitro
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.
Clinical_Measurement.ontology
CMO:0000000
clinical measurement
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.
JSmith
2013-01-08T18:17:44Z
Clinical_Measurement.ontology
CMO:0001276
serum immunoglobulin measurement
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.
JSmith
2013-01-30T12:00:54Z
Clinical_Measurement.ontology
CMO:0001531
blood immunoglobulin measurement
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.
JSmith
2014-01-27T12:21:14Z
serum IgA level
Clinical_Measurement.ontology
CMO:0002095
serum immunoglobulin A level
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.
JSmith
2014-01-27T12:33:22Z
serum IgG level
Clinical_Measurement.ontology
CMO:0002102
serum immunoglobulin G level
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.
JSmith
2014-01-27T12:35:25Z
serum IgM level
Clinical_Measurement.ontology
CMO:0002104
serum immunoglobulin M level
An intestinal disease characterized by inflammation located_in all parts of digestive tract.
EFO:0003767
KEGG:05321
MESH:D015212
NCI:C3138
OMIM:PS266600
SNOMEDCT_US_2018_03_01:24526004
UMLS_CUI:C0021390
disease_ontology
DOID:0050589
Xref MGI.
OMIM mapping confirmed by DO. [SN].
inflammatory bowel disease
A cancer that is classified based on the organ it starts in.
snadendla
2011-06-13T03:28:33Z
MESH:D009371
disease_ontology
DOID:0050686
organ system cancer
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.
disease_ontology
DOID:0060032
autoimmune disease of musculoskeletal system
A gastrointestinal system cancer that is located_in the hepatobiliary system
disease_ontology
DOID:0080355
hepatobiliary system cancer
A gastrointestinal system cancer that is located_in the intestine.
ICD10CM:C26.0
ICD9CM:159.0
MESH:D007414
NCI2004_11_17:C4572
NCI:C4572
SNOMEDCT_US_2018_03_01:93838000
UMLS_CUI:C0346627
malignant intestinal tumors
malignant neoplasm of intestine
disease_ontology
DOID:10155
intestinal cancer
A gastrointestinal system cancer that is located_in the stomach.
DOID:10539
DOID:10542
DOID:10543
DOID:4713
GARD:7704
ICD10CM:C16
ICD10CM:C16.2
ICD10CM:C16.5
ICD10CM:C16.6
ICD10CM:C16.9
ICD9CM:151
ICD9CM:151.4
ICD9CM:151.5
ICD9CM:151.6
ICD9CM:151.9
MESH:D013274
NCI:C3387
NCI:C9331
OMIM:137215
OMIM:613659
SNOMEDCT_US_2018_03_01:93717002
SNOMEDCT_US_2018_03_01:93818001
SNOMEDCT_US_2018_03_01:93867004
SNOMEDCT_US_2018_03_01:94074003
UMLS_CUI:C0024623
UMLS_CUI:C0038356
UMLS_CUI:C0153421
UMLS_CUI:C0153422
UMLS_CUI:C0153423
Ca body - stomach
Ca lesser curvature - stomach
ca greater curvature of stomach
gastric cancer
gastric neoplasm
malignant neoplasm of body of stomach
malignant neoplasm of lesser curve of stomach
malignant tumor of body of stomach
malignant tumor of greater curve of stomach
malignant tumor of lesser curve of stomach
disease_ontology
DOID:10534
OMIM mapping confirmed by DO. [SN].
stomach cancer
An arthritis that has_material_basis_in uric acid crystal deposits located_in joint.
DOID:14144
EFO:0004274
ICD10CM:M10
ICD10CM:M10.9
ICD9CM:274
ICD9CM:274.0
ICD9CM:274.00
ICD9CM:274.9
MESH:D006073
MESH:D015210
NCI:C34650
SNOMEDCT_US_2018_03_01:48440001
SNOMEDCT_US_2018_03_01:90560007
UMLS_CUI:C0003868
UMLS_CUI:C0018099
Articular gout
Gouty arthropathy
gouty arthritis
disease_ontology
DOID:13189
gout
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.
DOID:0050006
ICD9CM:009.2
MESH:D003967
SNOMEDCT_US_2018_03_01:19213003
UMLS_CUI:C0013369
disease_ontology
diarrhea of presumed infectious origin
diarrhoea
DOID:13250
diarrhea
An autoimmune hypersensitivity disease that involves inflammation or pain in the muscles, joints, or fibrous tissue.
disease_ontology
DOID:1575
rheumatic disease
A disease of cellular proliferation that is malignant and primary, characterized by uncontrolled cellular proliferation, local cell invasion and metastasis.
ICD10CM:C80
ICD10CM:C80.1
ICD9CM:199
MESH:D009369
NCI:C9305
SNOMEDCT_US_2018_03_01:38807002
UMLS_CUI:C0006826
stedman:rlc
malignant neoplasm
malignant tumor
primary cancer
disease_ontology
DOID:162
Updating out dated UMLS CUI.
cancer
A disease of anatomical entity that occurs in the muscular and/or skeletal system.
MESH:D009140
NCI:C107377
SNOMEDCT_US_2018_03_01:928000
UMLS_CUI:C0026857
disease_ontology
DOID:17
musculoskeletal system disease
An organ system cancer located_in endocrine system that is characterized by uncontrolled cellular proliferation of the hormone producing glands of the endocrine system.
DOID:10009
CSP2005:2009-5861
ICD10CM:C75.9
ICD9CM:194.9
MESH:D004701
NCI2004_11_17:C3010
NCI2004_11_17:C3575
NCI:C3010
NCI:C3575
SNOMEDCT_US_2018_03_01:93780007
UMLS_CUI:C0014132
UMLS_CUI:C0153658
Endocrine tumor
endocrine neoplasm
malignant Endocrine tumor
malignant neoplasm of endocrine gland
malignant tumour of endocrine gland
neoplasm of endocrine gland
neoplasm of endocrine system
disease_ontology
DOID:170
endocrine gland cancer
An endocrine gland cancer located_in the pancreas.
DOID:14356
DOID:1797
DOID:3588
DOID:9859
CSP2005:2014-4876
GARD:9364
ICD10CM:C25.0
ICD10CM:C25.1
ICD10CM:C25.2
ICD9CM:157.0
ICD9CM:157.1
ICD9CM:157.2
ICD9CM:157.8
KEGG:05212
MESH:D010190
MTH:NOCODE
NCI2004_11_17:C3305
NCI:C3305
ORDO:1333
ORDO:217074
SNOMEDCT_US_2018_03_01:93715005
SNOMEDCT_US_2018_03_01:93823001
SNOMEDCT_US_2018_03_01:94082003
UMLS_CUI:C0030297
UMLS_CUI:C0153458
UMLS_CUI:C0153459
UMLS_CUI:C0153460
UMLS_CUI:C0153463
Ca body of pancreas
Ca head of pancreas
Ca tail of pancreas
malignant neoplasm of body of pancreas
malignant neoplasm of head of pancreas
malignant neoplasm of tail of pancreas
pancreas neoplasm
pancreatic neoplasm
pancreatic tumor
disease_ontology
DOID:1793
Xref MGI.
pancreatic cancer
A large intestine cancer that is located_in the colon.
ICD10CM:C18
ICD10CM:C18.9
ICD9CM:153
ICD9CM:153.9
MESH:D003110
NCI:C9242
SNOMEDCT_US_2018_03_01:93761005
UMLS_CUI:C0007102
disease_ontology
DOID:219
colon cancer
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.
ICD10CM:E34.9
ICD9CM:259.9
MESH:D004700
NCI:C3009
SNOMEDCT_US_2018_03_01:67432001
UMLS_CUI:C0014130
disease_ontology
DOID:28
endocrine system disease
A disease of anatomical entity that is located_in the immune system.
EFO:0000540
ICD10CM:D89.9
ICD9CM:279
ICD9CM:279.9
UMLS_CUI:C0041806
disease_ontology
DOID:2914
immune system disease
A cell type cancer that has_material_basis_in abnormally proliferating cells derives_from epithelial cells.
DOID:2428
DOID:6570
CSP2005:2000-5801
MESH:D002277
MESH:D009375
NCI2004_11_17:C6927
NCI:C2916
NCI:C3709
SNOMEDCT_US_2018_03_01:68453008
SNOMEDCT_US_2018_03_01:71298006
UMLS_CUI:C0007097
UMLS_CUI:C0553707
UMLS_CUI:C1368683
epithelioma
malignant Epithelioma
disease_ontology
DOID:305
carcinoma
DOID:11500
DOID:6144
CSP2005:4004-0004
EFO:0000341
ICD10CM:J44.9
MESH:D029424
NCI2004_11_17:C3199
NCI:C3199
OMIM:606963
SNOMEDCT_US_2018_03_01:13645005
UMLS_CUI:C0024117
COLD
COPD
chronic obstructive airway disease
chronic obstructive lung disease
disease_ontology
DOID:3083
chronic obstructive pulmonary disease
A gastrointestinal system disease that is located_in the liver and/or biliary tract.
NCI:C3959
UMLS_CUI:C0267792
liver and biliary tract disease
disease_ontology
DOID:3118
hepatobiliary disease
An organ system cancer located_in gastrointestinal tract that is manifested in organs of the gastrointestinal system.
DOID:4945
DOID:8377
ICD10CM:C26.9
ICD9CM:239.0
MESH:D004067
MESH:D005770
NCI2004_11_17:C3052
NCI2004_11_17:C4890
NCI:C3052
NCI:C4890
SNOMEDCT_US_2018_03_01:93811007
UMLS_CUI:C0012243
UMLS_CUI:C0017185
UMLS_CUI:C0685938
GI tumor
digestive system cancer
gastrointestinal tract cancer
disease_ontology
DOID:3119
gastrointestinal system cancer
A bone disease that results_in inflammation of the located_in bone.
CSP2005:2715-2703
MESH:D010000
SNOMEDCT_US_2018_03_01:44462005
UMLS_CUI:C0029400
Inflammatory disorder of bone
bone inflammatory disease
osteitis
disease_ontology
DOID:3342
bone inflammation disease
A hepatobiliary system cancer that is located_in the liver.
DOID:12300
DOID:269
DOID:7330
DOID:915
DOID:919
CSP2005:2003-2810
ICD10CM:C22.0
ICD10CM:C22.9
ICD9CM:155.0
ICD9CM:155.2
ICD9CM_2006:155.0
ICD9CM_2006:155.2
MESH:D008113
NCI2004_11_17:C34803
NCI2004_11_17:C7692
NCI:C34803
NCI:C7692
SNOMEDCT_US_2018_03_01:93870000
SNOMEDCT_US_2018_03_01:95214007
UMLS_CUI:C0023903
UMLS_CUI:C0024620
UMLS_CUI:C0345904
UMLS_CUI:C0854795
Ca liver - primary
Resectable malignant neoplasm of Liver
ca liver - primary
hepatic cancer
hepatic neoplasm
malignant hepato-biliary neoplasm
malignant neoplasm of liver
malignant neoplasm of liver, not specified as primary or secondary
malignant neoplasm of liver, primary
malignant tumor of liver
neoplasm of liver
non-resectable primary hepatic malignant neoplasm
primary liver cancer
primary malignant neoplasm of Liver
primary malignant neoplasm of liver
resectable malignant neoplasm of the liver
disease_ontology
DOID:3571
liver cancer
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.
MESH:D004194
NCI:C2991
SNOMEDCT_US_2018_03_01:64572001
UMLS_CUI:C0012634
disease_ontology
DOID:4
disease
DOID:2164
DOID:2165
DOID:46
ICD10CM:K70-K77
ICD10CM:K76.9
ICD9CM:573.9
MESH:D008107
NCI2004_11_17:C3196
NCI:C3196
SNOMEDCT_US_2018_03_01:62857009
UMLS_CUI:C0023895
disorder of liver
hepatic disorder
disease_ontology
DOID:409
liver disease
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.
ICD9CM:720
OMIM:109100
UMLS_CUI:C0003089
ls:IEDB
autoimmune disease
hypersensitivity reaction type II disease
disease_ontology
DOID:417
Xref MGI.
autoimmune hypersensitivity disease
A biliary tract cancer that is located_in the bile duct.
DOID:10019
ICD10CM:C24.0
ICD9CM:156.1
MESH:D001650
NCI2004_11_17:C2898
NCI2004_11_17:C7483
NCI:C2898
NCI:C7483
SNOMEDCT_US_2018_03_01:93790004
UMLS_CUI:C0005396
UMLS_CUI:C0153453
Ca extrahepatic bile ducts
bile duct tumor
malignant neoplasm of the extrahepatic bile duct
disease_ontology
DOID:4606
bile duct cancer
A gastrointestinal system cancer that is located_in the esophagus.
DOID:10291
DOID:10292
DOID:10448
DOID:1102
DOID:1104
GARD:6383
ICD10CM:C15.3
ICD10CM:C15.4
ICD10CM:C15.5
ICD9CM:150.2
ICD9CM:150.3
ICD9CM:150.4
ICD9CM:150.5
ICD9CM:150.8
MESH:D004938
MTHICD9_2006:150.3
MTHICD9_2006:150.5
NCI2004_11_17:C3533
NCI2004_11_17:C3534
NCI2004_11_17:C3535
NCI2004_11_17:C4764
NCI:C3028
NCI:C3533
NCI:C3534
NCI:C3535
NCI:C4764
OMIM:133239
SNOMEDCT_US_2018_03_01:93656003
SNOMEDCT_US_2018_03_01:93877002
SNOMEDCT_US_2018_03_01:93895004
SNOMEDCT_US_2018_03_01:94119000
UMLS_CUI:C0014859
UMLS_CUI:C0153413
UMLS_CUI:C0153414
UMLS_CUI:C0153415
UMLS_CUI:C0153416
UMLS_CUI:C0496775
Ca lower third oesophagus
Ca middle third oesophagus
esophagus cancer
malignant neoplasm of distal third of esophagus
malignant neoplasm of lower third of oesophagus
malignant neoplasm of middle third of oesophagus
malignant neoplasm of proximal third of esophagus
malignant neoplasm of upper third esophagus
malignant tumor of Distal Third of esophagus
malignant tumor of Proximal Third of esophagus
malignant tumor of abdominal esophagus
malignant tumor of the middle Third of the esophagus
disease_ontology
DOID:5041
esophageal cancer
A gastrointestinal system disease that is located_in the intestine.
DOID:10759
DOID:11222
DOID:11789
DOID:8531
DOID:8558
DOID:8591
ICD10CM:K63.9
ICD9CM:569.9
MESH:D007410
NCI:C26801
SNOMEDCT_US_2018_03_01:85919009
UMLS_CUI:C0021831
disease_ontology
DOID:5295
intestinal disease
A stomach cancer that is located_in the stomach.
EFO:0000178
NCI2004_11_17:C4911
NCI:C4911
UMLS_CUI:C0699791
cancer of the stomach
carcinoma of stomach
gastric carcinoma
disease_ontology
DOID:5517
stomach carcinoma
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.
DOID:1994
DOID:1997
ICD10CM:C18.9
MESH:D015179
NCI:C2955
NCI:C4978
NCI:C5105
SNOMEDCT_US_2018_03_01:93854002
UMLS_CUI:C0009402
UMLS_CUI:C0346629
UMLS_CUI:C1319315
disease_ontology
DOID:5672
large intestine cancer
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]
Fiessinger Leroy Reiter syndrome; Post-bacterial arthropathy; postdysenteric arthropathy; Reiter's disease; Reactive arthritis; Reiter disease
reactive arthritis
A musculoskeletal system disease that affects tissues such as skin, tendons, and cartilage.
CSP2005:0729-7208
MESH:D003240
NCI:C26729
UMLS_CUI:C0009782
connective tissue disorder
disorder of connective tissue
disease_ontology
DOID:65
connective tissue disease
A rheumatoid arthritis that involves an autoimmune disease onset in children under 16 which attacks the healthy cells and tissue of located_in joint.
DOID:10129
DOID:1264
DOID:675
ICD10CM:M08.4
ICD10CM:M08.40
ICD9CM:714.3
ICD9CM:714.31
ICD9CM:714.32
ICD9CM:714.33
NCI:C26979
NCI:C61279
OMIM:604302
ORDO:92
SNOMEDCT_US_2018_03_01:74391003
SNOMEDCT_US_2018_03_01:7441009
SNOMEDCT_US_2018_03_01:75822003
SNOMEDCT_US_2018_03_01:83793004
UMLS_CUI:C0157916
UMLS_CUI:C0157917
UMLS_CUI:C0157918
UMLS_CUI:C0409667
Pauciarticular onset juvenile chronic arthritis
acute juvenile rheumatoid arthritis
juvenile chronic polyarthritis
juvenile idiopathic arthritis
monarticular juvenile rheumatoid arthritis
pauciarticular juvenile arthritis
systemic juvenile rheumatoid arthritis
disease_ontology
DOID:676
Xref MGI.
juvenile rheumatoid arthritis
A liver carcinoma that has_material_basis_in undifferentiated hepatocytes.
DOID:5005
EFO:0000182
NCI2004_11_17:C3099
NCI2004_11_17:C7956
NCI:C7956
OMIM:114550
UMLS_CUI:C0279607
HCC
Hepatoma
adult Hepatoma
adult primary hepatocellular carcinoma
disease_ontology
DOID:684
OMIM mapping confirmed by DO. [SN].
hepatocellular carcinoma
A liver cancer that has_material_basis_in epithelial cells.
NCI2004_11_17:C7927
NCI:C7927
UMLS_CUI:C0279000
Liver and Intrahepatic bile duct carcinoma
disease_ontology
DOID:686
liver carcinoma
A disease that manifests in a defined anatomical structure.
DOID:1
DOID:2
DOID:5
DOID:71
DOID:72
DOID:8
disease_ontology
DOID:7
disease of anatomical entity
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.
EFO:0003898
GARD:9518
ICD10CM:M45
ICD9CM:720.0
MESH:D013167
NCI:C84564
ORDO:825
SNOMEDCT_US_2018_03_01:9631008
UMLS_CUI:C0038013
ls:IEDB
Bekhterev syndrome
Bekhterev's disease
Marie-Strumpell disease
disease_ontology
DOID:7147
ankylosing spondylitis
An arthritis that is an autoimmune disease which attacks healthy cells and tissue located_in joint.
EFO:0000685
ICD10CM:M06.9
ICD9CM:714.0
KEGG:05323
MESH:D001172
MTHICD9_2006:714.0
NCI2004_11_17:C27206
NCI:C2884
OMIM:180300
SNOMEDCT_US_2018_03_01:69896004
UMLS_CUI:C0003873
Arthritis or polyarthritis, rheumatic
atrophic Arthritis
disease_ontology
DOID:7148
OMIM mapping confirmed by DO. [SN].
rheumatoid arthritis
A disease of anatomical entity that is located_in the gastrointestinal tract.
DOID:27
DOID:944
CSP2005:1248-3545
ICD10CM:K92.9
ICD9CM:520-579.99
MESH:D004066
SNOMEDCT_US_2018_03_01:53619000
UMLS_CUI:C0012242
GIT disease
Gastroenteropathy
alimentary system disease
digestive system disorder
gastrointestinal disease
gastrointestinal disorder
disease_ontology
DOID:77
gastrointestinal system disease
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.
ICD10CM:M19.90
MESH:D001168
NCI:C2883
SNOMEDCT_US_2018_03_01:3723001
UMLS_CUI:C0003864
ls:IEDB
Inflammatory disorder of joint
disease_ontology
DOID:848
arthritis
A syndrome that occurs in humans with psoriasis who also experience symptoms similar to arthritis.
EFO:0003778
ICD10CM:L40.5
ICD10CM:L40.50
ICD9CM:696.0
MESH:D015535
NCI:C61277
SNOMEDCT_US_2018_03_01:33339001
UMLS_CUI:C0003872
arthritis psoriatica
arthropathic psoriasis
disease_ontology
psoriatic arthropathy
DOID:9008
psoriatic arthritis
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.
CSP2005:0729-7721
EFO:0002690
GARD:10253
ICD10CM:M32
ICD10CM:M32.9
ICD9CM:710.0
KEGG:05322
MESH:D008180
MTH:U002054
NCI2004_11_17:C3201
NCI:C3201
OMIM:152700
OMIM:300809
OMIM:605480
OMIM:608437
OMIM:609903
OMIM:609939
OMIM:610065
OMIM:610066
OMIM:612254
OMIM:612378
OMIM:613145
OMIM:614420
ORDO:536
SNOMEDCT_US_2018_03_01:55464009
UMLS_CUI:C0024141
ls:IEDB
Lupus Erythematosus, systemic
SLE - Lupus Erythematosus, systemic
disseminated lupus erythematosus
disease_ontology
DOID:9074
Xref MGI.
systemic lupus erythematosus
A large intestine cancer that is located_in the colon and/or located_in the rectum.
KEGG:05210
MESH:D015179
OMIM:114500
OMIM:611469
OMIM:612230
OMIM:612231
OMIM:612232
OMIM:612589
OMIM:612590
OMIM:612592
UMLS_CUI:C1527249
disease_ontology
DOID:9256
Xref MGI.
OMIM mapping confirmed by DO. [SN].
colorectal cancer
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
William Hogan
William Hogan
drug product
A biome is an ecosystem to which resident ecological communities have evolved adaptations.
EcoLexicon:biome
LTER:173
major habitat type
EcosytemType
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.
biome
environmental material
A portion of environmental material is a fiat object which forms the medium or part of the medium of an environmental system.
environmental material
A system which has the disposition to environ one or more material entities.
2013-09-23T16:04:08Z
EcoLexicon:environment
environment
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.
environmental system
An environmental system which can sustain and allow the growth of an ecological population.
EcoLexicon:habitat
LTER:238
SWEETRealm:Habitat
https://en.wikipedia.org/wiki/Habitat
A habitat's specificity to an ecological population differentiates it from other environment classes.
habitat
An environmental system which includes both living and non-living components.
This class will be primarily filled by inference, any environmental system which necessarily includes living parts should be autoclassified here.
ecosystem
biological_process
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.
janelomax
2012-09-19T15:05:24Z
GO:0000004
GO:0007582
GO:0044699
Wikipedia:Biological_process
biological process
physiological process
biological_process
single organism process
single-organism process
GO:0008150
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.
biological_process
gene expression
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.
gene expression
Any process in which an organism has an effect on an organism of a different species.
interaction with another species
interspecies interaction
interspecies interaction with other organisms
biological_process
GO:0044419
interspecies interaction between organisms
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.
biological_process
GO:0051701
interaction with host
A biological process which involves another organism of the same or different species.
GO:0051706
interaction between organisms
physiological interaction between organisms
physiological interaction with other organism
biological_process
GO:0051704
multi-organism process
A phenotypic abnormality.
UMLS:C4021819
Organ abnormality
human_phenotype
HP:0000118
This is the root of the phenotypic abnormality subontology of the HPO.
Phenotypic abnormality
Accumulation of substantial excess body fat.
MSH:D009765
SNOMEDCT_US:414915002
SNOMEDCT_US:414916001
UMLS:C0028754
Having too much body fat
Obesity
human_phenotype
HP:0001513
Obesity
Abnormally increased frequency of loose or watery bowel movements.
MSH:D003967
SNOMEDCT_US:267060006
SNOMEDCT_US:62315008
UMLS:C0011991
Diarrhea
Diarrhoea
Watery stool
human_phenotype
HP:0002014
Diarrhea
The presence of chronic diarrhea, which is usually taken to mean diarrhea that has persisted for over 4 weeks.
SNOMEDCT_US:236071009
UMLS:C0401151
Chronic diarrhea
human_phenotype
Diarrhea, recurrent
Recurrent diarrhea
HP:0002028
Chronic diarrhea
measurement unit label
Examples of measurement unit labels are liters, inches, weight per volume.
A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure.
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.
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.
PERSON: Alan Ruttenberg
PERSON: Melanie Courtot
measurement unit label
objective specification
In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction.
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.
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."
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.
Answers the question, why did you do this experiment?
PERSON: Alan Ruttenberg
PERSON: Barry Smith
PERSON: Bjoern Peters
PERSON: Jennifer Fostel
goal specification
OBI Plan and Planned Process/Roles Branch
OBI_0000217
objective specification
Pour the contents of flask 1 into flask 2
a directive information entity that describes an action the bearer will take
Alan Ruttenberg
OBI Plan and Planned Process branch
action specification
datum label
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
http://www.golovchenko.org/cgi-bin/wnsearch?q=label#4n
GROUP: IAO
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.
datum label
data item
Data items include counts of things, analyte concentrations, and statistical summaries.
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.
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.
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.
2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym.
2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/
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
PERSON: Alan Ruttenberg
PERSON: Chris Stoeckert
PERSON: Jonathan Rees
data
data item
information content entity
Examples of information content entites include journal articles, data, graphical layouts, and graphs.
A generically dependent continuant that is about some thing.
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).
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.
PERSON: Chris Stoeckert
OBI_0000142
information content entity
1
1
10 feet. 3 ml.
a scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label.
2009-03-16: we decided to keep datum singular in scalar measurement datum, as in
this case we explicitly refer to the singular form
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.
PERSON: Alan Ruttenberg
PERSON: Melanie Courtot
scalar measurement datum
An information content entity whose concretizations indicate to their bearer how to realize them in a process.
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.
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.
8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO
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
PERSON: Alan Ruttenberg
PERSON: Bjoern Peters
directive information entity
curation status specification
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.
Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)
PERSON:Bill Bug
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
OBI_0000266
curation status specification
data about an ontology part is a data item about a part of an ontology, for example a term
Person:Alan Ruttenberg
data about an ontology part
plan specification
PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice.
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.
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.
2014-03-31: A plan specification can have other parts, such as conditional specifications.
Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved
Alan Ruttenberg
OBI Plan and Planned Process branch
OBI_0000344
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
plan specification
measurement datum
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,}.
A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device.
2/2/2009 is_specified_output of some assay?
person:Chris Stoeckert
OBI_0000305
group:OBI
measurement datum
A scalar measurement datum that is the result of measuring a temporal interval
2009/09/28 Alan Ruttenberg. Fucoidan-use-case
Person:Alan Ruttenberg
time measurement datum
infection
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.
infection
Interaction is a processual entity that has two or more participants (i.e., interactors) that have an effect upon one another.
YH, ZX
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
interaction
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 .
GARD:0010969
ICD10:M08.8
NCIT:C119024
Orphanet:85438
SCTID:410801005
enthesitis-related JIA
era
enthesitis related arthritis, juvenile
enthesitis-related arthritis
juvenile enthesitis-related arthritis
juvenile spondylarthropathy
MONDO:0019437
enthesitis-related juvenile idiopathic arthritis
https://rarediseases.info.nih.gov/diseases/10969/enthesitis-related-juvenile-idiopathic-arthritis
Coprobacillus
Coprobacillus
Mus musculus
house mouse
mouse
Mus musculus
Rattus
rat
rats
Rattus
Rattus norvegicus
Norway rat
Rattus sp. strain Wistar
brown rat
rat
rats
Rattus norvegicus
Capnocytophaga
Capnocytophaga
Capnocytophaga gingivalis
Beggiatoa
Beggiatoa
Collinsella
Collinsella
Solobacterium moorei
Solobacterium moorei
Viruses
Viruses
Hepatitis B virus
Hepatitis B virus
Leptotrichia sp.
Leptotrichia sp.
Badula fragilis
Badula fragilis
Anaerovorax
Anaerovorax
Hepacivirus C
Hepacivirus C
Leptotrichiaceae
Leptotrichiaceae
Fusicatenibacter saccharivorans
Fusicatenibacter saccharivorans
Parasporobacterium
Parasporobacterium
Coprococcus catus
Coprococcus catus
Euteleostomi
bony vertebrates
Euteleostomi
Cutibacterium acnes 17B
Cutibacterium acnes 17B
Methylobacteriaceae
Methylobacteriaceae
Burkholderiaceae
Burkholderiaceae
Ecdysozoa
Ecdysozoa
Solobacterium sp. S4-A19
Solobacterium sp. S4-A19
Proteobacteria
purple bacteria
purple bacteria and relatives
purple non-sulfur bacteria
purple photosynthetic bacteria
purple photosynthetic bacteria and relatives
Proteobacteria
Solobacterium
Solobacterium
Gammaproteobacteria
Gammaproteobacteria
Firmicutes
low G+C Gram-positive bacteria
low GC Gram+
Firmicutes
Peptostreptococcus
Peptostreptococcus
Peptostreptococcus anaerobius
Peptostreptococcus anaerobius
Ruminococcus
Ruminococcus
Ruminococcus albus
Ruminococcus albus
Micrococcaceae
Micrococcaceae
Micrococcus
Human immunodeficiency virus
Human immunodeficiency virus
Erysipelotrichaceae
Erysipelotrichaceae
Acidovorax
Acidivorax
Acidovorax
Streptococcaceae
Streptococcaceae
Streptococcus
Streptococcus
Streptococcus sanguinis
Streptococcus thermophilus
Streptococcus salivarius thermophilus
Streptococcus thermophilus
Streptococcus pyogenes
Streptococcus pyogenes
Streptococcus equinus
Streptococcus equinus
Enterococcus
Enterococcus
Enterococcus faecalis
Enterococcus faecalis
Escherichia coli #1/H766
Escherichia coli #1/H766
Spirochaetaceae
Spirochaetaceae
Atopobium
Atopobium
Atopobium parvulum
Atopobium parvulum
Lachnobacterium bovis
Lachnobacterium bovis
Fretibacterium
Fretibacterium
Mesangiospermae
Mesangiospermae
Pentapetalae
Pentapetalae
Clostridium
Clostridium
Clostridioides difficile
[Clostridium] difficile
Clostridioides difficile
Clostridium perfringens
Clostridium perfringens
Anoxybacillus
Anoxybacillus
Erysipelatoclostridium
Erysipelatoclostridium
Lachnoclostridium
Lachnoclostridium
[Clostridium] clostridioforme
Clostridium clostridioforme
[Clostridium] clostridioforme
Blautia coccoides
Blautia coccoides
Candida <Debaryomycetaceae>
Candida
Candida <Debaryomycetaceae>
Fusobacterium nucleatum subsp. vincentii
Fusibacterium nucleatum subsp. fusiforme
Fusibacterium nucleatum subsp. vincentii
Fusobacterium nucleatum subsp. vincentii
Treponema
Treponema
Treponema
Lactobacillus
Lactobacillus
Lactobacillus acidophilus
Lactobacillus acidophilus
Treponema denticola
Lactobacillus casei
Lactobacillus casei
Fusobacterium hwasookii
Fusobacterium hwasookii
Megamonas hypermegale
Megamonas hypermegale
Lactobacillus sp.
Lactobacillus sp.
Lactobacillus reuteri
Lactobacillus reuteri
Lactobacillus fermentum
Lactobacillus fermentum
Lactobacillus murinus
Lactobacillus murinus
Lactobacillus salivarius
Lactobacillus salivarius
Eggerthellaceae
Eggerthellaceae
Prevotella copri
Prevotella copri
Actinomyces
Actinomyces
Bifidobacterium
Bifidobacterium
Bifidobacterium bifidum
Bifidobacterium bifidum
Bifidobacterium dentium
Bifidobacterium dentium
Bacteroidales
Bacteroidales
Rikenellaceae
Rikenellaceae
Rikenellaceae
Porphyromonadaceae
Porphyromonadaceae
Prevotellaceae
Prevotellaceae
Corynebacterium diphtheriae
Corynebacterium diphtheriae
Rothia aeria
Rothia aeria
Eubacterium
Propionibacterium
Propionicibacterium
Propionibacterium
Actinobacteria <class>
Actinobacteria
high G+C Gram-positive bacteria
Actinobacteria <class>
Mycobacterium
Mycobacterium
Mycobacterium avium
Mycobacterium avium
PVC group
PVC group
Terrabacteria group
Terrabacteria group
Rhodococcus
Selenomonadaceae
Selenomonadaceae
Pseudonocardia
Clostridia
Clostridia
Clostridiales
Clostridiales
Lachnospiraceae
Lachnospiraceae
Peptostreptococcaceae
Peptostreptococcaceae
Eubacteriaceae
Eubacteriaceae
unclassified Clostridiales
unclassified Clostridiales
Bacillaceae
Bacillaceae
Lactobacillales
Lactobacillales
Atopobium sp.
Atopobium sp.
Subdoligranulum sp. 60_17
Subdoligranulum sp. 60_17
Lachnospiraceae bacterium
Lachnospiraceae bacterium
Yersiniaceae
Yersiniaceae
Morganellaceae
Morganellaceae
Neisseria sp.
Neisseria sp.
Campylobacter
Campylobacter
Campylobacter
Desulfovibrionaceae
Desulfovibrionaceae
Campylobacter jejuni
Campylobacter jejuni
Pancrustacea
Pancrustacea
Bacteria
eubacteria
Bacteria
Tannerellaceae
Tannerellaceae
Bacteroidia
Bacteroidia
Crenothrix
Crenothrix
Chloroflexi
Actinobacteria <phylum>
Actinobacteria
Actinobacteria <phylum>
Fusobacteriales
Fusobacteriales
Fusobacteriaceae
Fusobacteriaceae
Pseudonocardiaceae
Pseudonocardiaceae
Helicobacter
Helicobacter
Helicobacter pylori
Helicobacter pylori
Mycoplasma fermentans
Mycoplasma fermentans
Campylobacterales
Campylobacterales
Archaea
Archaea
Bifidobacterium longum
Bifidobacterium longum
Faecalibacterium
Faecalibacterium
Dialister invisus
Dialister invisus
Moniliophthora
Moniliophthora
Candidatus Portiera
Candidatus Portiera
Alistipes
Alistipes
Akkermansia
Akkermansia
Akkermansia muciniphila
Akkermansia muciniphila
Anaerotruncus
Anaerotruncus
Acetanaerobacterium
Acetanaerobacterium
Sulfurovum
Sulfurovum
Cardiobacterium
Cardiobacterium
Eukaryota
eucaryotes
eukaryotes
Eukaryota
Bifidobacterium animalis
Bifidobacterium animalis
Lachnospira pectinoschiza
Lachnospira pectinoschiza
Tannerella forsythia
Tannerella forsythia
Bacteroides ovatus
Bacteroides ovatus
Alistipes putredinis
Alistipes putredinis
Prevotella intermedia
Prevotella intermedia
Prevotella oris
Prevotella oris
Prevotella oulorum
Betaproteobacteria
Betaproteobacteria
Odoribacter
Odoribacter
Pseudomonas
Pseudomonas
Salmonella enterica
Salmonella enterica
Anaerolineae
Anaerolineaceae
Anaerolineales
Anaerolineales
Subdoligranulum
Subdoligranulum
[Clostridium] scindens
Clostridium scindens
[Clostridium] scindens
Veillonella
Veillonella
Bacteroides sp.
Bacteroides sp.
Epsilonproteobacteria
Epsilonproteobacteria
Roseburia hominis
Roseburia hominis
Bifidobacterium animalis subsp. lactis
Bifidobacterium animalis subsp. lactis
Clostridium sp. cp01.19
Clostridium sp. cp01.19
Pseudomonas sp.
Bacteroides plebeius
Bacteroides plebeius
Euarchontoglires
Euarchontoglires
Streptococcus gallolyticus
Streptococcus gallolyticus
Propionibacteriaceae
Propionicibacteriaceae
Propionibacteriaceae
Veillonellaceae
Veillonellaceae
Clostridiaceae
Clostridiaceae
Burkholderia
Helicobacter hepaticus
Helicobacter hepaticus
unclassified Proteobacteria
unclassified Proteobacteria
Fusobacteria
Fusobacteria
Leptotrichia
Leptotrichia
Kingella
Kingella
Tetrapoda
tetrapods
Tetrapoda
Amniota
amniotes
Amniota
Bacteroides intestinalis
Bacteroides intestinalis
Phascolarctobacterium
Phascolarctobacterium
Parvimonas micra
Parvimonas micra
Coprococcus
Coprococcus
Opisthokonta
Opisthokonta
Bilateria
Bilateria
[Clostridium] asparagiforme
Clostridium asparagiforme
[Clostridium] asparagiforme
Bacteroides finegoldii
Bacteroides finegoldii
Microbacterium
Aureibacterium
Microbacterium
Lactobacillaceae
Lactobacillaceae
Streptobacillus
Streptobacillus
Peptostreptococcus stomatis
Peptostreptococcus stomatis
Bilophila
Bilophila
Bilophila wadsworthia
Bilophila wadsworthia
Prevotella stercorea
Prevotella stercorea
Streptococcus sp. 'group A'
Streptococcus sp. 'group A'
Arabidopsis thaliana
mouse-ear cress
thale cress
thale-cress
Arabidopsis thaliana
Bacteroides xylanisolvens
Bacteroides xylanisolvens
Parabacteroides
Parabacteroides
Escherichia coli B
Escherichia coli B
Murinae
Murinae
Dorea formicigenerans
Dorea formicigenerans
Eubacterium ventriosum
[Eubacterium] ventriosum
Eubacterium ventriosum
Barnesiella
Barnesiella
Dialister
Dialister
Dialister pneumosintes
Dialister pneumosintes
Blautia obeum
Blautia obeum
Sutterella wadsworthensis
Sutterella wadsworthensis
Mammalia
mammals
Mammalia
Methylobacterium
Prevotella pleuritidis
Cronobacter
Cronobacter
Aggregatibacter
Aggregatibacter
Ruminococcus sp.
Ruminococcus sp.
Filifactor
Filifactor
Dictyostelium discoideum
Dictyostelium discoideum
Eleutherodactylus lentus
Virgin Islands robber frog
Eleutherodactylus lentus
Dikarya
Dikarya
Oscillibacter
Oscillibacter
Pseudobutyrivibrio
Pseudobutyrivibrio
Pseudobutyrivibrio ruminis
Pseudobutyrivibrio ruminis
Ruminococcus lactaris
Ruminococcus lactaris
Acinetobacter
Acinetobacter
Gordonibacter pamelaeae
Gordonibacter pamelaeae
Natronobacillus
Natronobacillus
Fungi
fungi
Fungi
Bacteroides caccae
Bacteroides caccae
Lactobacillus rhamnosus
Lactobacillus rhamnosus
Neisseriaceae
Neisseriaceae
Ascomycota
ascomycetes
sac fungi
Ascomycota
Saccharomycetales
budding yeasts
Saccharomycetales
Schizosaccharomyces pombe
fission yeast
Schizosaccharomyces pombe
Saccharomyces cerevisiae
baker's yeast
brewer's yeast
Saccharomyces cerevisiae
Treponema maltophilum
Neurospora
Neurospora
Basidiomycota
basidiomycetes
Basidiomycota
Eikenella
Eikenella
Clostridiales incertae sedis
Clostridiales incertae sedis
Ruminococcaceae
Ruminococcaceae
Enterobacteriaceae
Enterobacteriaceae
Parvimonas
Parvimonas
Clostridiales Family XIII. Incertae Sedis
Clostridiales Family XIII. Incertae Sedis
Citrobacter
Citrobacter
Candida albicans
Candida albicans
Klebsiella aerogenes
[Enterobacter] aerogenes
Klebsiella aerogenes
Diutina rugosa
Diutina rugosa
Malassezia
Malassezia
Malassezia furfur
Pityriasis (Tinea) versicolor infection agent
Malassezia furfur
Escherichia
Escherichia
Escherichia coli
E. coli
Escherichia/Shigella coli
Escherichia coli
Klebsiella
Klebsiella
Blautia
Blautia
Klebsiella pneumoniae
Klebsiella pneumoniae
Paraprevotella
Paraprevotella
Kluyvera
Kluyvera
Proteus mirabilis
Proteus mirabilis
Providencia
Providencia
Robinsoniella
Robinsoniella
Salmonella
Salmonella
Salmonella enterica subsp. enterica
Salmonella enterica subsp. enterica
Holdemania
Holdemania
Serratia
Serratia
Shigella
Shigella
Shigella dysenteriae
Escherichia/Shigella dysenteriae
Shigella dysenteriae
Caenorhabditis elegans
roundworm
Caenorhabditis elegans
Yersinia
Yersinia enterocolitica
Yersinia enterocolitica
Vibrionaceae
Vibrionaceae
Fretibacterium fastidiosum
Acidaminobacter
Acidaminobacter
Photobacterium
Photobacterium
Bacteroides xylanisolvens XB1A
Bacteroides xylanisolvens str. XB1A
Bacteroides xylanisolvens strain XB1A
Bacteroides xylanisolvens XB1A
Vibrio
Vibrio
Daphnia
common water fleas
Daphnia
Citrobacter farmeri
Citrobacter farmeri
Citrobacter rodentium
Citrobacter rodentium
delta/epsilon subdivisions
delta/epsilon subdivisions
Fusobacterium sp.
Fusobacterium sp.
Escherichia coli ETEC TW03439
Escherichia coli ETEC TW03439
Catenisphaera adipataccumulans
Catenisphaera adipataccumulans
Pasteurellaceae
Pasteurellaceae
Aggregatibacter actinomycetemcomitans
Aggregatibacter actinomycetemcomitans
saccharomyceta
saccharomyceta
leotiomyceta
leotiomyceta
Drosophila melanogaster
fruit fly
Drosophila melanogaster
Pseudomonadales
Pseudomonadales
Campylobacteraceae
Campylobacteraceae
Haemophilus
Haemophilus
Haemophilus parainfluenzae
[Haemophilus] ducreyi
Haemophilus ducreyi
[Haemophilus] ducreyi
Haemophilus sp.
Verrucomicrobia
Verrucomicrobia
Collinsella aerofaciens
Collinsella aerofaciens
Escherichia coli NC101
Escherichia coli NC101
Escherichia coli EPEC 32/73
Escherichia coli str. EPEC 32/73
Escherichia coli strain EPEC 32/73
Escherichia coli EPEC 32/73
Malassezia restricta
Malassezia restricta
Malassezia sympodialis
Malassezia sympodialis
Fusobacterium nucleatum subsp. nucleatum
Fusibacterium nucleatum subsp. nucleatum
Fusobacterium nucleatum subsp. nucleatum
Fusobacterium nucleatum subsp. polymorphum
Fusibacterium nucleatum subsp. polymorphum
Fusobacterium nucleatum subsp. polymorphum
Fusobacterium nucleatum subsp. animalis
Fusibacterium nucleatum subsp. animalis
Fusobacterium nucleatum subsp. animalis
Malassezia pachydermatis
Malassezia pachydermatis
Vertebrata <Metazoa>
Vertebrata
vertebrates
Vertebrata <Metazoa>
Danio rerio
leopard danio
zebra danio
zebra fish
zebrafish
Danio rerio
Burkholderiales
Burkholderiales
Chlamydia
Chlamydia
Chlamydia trachomatis
Bacteroidaceae
Bacteroidaceae
Bacteroides
Bacteroides
Bacteroides fragilis
Bacteroides fragilis
Enterococcaceae
Enterococcaceae
Bacteroides uniformis
Bacteroides uniformis
Bacteroides vulgatus
Bacteroides vulgatus
Anura
anurans
frogs
frogs and toads
Anura
Xenopus <genus>
Xenopus
Xenopus <genus>
Porphyromonas
Porphyromonas
Porphyromonas gingivalis
Porphyromonas gingivalis
Prevotella
Prevotella
Roseburia
Roseburya
Roseburyella
Roseburia
Coriobacteriaceae
Coriobacteriaceae
Slackia
Slackia
Eggerthella
Eggerthella lenta
Eggerthella lenta
Cryptobacterium curtum
Cryptobacterium curtum
Dolosicoccus paucivorans
Dolosicoccus paucivorans
Fusobacterium
Fusibacterium
Fusobacterium
Fusobacterium
Coriobacteriia
Coriobacteriia
Coriobacteriales
Coriobacteriales
Bifidobacteriales
Bifidobacteriales
Micrococcales
Micrococcales
Corynebacteriales
Corynebacteriales
Nocardiaceae
Nocardiaceae
Fusobacterium nucleatum
Fusibacterium nucleatum
Fusobacterium nucleatum
Faecalibacterium prausnitzii
[Fusobacterium] prausnitzii
Faecalibacterium prausnitzii
Mogibacterium
Mogibacterium
Magnolia globosa
Magnolia globosa
Umbilicariaceae
Umbilicariaceae
[Clostridium] hiranonis
Clostridium hiranonis
[Clostridium] hiranonis
[Clostridium] hylemonae
Clostridium hylemonae
[Clostridium] hylemonae
Gallus gallus
bantam
chicken
chickens
Gallus gallus
Salmonella enterica subsp. enterica serovar Typhi
Salmonella enterica subsp. enterica serovar Typhi
Salmonella enterica subsp. enterica serovar Typhimurium
Salmonella enterica subsp. enterica serovar Typhimurium
Selenomonadales
Negativicutes
Negativicutes
Bacilli
Bacilli
Enterobacterales
Enterobacterales
Flavonifractor
Homo sapiens
human
man
Homo sapiens
Selenomonas
Selenomonas
Selenomonas
Bacteroidetes
Bacteroidetes
Rodentia
rodent
Rodentia
Porphyromonas macacae
planned process
planned process
Injecting mice with a vaccine in order to test its efficacy
A processual entity that realizes a plan which is the concretization of a plan specification.
'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.)
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.
Bjoern Peters
branch derived
6/11/9: Edited at workshop. Used to include: is initiated by an agent
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)
planned process
biological feature identification objective
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.
Jennifer Fostel
biological feature identification objective
processed material
Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples
Is a material entity that is created or changed during material processing.
PERSON: Alan Ruttenberg
processed material
evaluant role
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.
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
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)
examples of features that could be described in an evaluant: quality.... e.g. "contains 10 pg/ml IL2", or "no glucose detected")
GROUP: Role Branch
OBI
Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term.
evaluant role
assay
Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house.
A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies.
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.
PlanAndPlannedProcess Branch
measuring
scientific observation
OBI branch derived
study assay
any method
assay
sample preparation for assay
A sample_preparation_for_assay is a protocol_application including material_enrollments and biomaterial_transformations. definition_source: OBI.
PlanAndPlannedProcess Branch
study
OBI branch derived
sample preparation for assay
culture medium
A growth medium or culture medium is a substance in which microorganisms or cells can grow. Wikipedia, growth medium, Feb 29, 2008
a processed material that provides the needed nourishment for microorganisms or cells grown in vitro.
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.
Person: Jennifer Fostel, Jie Zheng
OBI
culture medium
reagent role
Buffer, dye, a catalyst, a solvating agent.
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.
PERSON:Matthew Brush
reagent
PERSON:Matthew Brush
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.
(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 that of some modified cell specimen which shares identity with the input unmodified cell specimen, and not with the biotin label. Thus, we see that an important criteria of 'reagent-ness' is that it is a facilitator, and not the primary focus of an investigation or material processing technique (ie not the specified subject/evaluant about which knowledge is sought, or the specified output material of the technique).
reagent role
material processing
A cell lysis, production of a cloning vector, creating a buffer.
A planned process which results in physical changes in a specified input material
PERSON: Bjoern Peters
PERSON: Frank Gibson
PERSON: Jennifer Fostel
PERSON: Melanie Courtot
PERSON: Philippe Rocca Serra
material transformation
OBI branch derived
material processing
specimen role
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.
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
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.
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.
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.
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.
GROUP: Role Branch
OBI
specimen role
molecular feature identification objective
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.
Jennifer Fostel
molecular feature identification objective
DNA extraction
A DNA extraction is a nucleic acid extraction where the desired output material is DNA.
PlanAndPlannedProcess Branch
OBI branch derived
DNA extraction
analyte role
Glucose in blood (measured in an assay to determine the concentration of glucose).
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.
interestingly, an analyte is still an analyte even if it is not detected. for this reason it does not bear a specified input role
pH (technically the inverse log of [H+]) may be considered a quality; this remains to be tested.
qualities such as weight, color are not assayed but measured, so they do not fall into this category.
GROUP: Role Branch
OBI
Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term.
analyte role
extract
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
an extract is a material entity which results from an extraction process
PERSON: Philippe Rocca-Serra
extracted material
GROUP: OBI Biomatrial Branch
extract
transcription profiling assay
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
An assay that determines gene expression and transcription activity using ribonucleic acids collected from a material entity.
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.
Philippe Rocca-Serra
gene expression profiling
transcription profiling
OBI
transcription profiling assay
assay objective
the objective to determine the weight of a mouse.
an objective specification to determine a specified type of information about an evaluated entity (the material entity bearing evaluant role)
PPPB branch
PPPB branch
assay objective
measure function
A glucometer measures blood glucose concentration, the glucometer has a measure function.
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.
PERSON: Daniel Schober
PERSON: Helen Parkinson
PERSON: Melanie Courtot
PERSON:Frank Gibson
measure function
material transformation objective
The objective to create a mouse infected with LCM virus. The objective to create a defined solution of PBS.
an objective specifiction that creates an specific output object from input materials.
PERSON: Bjoern Peters
PERSON: Frank Gibson
PERSON: Jennifer Fostel
PERSON: Melanie Courtot
PERSON: Philippe Rocca-Serra
artifact creation objective
GROUP: OBI PlanAndPlannedProcess Branch
material transformation objective
DNA sequencing assay
Illumina (Solexa) sequencing is an example of DNA sequencing
A sequencing assay which determines information on the sequence of a DNA molecule.
Philippe Rocca-Serra
nucleotide sequencing
url:https://en.wikipedia.org/wiki/DNA_sequencing
DNA sequencing assay
material separation objective
The objective to obtain multiple aliquots of an enzyme preparation. The objective to obtain cells contained in a sample of blood.
is an objective to transform a material entity into spatially separated components.
PPPB branch
PPPB branch
material separation objective
specimen collection process
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
A planned process with the objective of collecting a specimen.
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.
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.
Philly2013: The specimen_role for the specimen is created during the specimen collection process.
label changed to 'specimen collection process' on 10/27/2014, details see tracker:
http://sourceforge.net/p/obi/obi-terms/716/
Bjoern Peters
specimen collection
5/31/2012: This process is not necessarily an acquisition, as specimens may be collected from materials already in posession
6/9/09: used at workshop
specimen collection process
sample from organism
a material obtained from an organism in order to be a representative of the whole
5/29: This is a helper class for now
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.
sample from organism
portioning objective
The objective to obtain multiple aliquots of an enzyme preparation.
A material separation objective aiming to separate material into multiple portions, each of which contains a similar composition of the input material.
portioning objective
separation into different composition objective
The objective to obtain cells contained in a sample of blood.
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).
We should be using has the grain relations or concentrations to distinguish the portioning and other sub-objectives
separation into different composition objective
specimen collection objective
The objective to collect bits of excrement in the rainforest. The objective to obtain a blood sample from a patient.
A objective specification to obtain a material entity for potential use as an input during an investigation.
Bjoern Peters
Bjoern Peters
specimen collection objective
host role
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
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
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
GROUP: Role Branch
30 Mar09 submitted by vaccine community
OBI
http://en.wikipedia.org/wiki/Host_(biology)
host role
material sample role
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.
A material sample role is a specimen role borne by a material entity that is the output of a material sampling process.
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.
material sample role
material sampling process
A specimen gathering process with the objective to obtain a specimen that is representative of the input material entity
material sampling process
material sample
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.
A material entity that has the material sample role
OBI: workshop
sample population
sample
material sample
material maintenance objective
An objective specification maintains some or all of the qualities of a material over time.
PERSON: Bjoern Peters
PERSON: Bjoern Peters
material maintenance objective
primary structure of DNA macromolecule
a quality of a DNA molecule that inheres in its bearer due to the order of its DNA nucleotide residues.
placeholder for SO
BP et al
primary structure of DNA macromolecule
measurement device
A ruler, a microarray scanner, a Geiger counter.
A device in which a measure function inheres.
GROUP:OBI Philly workshop
OBI
measurement device
material maintenance
a process with that achieves the objective to maintain some or all of the characteristics of an input material over time
material maintenance
RNA extract
an extract which is the output of an extraction process in which RNA molecules are isolated from a specimen.
PERSON: Chris Stoeckert
PERSON: Jie Zheng
Group: UPenn Group
RNA extract
processed specimen
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.
A specimen that has been intentionally physically modified.
Bjoern Peters
Bjoern Peters
A tissue sample that has been sliced and stained for a histology study.
processed specimen
device
A voltmeter is a measurement device which is intended to perform some measure function.
An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure.
A material entity that is designed to perform a function in a scientific investigation, but is not a reagent.
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 role is not transitive across the part_of relation). In this way, the asserted disjointness between a reagent and device holds, as both roles are never realized in the same bearer during execution of an assay.
PERSON: Helen Parkinson
instrument
OBI development call 2012-12-17.
device
sequence data
example of usage: the representation of a nucleotide sequence in FASTA format used for a sequence similarity search.
A measurement datum that representing the primary structure of a macromolecule(it's sequence) sometimes associated with an indicator of confidence of that measurement.
Person:Chris Stoeckert
GROUP: OBI
sequence data
nucleic acid extract
An extract that is the output of an extraction process in which nucleic acid molecules are isolated from a specimen.
PERSON: Jie Zheng
UPenn Group
nucleic acid extract
DNA extract
The output of an extraction process in which DNA molecules are purified in order to exclude DNA from organellas.
Person: Jie Zheng
Group: UPenn group
DNA extract
nucleic acid sequencer
An device that is used to determine the order of nucleotides in nucleic acid sequences.
PERSON: Erik Segerdell
PERSON: Erik Segerdell
nucleic acid sequencer
protein sequencer
An device that is used to determine the order of amino acids in protein sequences.
PERSON: Erik Segerdell
PERSON: Erik Segerdell
protein sequencer
RNA-seq assay
An transcription profiling assay that determines an RNA sequence by analyzing the transcibed regions of the genome and or to quantitate transcript abundance.
James Malone
transcription profiling by high throughput sequencing
EFO:0002770
RNA-seq assay
transcription profiling identification objective
A molecular feature identification objective that aims to characterize the abundance of transcripts
Person: Chris Stoeckert, Jie Zheng
Group: Penn Group
transcription profiling identification objective
specimen from organism
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).
PERSON: Chris Stoeckert, Jie Zheng
tissue specimen
MO_954 organism_part
specimen from organism
sampling time measurement datum
A time measurement datum when an observation is made or a sample is taken from a material as measured from some reference point.
Person: Chris Stoeckert
time point
MO_738 timepoint
sampling time measurement datum
DNA sequence data
The part of a FASTA file that contains the letters ACTGGGAA
A sequence data item that is about the primary structure of DNA
OBI call; Bjoern Peters
OBI call; Melanie Courtout
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.
DNA sequence data
specimen collection time measurement datum
A time measurement datum that is the measure of the time when the specimens are collected.
Person: Chris Stoeckert, Jie Zheng
collection date
NIAID GSCID-BRC metadata working group
Specimen Collection Date
NIAID GSCID-BRC
specimen collection time measurement datum
sample preparation for sequencing assay
A sample preparation for assay that preparation of nucleic acids for a sequencing assay
PERSON: Chris Stoeckert, Jie Zheng
NIAID GSCID-BRC metadata working group
Nucleic Acid Preparation Method
NIAID GSCID-BRC
sample preparation for sequencing assay
cell freezing medium
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.
PERSON: Matthew Brush
cell freezing medium
1
1
scalar value specification
A value specification that consists of two parts: a numeral and a unit label
PERSON:Bjoern Peters
scalar value specification
value specification
The value of 'positive' in a classification scheme of "positive or negative"; the value of '20g' on the quantitative scale of mass.
An information content entity that specifies a value within a classification scheme or on a quantitative scale.
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.
PERSON:Bjoern Peters
value specification
whole genome sequencing assay
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.
A DNA sequencing assay that intends to provide information about the sequence of an entire genome of an organism.
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.
ImmPort
WGS
PMID:23095910
PMID:25827230
whole genome sequencing assay
measurand role
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.
Person: Alan Ruttenberg, Jie Zheng
https://en.wiktionary.org/wiki/measurand
https://github.com/obi-ontology/obi/issues/778
measurand role
organism
animal
fungus
plant
virus
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.
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')
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.
GROUP: OBI Biomaterial Branch
WEB: http://en.wikipedia.org/wiki/Organism
organism
specimen
Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen.
A material entity that has the specimen role.
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.
PERSON: James Malone
PERSON: Philippe Rocca-Serra
GROUP: OBI Biomaterial Branch
specimen
cultured cell population
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).
A processed material comprised of a collection of cultured cells that has been continuously maintained together in culture and shares a common propagation history.
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.
PERSON:Matthew Brush
cell culture sample
PERSON:Matthew Brush
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.
cultured cell population
extraction
nucleic acid extraction using phenol chloroform
A material separation in which a desired component of an input material is separated from the remainder
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.
Person:Bjoern Peters
Philippe Rocca-Serra
extraction
DNA sequencer
ABI 377 DNA Sequencer, ABI 310 DNA Sequencer
A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences.
Trish Whetzel
MO
DNA sequencer
collecting specimen from organism
taking a sputum sample from a cancer patient, taking the spleen from a killed mouse, collecting a urine sample from a patient
a process with the objective to obtain a material entity that was part of an organism for potential future use in an investigation
PERSON:Bjoern Peters
IEDB
collecting specimen from organism
environmental material collection
Taking 1 liter of surface ocean water from the San Diego Mission Bay Jetty. Capturing mice living in rural Arkansas
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.
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/
Bjoern Peters, Alan Ruttenberg
IEDB
the researcher is very interested in the location
environmental material collection process
material component separation
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
a material processing in which components of an input material become segregated in space
Bjoern Peters
IEDB
material component separation
maintaining cell culture
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
a protocol application in which cells are kept alive in a defined environment outside of an organism. part of cell_culturing
PlanAndPlannedProcess Branch
OBI branch derived
maintaining cell culture
'establishing cell culture'
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).
PERSON:Matthew Brush
PERSON:Matthew Brush
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.
establishing cell culture
sequencing assay
The use of the Sanger method of DNA sequencing to determine the order of the nucleotides in a DNA template
An assay the uses chemical or biochemical means to infer the sequence of a biomaterial
PlanAndPlannedProcess Branch
OBI branch derived
sequencing assay
RNA extraction
A RNA extraction is a nucleic acid extraction where the desired output material is RNA
PlanAndPlannedProcess Branch
OBI branch derived
requested by Helen Parkinson for MO
RNA extraction
nucleic acid extraction
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.
a material separation to recover the nucleic acid fraction of an input material
PlanAndPlannedProcess Branch
OBI branch derived
requested by Helen Parkinson for MO. Could be defined class
nucleic acid extraction
infection process
the detrimental process in which an infectious agent colonizes or replicates in a host environment
IEDB
IEDB
infection process
disposition to infect an organism
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
IEDB
IEDB
disposition to infect an organism
pathologic process
abnormal, harmful processes caused by or associated with a disease
IEDB
IEDB
pathologic process
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.
Oliver He
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
WEB: http://en.wikipedia.org/wiki/Genome
genome
A gene is a material entity that represents the entire DNA sequence required for synthesis of a functional protein or RNA molecule.
Oliver He
WEB: http://www.ncbi.nlm.nih.gov/books/NBK21640/
gene
A biological interaction between a microbiome and its host
Oliver He, Jie Zheng, Jihad Obeid, Anna Maria Masci
microbiome-host interaction
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1669-4
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4644880/
host-microbiome interaction
A microbiome located in a human body
JZ, YH
https://www.ncbi.nlm.nih.gov/pubmed/3418802/
human microbiome
A biome that consists of a collection of microorganisms (i.e., microbiota) and the surrounding environment where the microorganisms reside.
Oliver He, Jie Zheng, Jihad Obeid, Anna Maria Masci
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4520061/
microbiome
A microbiome located in a mouse body
JZ, YH
mouse microbiome
A microbiome that includes a collective population of bacterial organisms.
YH, JZ, JO, AA
bacterial microbiome
A microbiome that includes a collective population of fungal microorganisms.
YH, JZ, JO, AA
https://www.ncbi.nlm.nih.gov/pubmed/3708484/
fungal microbiome
A microbiome that includes a collective population of virus
viral microbiome
A fungal microbiome that is located in the skin of a host organism
YH, JZ, JO, AA
https://www.ncbi.nlm.nih.gov/pubmed/3708484/
fungal microbiome of skin
A fungal microbiome that is located in a mucosal site of a host organism (e.g., urogenital tract, oral cavity, and gastrointestinal tract)
YH, JZ, JO, AA
https://www.ncbi.nlm.nih.gov/pubmed/3708484/
fungal microbiome of mucosal site
A fungal microbiome that is located in a lung of a host organism
YH, JZ, JO, AA
https://www.ncbi.nlm.nih.gov/pubmed/3708484/
fungal microbiome of lung
A host-microbiome interaction where the microbiome interacts with the host immune system
YH, JZ, JO, AA
interaction between microbiome and host immune system
A interaction between microbiome and host immune system where the immune system is the host adaptive immune system
YH, JZ, JO, AA
https://www.ncbi.nlm.nih.gov/pubmed/27366226
interaction between microbiome and adaptive immune system
a human microbiome that is located in a human respiratory system
JO, AA, YH
microbiome in human lung
a human microbiome that is located in a human lung
JO, AA, YH
microbiome in human respiratory system
a human microbiome that is located in a human oral system
JO, AA, YH
microbiome in human oral
a human microbiome that is located in a human gastrointestinal system
JO, AA, YH
microbiome in human gastrointestinal system
a human microbiome that is located in a human cutaneous system
JO, AA, YH
microbiome in human cutaneous system
a human microbiome that is located in a human urogenital system
JO, AA, YH
microbiome in human urogenital system
A host-microbiome interaction where the host is human
YH, HW
human-microbiome interaction
A microbiome located in a human gut.
YH
human gut microbiota
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
An interaction between human and gut microbiome.
YH
human-gut microbiome interaction
A human-gut microbiome interaction that is associated with bowel syndrome.
YH
https://www.ncbi.nlm.nih.gov/pubmed/25864640
human gut microbiome interaction in bowel syndrome
A human-gut microbiome interaction that is associated with Crohn's disease.
YH
https://www.ncbi.nlm.nih.gov/pubmed/25864640
human gut microbiome interaction in Crohn's disease
A human-gut microbiome interaction that is associated with colon cancer.
YH
https://www.ncbi.nlm.nih.gov/pubmed/25864640
colon cancer human-gut microbiome interaction
A human-gut microbiome interaction that involves in Clostridium difficile
YH
https://www.ncbi.nlm.nih.gov/pubmed/4892173/
human gut microbiome and Clostridium difficile interaction
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.
YH
https://www.ncbi.nlm.nih.gov/pubmed/4892173/
antibiotics reducing colonization resistance against C. difficile in human gut
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.
YH
restoring human gut microbiome resistance to CDI by FMT
https://www.ncbi.nlm.nih.gov/pubmed/4328137/
restoring human gut microbiome resistance to C. difficile infection by fecal microbiota transplantation
An infection process that is caused by Clostridioides difficile.
YH
CDI
Clostridioides difficile infection
A human gut-microbiome interaction that is associated with rheumatoid arthritis (RA).
YH
https://www.ncbi.nlm.nih.gov/pubmed/4840970/
RA human-gut microbiome interaction
An association of human gut microbiota with rheumatoid arthritis (RA) that shows a patient with RV exhibits decreased gut microbial diversity
YH
https://www.ncbi.nlm.nih.gov/pubmed/4840970/
patient with RA having decreased gut microbial diversity
A quality with an increased quantity of a type of organism (e.g., bacteria inside human gut) compared with control.
YH, HW, HY
increased organism quantity compared with healthy control
A quality with an decreased microbiome organism dirversity in a host microbiome environment (e.g., gut).
YH, HW, HY
descreased microbiome organism diversity
a RA human-gut microbiome interaction that shows an decrease of Klebsiella pneumoniae in patients with RA compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/?term=26214836
depletion of Klebsiella pneumoniae in RA human gut
A quality with a depleted quantity of a type of organism (e.g., bacteria inside human gut) compared with control.
YH, HW, HY
decreased organism quantity compared with healthy controls
An interaction between human and oral microbiome.
YH WH YH
human oral cavity microbiome interaction
a RA human-gut microbiome interaction that shows an expansion of Gordonibacter pamelaeae in patients with RA compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/26214836/
expansion of Gordonibacter pamelaeae in RA human gut
a RA human-gut microbiome interaction that shows an expansion of Prevotellaceae in patients with chronic RA compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pmc/articles/PMID:24192039/
expansion of Prevotellaceae in RA human gut
a RA human-gut microbiome interaction that shows an decrease of Bifidobacterium bifidum in patients with RA compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/?term=26214836
depletion of Bifidobacterium bifidum in RA human gut
a RA human-gut microbiome interaction that shows an decrease of Veillonellain in patients with RA compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/?term=26214836
depletion of Veillonella in RA human gut
RA human-gut microbiome interaction that shows an decrease of Sutterella wadsworthensis in patients with RA compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/?term=26214836
depletion of Sutterella wadsworthensis in RA human gut
a RA human-gut microbiome interaction that shows an decrease of Megamonas hypermegale in patients with RA compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/?term=26214836
depletion of Megamonas hypermegale in RA human gut
a RA human-gut microbiome interaction that shows an expansion of [Clostridium] asparagiforme in patients with RA compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/26214836/
expansion of [Clostridium] asparagiforme in RA human gut
A colorectal cancer human-gut microbiome interaction where B. fragilis is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/24967088
https://www.ncbi.nlm.nih.gov/pubmed/27810411
expansion of B. fragilis in colorectal cancer human gut
a RA human-gut microbiome interaction that shows an expansion of Eggerthella lenta in patients with RA compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/26214836/
expansion of Eggerthella lenta in RA human gut
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.
YH, HW, HY
decreased organism quantity in acute disease patient compared with chronic disease control
A host-microbiome interaction where the host is rattus.
YH, HW
rat-microbiome interaction
a RA human-gut microbiome interaction that shows an expansion of Bifidobacterium dentium in patients with RA compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/26214836/
expansion of Bifidobacterium dentium in RA human gut
a RA human-gut microbiome interaction that shows an expansion of Lactobacillus sp in patients with RA compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/26214836/
expansion of Lactobacillus sp in RA human gut
a RA human-gut microbiome interaction that shows an expansion of Ruminococcus lactaris in patients with chronic RA compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/26214836/
expansion of Ruminococcus lactaris in RA human gut
a RA human-gut microbiome interaction that shows high Prevotella or high Bacteroides relative abundance, but rarely a high relative abundance of both.
Haihe Wang, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/24192039
segregation of Prevotella or Bacteroides dominance in RA human gut
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.
YH, HW, HY
decreased organism quantity compared with fibromyalgia patients
A human gut-microbiome interaction that is associated with systemic lupus erythematosus (SLE).
Haihe Wang, Hong Yu, Yongqun He
SLE human-gut microbiome interaction
A human-gut microbiome interaction that is associated with colorectal cancer.
YH, HW
colorectal cancer human-gut microbiome interaction
A colorectal cancer human-gut microbiome interaction where Fusobacterium sp. is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/23733170
https://www.ncbi.nlm.nih.gov/pubmed/23954159
https://www.ncbi.nlm.nih.gov/pubmed/25104642
expansion of Fusobacterium sp. in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Citrobacter is decreased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/21647227
depletion of Citrobacter in colorectal cancer human gut
a RA human-gut microbiome interaction that shows an expansion of Porphyromonas gingivalis in patients with RA compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/20436074 /
https://www.ncbi.nlm.nih.gov/pubmed/24873878/
expansion of Porphyromonas gingivalis in RA human gut
A colorectal cancer human-gut microbiome interaction where Shigella is decreased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/21647227
depletion of Shigella in colorectal cancer human gut
a RA human oral cavity microbiome interaction that shows an expansion of rare taxa,Prevotella intermedia in patients with RA compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/22576262
https://www.ncbi.nlm.nih.gov/pubmed/27789760
expansion of Prevotella intermedia in RA human oral cavity
a RA human oral cavity microbiome interaction that shows an expansion of Porphyromonas gingivalis in patients with RA compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/19554393
https://www.ncbi.nlm.nih.gov/pubmed/23902301
https://www.ncbi.nlm.nih.gov/pubmed/27641915
https://www.ncbi.nlm.nih.gov/pubmed/27789760
expansion of Porphyromonas gingivalis in RA human oral cavity
a RA human-gut microbiome interaction that shows an expansion of Proteus mirabilis in patients with RA compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/19895906/
https://www.ncbi.nlm.nih.gov/pubmed/24873878/
expansion of Proteus mirabilis in RA human gut
a RA human-gut microbiome interaction that shows an expansion of Collinsella aerofaciens in patients with RA compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/27102666/
expansion of Collinsella aerofaciens in RA human gut
A human gut-microbiome interaction that is associated with the diarrhea disease
YH
diarrheal patient-gut microbiome interaction
a SLE human-gut microbiome interaction that shows an expansion of Klebsiella in patients with SLE compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/27980687/
expansion of Klebsiella in SLE human gut
a RA human oral cavity microbiome interaction that shows an expansion of Lactobacillus salivarius in patients with RA compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/26214836
https://www.ncbi.nlm.nih.gov/pubmed/27789760
https://www.ncbi.nlm.nih.gov/pubmed/26214836
expansion of Lactobacillus salivarius in RA human oral cavity
a RA human-gut microbiome interaction that shows an expansion of Clostridia in patients with RA compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/26385261/
https://www.ncbi.nlm.nih.gov/pubmed/2889500/
expansion of Clostridia in RA human gut
a RA human-gut microbiome interaction that shows an expansion of Clostridium perfringens in patients with RA compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/2889500
expansion of Clostridium perfringens in RA human gut
a SLE human-gut microbiome interaction that shows an expansion of Prevotella in patients with SLE compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/27980687/
expansion of Prevotella in SLE human gut
a SLE human-gut microbiome interaction that shows a depletion of Dialister in patients with SLE compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/27980687/
depletion of Dialister in SLE human gut
a RA human-gut microbiome interaction that shows an decrease of Bacteroides in patients with RA compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/?term=26385261
depletion of Bacteroides in RA human gut
a RA human-gut microbiome interaction that shows an decrease of Porphyromonas in patients with RA compared to fibromyalgia patients
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/18528968
https://www.ncbi.nlm.nih.gov/pubmed/?term=26385261
depletion of Porphyromonas in RA human gut compared to fibromyalgia patients
a RA human-gut microbiome interaction that shows an decrease of Prevotella in patients with RA compared to fibromyalgia patients
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/?term=26385261
depletion of Prevotella in RA human gut compared to fibromyalgia patients
An interaction between human and respiratory airway microbiome.
Haihe Wang, Hong Yu, Yongqun He
human respiratory airway microbiome interaction
A human respiratory airway microbiome interaction that is associated with rheumatoid arthritis (RA).
Haihe Wang, Hong Yu, Yongqun He
RA human respiratory airway microbiome interaction
RA human respiratory airway microbiome interaction that shows an decrease of Porphyromonas in patients with RA compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/?term=27855721
depletion of Porphyromonas in RA human respiratory airway
RA human respiratory airway microbiome interaction that shows an decrease of Prevotella in patients with RA compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/?term=27855721
depletion of Prevotella in RA human respiratory airway
a SLE human-gut microbiome interaction that shows a depletion of Pseudobutyrivibrio in patients with SLE compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/27980687/
depletion of Pseudobutyrivibrio in SLE human gut
A human oral cavity microbiome interaction that is associated with systemic lupus erythematosus (SLE).
YH
SLE human oral cavity microbiome interaction
A human oral cavity microbiome interaction that is associated with rheumatoid arthritis (RA).
YH
RA human oral cavity microbiome interaction
a RA human oral cavity microbiome interaction that shows an decrease of Haemophilus in patients with RA compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/?term=26214836
depletion of Haemophilus in RA human oral cavity
a RA human-gut microbiome interaction that shows an expansion of Actinobacteria<phylum> in patients with RA compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/28376066/
expansion of Actinobacteria<phylum> in RA human gut
a RA human oral cavity microbiome interaction that shows an decrease of Cardiobacterium in patients with RA compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/?term=26214836
depletion of Cardiobacterium in RA human oral cavity
a RA human oral cavity microbiome interaction that shows an decrease of Eikenella in patients with RA compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/?term=26214836
depletion of Eikenella in RA human oral cavity
a RA human oral cavity microbiome interaction that shows an expansion of Kingella in patients with RA compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/?term=26214836
depletion of Kingella in RA human oral cavity
a RA human oral cavity microbiome interaction that shows an expansion of Rothia aeria in patients with RA compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/?term=26214836
depletion of Rothia aeria in RA human oral cavity
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.
YH
http://microbiomedb.org/mbio/app/
depletion of Prevotella in diarrheal patient gut
a RA human-gut microbiome interaction that shows an expansion of Prevotella copri in patients with RA compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/27333153
expansion of Prevotella copri in RA human gut
a RA human oral cavity microbiome interaction that shows an decrease of Haemophilus sp in patients with RA compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/?term=26214836
depletion of Haemophilus spp. in RA human oral cavity
a RA human oral cavity microbiome interaction that shows an increase of Cryptobacterium curtum in patients with RA compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/?term=26214836
expansion of Cryptobacterium curtum in RA human oral cavity
a RA human oral cavity microbiome interaction that shows an expansion of Veillonella in patients with RA compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/?term=26214836
expansion of Veillonella in RA human oral cavity
An interaction between rattus and gut microbiome.
YH
rat gut microbiome interaction
a RA human-gut microbiome interaction that shows an expansion of Escherichia coli in patients with RA compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/20360042/
expansion of Escherichia coli in RA human gut
a SLE human oral cavity microbiome interaction that shows an decrease of Clostridiales in patients with SLE compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/?term=28320468
depletion of Clostridiales in SLE human oral cavity
a RA human-gut microbiome interaction that shows an decrease of Faecalibacterium in patients with RA compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/?term=27333153
depletion of Faecalibacterium in RA human gut
A human gut-microbiome interaction that is associated with ankylosing spondylitis (AS).
Haihe Wang, Hong Yu, Yongqun He
AS human-gut microbiome interaction
an AS human-gut microbiome interaction that shows an expansion of Ruminococcaceae in patients with AS compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/25417597/
https://www.ncbi.nlm.nih.gov/pubmed/26362739/
expansion of Ruminococcaceae in AS human gut
an AS human-gut microbiome interaction that shows an expansion of Lachnospiraceae in patients with AS compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/25417597/
https://www.ncbi.nlm.nih.gov/pubmed/25434931/
https://www.ncbi.nlm.nih.gov/pubmed/26331579/
expansion of Lachnospiraceae in AS human gut
an AS human-gut microbiome interaction that shows an expansion of Bacteroidaceae in patients with AS compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/25417597/
expansion of Bacteroidaceae in AS human gut
an AS human-gut microbiome interaction that shows an expansion of Prevotellaceae in patients with AS compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/25417597/
expansion of Prevotellaceae in AS human gut
an AS human-gut microbiome interaction that shows an expansion of rare taxa,Veillonellaceae in patients with AS compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/25417597/
https://www.ncbi.nlm.nih.gov/pubmed/25434931/
https://www.ncbi.nlm.nih.gov/pubmed/26331579/
expansion of Veillonellaceae in AS human gut
an AS human-gut microbiome interaction that shows an expansion of Klebsiella pneumoniae in patients with AS compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/1001180/
expansion of Klebsiella pneumoniae in AS human gut
A human oral cavity microbiome interaction that is associated with ankylosing spondylitis (AS).
YH
AS human oral cavity microbiome interaction
an AS human oral cavity microbiome interaction that shows an expansion of Klebsiella pneumoniae in patients with AS compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/17458395/
expansion of Klebsiella pneumoniae in AS human oral cavity
an AS human oral cavity microbiome interaction that shows an expansion of Prevotella intermedia in patients with AS compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/26002454/
expansion of Prevotella intermedia in AS human oral cavity
an AS human oral cavity microbiome interaction that shows an expansion of rare taxa,Tannerella forsythia in patients with AS compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/26002454/
expansion of Tannerella forsythia in AS human oral cavity
A rattus gut-microbiome interaction that is associated with ankylosing spondylitis (AS).
Haihe Wang, Hong Yu, Yongqun He
association of rat gut microbiota with ankylosing spondylitis
AS rat-gut microbiome interaction
a SLE human oral cavity microbiome interaction that shows an expansion of Prevotella in patients with SLE compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/28320468/
expansion of Prevotella in SLE human oral cavity
a SLE human-gut microbiome interaction that shows an decrease of Firmicutes in patients with SLEcompared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/?term=28167944
depletion of Firmicutes in SLE human gut
a SLE human-gut microbiome interaction that shows an expansion of Bacteroidetes in patients with SLE compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/25271284/
expansion of Bacteroidetes in SLE human gut
A human gut-microbiome interaction that is associated with gout.
Haihe Wang, Hong Yu, Yongqun He
gout human-gut microbiome interaction
a Gout human-gut microbiome interaction that shows an decrease of rare taxa,Bacteroidetes in patients with gout compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/28270806/
expansion of Bacteroidetes in gout human gut
a Gout human-gut microbiome interaction that shows an expansion of Bacteroides in patients with gout compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/28270806/
expansion of Bacteroides in gout human gut
a Gout human-gut microbiome interaction that shows an expansion of Bacteroidales in patients with gout compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/28270806/
expansion of Bacteroidales in gout human gut
a Gout human-gut microbiome interaction that shows an expansion of Porphyromonadaceae in patients with gout compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/28270806/
expansion of Porphyromonadaceae in gout human gut
a Gout human-gut microbiome interaction that shows an expansion of Bacteroidaceae in patients with gout compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/28270806/
expansion of Bacteroidaceae in gout human gut
a Gout human-gut microbiome interaction that shows an expansion of Negativicutes in patients with gout compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/28270806/
expansion of Negativicutes in gout human gut
An interaction between human and zone of skin microbiome.
YH
human skin microbiome interaction
A human skin microbiome interaction that is associated with psoriatic arthritis (PsA).
Haihe Wang, Hong Yu, Yongqun He
PsA human zone of skin microbiome interaction
a Gout human-gut microbiome interaction that shows an decrease of Vibrionaceae in patients with gout compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/?term=28270806
depletion of Vibrionaceae in gout human gut
a Gout human-gut microbiome interaction that shows an decrease of Photobacterium in patients with gout compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/?term=28270806
depletion of Photobacterium in gout human gut
a Gout human-gut microbiome interaction that shows an decrease of Vibrio in patients with gout compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/?term=28270806
depletion of Vibrio in gout human gut
A colorectal cancer human-gut microbiome interaction where Eubacterium ventriosum is decreased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/26408641
depletion of Eubacterium ventriosum in colorectal cancer human gut
a Gout human-gut microbiome interaction that shows an decrease of Lachnospiraceae in patients with gout compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/?term=28270806
depletion of Lachnospiraceae in gout human gut
a Gout human-gut microbiome interaction that shows an decrease of Ruminococcaceae in patients with gout compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/?term=28270806
depletion of Ruminococcaceae in gout human gut
a Gout human-gut microbiome interaction that shows an expansion of Erysipelatoclostridium in patients with gout compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/28270806/
expansion of Erysipelatoclostridium in gout human gut
a Gout human-gut microbiome interaction that shows an expansion of Escherichia coli EPEC32/73 in patients with gout compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/23340314/
https://www.ncbi.nlm.nih.gov/pubmed/23811846/
expansion of Escherichia coli EPEC 32/73 in gout human gut
a Gout human-gut microbiome interaction that shows an expansion of Escherichia coli ETEC TW03439 in patients with gout compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/23340314/
https://www.ncbi.nlm.nih.gov/pubmed/23811846/
expansion of E. coli ETEC TW03439 in gout human gut
a Gout human-gut microbiome interaction that shows an expansion of Barnesiella in patients with gout compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/26852926/
https://www.ncbi.nlm.nih.gov/pubmed/27941389/
expansion of Barnesiella in gout human gut
a Gout human-gut microbiome interaction that shows an expansion of Parasporobacterium in patients with gout compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/26852926/
https://www.ncbi.nlm.nih.gov/pubmed/27941389/
expansion of Parasporobacterium in gout human gut
a Gout human-gut microbiome interaction that shows an expansion of Paraprevotella in patients with gout compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/26852926/
https://www.ncbi.nlm.nih.gov/pubmed/27941389/
expansion of Paraprevotella in gout human gut
a Gout human-gut microbiome interaction that shows an expansion of Anaerotruncus in patients with gout compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/26852926/
https://www.ncbi.nlm.nih.gov/pubmed/27941389/
expansion of Anaerotruncus in gout human gut
a Gout human-gut microbiome interaction that shows an expansion of Pseudobutyrivibrio in patients with gout compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/26852926/
https://www.ncbi.nlm.nih.gov/pubmed/27941389/
expansion of Pseudobutyrivibrio in gout human gut
a Gout human-gut microbiome interaction that shows an expansion of Bacteroides caccae in patients with gout compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/26852926/
https://www.ncbi.nlm.nih.gov/pubmed/27941389/
expansion of Bacteroides caccae in gout human gut
a Gout human-gut microbiome interaction that shows an expansion of Bacteroides sp in patients with gout compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/26852926/
https://www.ncbi.nlm.nih.gov/pubmed/27941389/
expansion of Bacteroides sp in gout human gut
a Gout human-gut microbiome interaction that shows an expansion of Bacteroides xylanisolvens XB1A in patients with gout compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/26852926/
https://www.ncbi.nlm.nih.gov/pubmed/27941389/
expansion of Bacteroides xylanisolvens XB1A in gout human gut
a Gout human-gut microbiome interaction that shows an expansion of Holdemania in patients with gout compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/26852926/
https://www.ncbi.nlm.nih.gov/pubmed/27941389/
expansion of Holdemania in gout human gut
a Gout human-gut microbiome interaction that shows an expansion of rare taxa,Acetanaerobacterium in patients with gout compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/26852926/
https://www.ncbi.nlm.nih.gov/pubmed/27941389/
expansion of Acetanaerobacterium in gout human gut
a Gout human-gut microbiome interaction that shows an decrease of Coprococcus catus in patients with gout compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/?term=26852926
https://www.ncbi.nlm.nih.gov/pubmed/?term=27941389
depletion of Coprococcus catus in gout human gut
a Gout human-gut microbiome interaction that shows an decrease of Faecalibacterium prausnitzii in patients with gout compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/?term=26852926
https://www.ncbi.nlm.nih.gov/pubmed/?term=27941389
depletion of Faecalibacterium prausnitzii in gout human gut
a Gout human-gut microbiome interaction that shows an decrease of Oscillibacter in patients with gout compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/?term=26852926
https://www.ncbi.nlm.nih.gov/pubmed/?term=27941389
depletion of Oscillibacter in gout human gut
a Gout human-gut microbiome interaction that shows an decrease of Ruminococcus sp. in patients with gout compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/?term=26852926
https://www.ncbi.nlm.nih.gov/pubmed/?term=27941389
depletion of Ruminococcus sp. in gout human gut
a Gout human-gut microbiome interaction that shows an decrease of Odoribacter in patients with gout compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/?term=26852926
https://www.ncbi.nlm.nih.gov/pubmed/?term=27941389
depletion of Odoribacter in gout human gut
a Gout human-gut microbiome interaction that shows an decrease of Subdoligranulum in patients with gout compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/?term=26852926
https://www.ncbi.nlm.nih.gov/pubmed/?term=27941389
depletion of Subdoligranulum in gout human gut
a Gout human-gut microbiome interaction that shows an decrease of Robinsoniella in patients with gout compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/?term=26852926
https://www.ncbi.nlm.nih.gov/pubmed/?term=27941389
depletion of Robinsoniella in gout human gut
a Gout human-gut microbiome interaction that shows an decrease of Dialister in patients with gout compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/?term=26852926
https://www.ncbi.nlm.nih.gov/pubmed/?term=27941389
depletion of Dialister in gout human gut
a Gout human-gut microbiome interaction that shows an decrease of Alistipes in patients with gout compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/?term=26852926
https://www.ncbi.nlm.nih.gov/pubmed/?term=27941389
depletion of Alistipes in gout human gut
a PsA human skin microbiome interaction that shows an decrease of Propionibacterium acnes 17B in patients with PsA compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/?term=18648509
depletion of Propionibacterium acnes 17B in PsA human skin
A human gut-microbiome interaction that is associated with juvenile psoriatic arthritis(PsA).
Haihe Wang, Hong Yu, Yongqun He
PsA human-gut microbiome interaction
a PsA human-gut microbiome interaction that shows an decrease of Akkermansia in patients with PsA compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/?term=25319745
depletion of Akkermansia in PsA human gut
a PsA human-gut microbiome interaction that shows an decrease of Ruminococcus in patients with PsA compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/?term=25319745
depletion of Ruminococcus in PsA human gut
a PsA human-gut microbiome interaction that shows an decrease of Pseudobutyrivibrio in patients with PsA compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/?term=25319745
depletion of Pseudobutyrivibrio in PsA human gut
a PsA human-gut microbiome interaction that shows an decrease of Verrucomicrobia in patients with PsA compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/?term=25319745
depletion of Verrucomicrobia in PsA human gut
a PsA human-gut microbiome interaction that shows an decrease of Parabacteroides in patients with PsA compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/?term=25319745
depletion of Parabacteroides in PsA human gut
a PsA human-gut microbiome interaction that shows an decrease of Coprobacillus in patients with PsA compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/?term=25319745
depletion of Coprobacillus in PsA human gut
a PsA human skin microbiome interaction that shows an expansion of Streptococcus in patients with PsA compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/18648509/
expansion of Streptococcus in PsA human skin
a PsA human skin microbiome interaction that shows an decrease of Propionibacterium in patients with PsA compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/?term=26362739
https://www.ncbi.nlm.nih.gov/pubmed/?term=22065152
depletion of Propionibacterium in PsA human skin
a PsA human skin microbiome interaction that shows an decrease of Actinobacteria <phylum> in patients with PsA compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/?term=18648509
https://www.ncbi.nlm.nih.gov/pubmed/?term=21407241
https://www.ncbi.nlm.nih.gov/pubmed/?term=3750937
depletion of Actinobacteria <phylum> in PsA human skin
a PsA human skin microbiome interaction that shows an decrease of Proteobacteria in patients with PsA compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/?term=18648509
https://www.ncbi.nlm.nih.gov/pubmed/?term=21407241
https://www.ncbi.nlm.nih.gov/pubmed/?term=3750937
depletion of Proteobacteria in PsA human skin
a PsA human skin microbiome interaction that shows an expansion of Firmicutes in patients with PsA compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/23750937/
https://www.ncbi.nlm.nih.gov/pubmed/18648509/
https://www.ncbi.nlm.nih.gov/pubmed/21407241 /
expansion of Firmicutes in PsA human skin
a PsA human skin microbiome interaction that shows an expansion of Bacteroidetes in patients with PsA compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/23750937/
https://www.ncbi.nlm.nih.gov/pubmed/18648509/
https://www.ncbi.nlm.nih.gov/pubmed/21407241 /
expansion of Bacteroidetes in PsA human skin
a PsA human-gut microbiome interaction that shows an expansion of Candida albicans in patients with PsA compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/11413927/
expansion of Candida albicans in PsA human gut
A human oral cavity microbiome interaction that is associated with psoriatic arthritis (PsA).
YH
PsA human oral cavity microbiome interaction
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.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/11413927/
expansion of Candida albicans in PsA human oral cavity
a PsA human skin microbiome interaction that shows an decrease of Malassezia restricta in patients with PsA compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/?term= 18294199
depletion of Malassezia restricta in PsA human skin
a PsA human skin microbiome interaction that shows an decrease of Malassezia sympodialis in patients with PsA compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/?term= 116891514
depletion of Malassezia sympodialis in PsA human skin
a PsA human skin microbiome interaction that shows an decrease of Malassezia pachydermatis in patients with PsA compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/?term= 116891514
depletion of Malassezia pachydermatis in PsA human skin
an AS human oral cavity microbiome interaction that shows an expansion of Porphyromonas gingivalis in patients with AS compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/26002454/
expansion of Porphyromonas gingivalis in AS human oral cavity
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.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/25261516/
depletion of Lactobacillus in SLE mouse gut
a RA human oral cavity microbiome interaction that shows an decrease of Aggregatibacter in patients with RA compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/?term=26214836
depletion of Aggregatibacter in RA human oral cavity
a RA human oral cavity microbiome interaction that shows an expansion of Neisseria sp. in patients with RA compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/?term=26214836
depletion of Neisseria sp. in RA human oral cavity
An association of rattus gut microbiota with ankylosing spondylitis(AS) that shows an expansion of Paraprevotella in rattus with AS compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/25140823/
expansion of Paraprevotella in AS rat gut
An association of rattus gut microbiota with ankylosing spondylitis(AS) that shows an expansion of Prevotella in rattus with AS compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/25140823/
expansion of Prevotella in AS rat gut
a RA human oral cavity microbiome interaction that shows an expansion of Actinomyces in patients with RA compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/26214836
expansion of Actinomyces in RA human oral cavity
a RA human oral cavity microbiome interaction that shows an expansion of Prevotella in patients with RA compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/22576262
expansion of Prevotella in RA human oral cavity
a RA human oral cavity microbiome interaction that shows an expansion of Leptotrichia sp. in patients with RA compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/22576262
expansion of Leptotrichia sp. in RA human oral cavity
a RA human oral cavity microbiome interaction that shows an expansion of rare taxa,Tannerella forsythia in patients with RA compared with healthy controls
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/19554393
https://www.ncbi.nlm.nih.gov/pubmed/22576262
https://www.ncbi.nlm.nih.gov/pubmed/23902301
expansion of Tannerella forsythia in RA human oral cavity
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.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/?term=25140823
Akkermansia muciniphila depletion in AS rat gut
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.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/10338507
https://www.ncbi.nlm.nih.gov/pubmed/25140823/
https://www.ncbi.nlm.nih.gov/pubmed/8770866
expansion of Bacteroides vulgatus in AS rat gut
A rattus gut-microbiome interaction that is associated with arthritis.
Haihe Wang, Hong Yu, Yongqun He
association of rat gut microbiota with arthritis
arthritis rat-gut microbiome interaction
An association of rattus gut microbiota with arthritis that shows an expansion of Bifidobacterium in rattus with arthritis compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/2931580/
expansion of Bifidobacterium in arthritis rat gut
An association of rattus gut microbiota with arthritis that shows an expansion of Propionibacterium acnes 17B in rattus with arthritis compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/2931580/
expansion of Propionibacterium acnes 17B in arthritis rat gut
An association of rattus gut microbiota with arthritis that shows an expansion of Lactobacillus casei in rattus with arthritis compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/2931580/
expansion of Lactobacillus casei in arthritis rat gut
An association of rattus gut microbiota with arthritis that shows an expansion of Lactobacillus fermentum in rattus with arthritis compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/2931580/
expansion of Lactobacillus fermentum in arthritis rat gut
An association of rattus gut microbiota with arthritis that shows an expansion of Lactobacillus murinus in rattus with arthritis compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/2931580/
expansion of Lactobacillus murinus in arthritis rat gut
An association of rattus gut microbiota with arthritis that shows an expansion of Lactobacillus acidophilus in rattus with arthritis compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/2931580/
expansion of Lactobacillus acidophilus in arthritis rat gut
An association of rattus gut microbiota with arthritis that shows an expansion of Escherichia coli in rattus with arthritis compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/2931580/
https://www.ncbi.nlm.nih.gov/pubmed/3518723/
expansion of E. coli in arthritis rat gut
An association of rattus gut microbiota with arthritis that shows an expansion of Lactobacillus in rattus with arthritis compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/27481047/
expansion of Lactobacillus in arthritis rat gut
An association of rattus gut microbiota with arthritis that shows an expansion of Bacteroidaceae in rattus with arthritis compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/27481047/
expansion of Bacteroidaceae in arthritis rat gut
An association of rattus gut microbiota with arthritis that shows a depleted quantity of Lachnospiraceae in rattus with arthritis compared with healty controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/?term=27481047
Lachnospiraceae depletion in arthritis rat gut
An association of rattus gut microbiota with arthritis that shows an expansion of Bacteroides fragilis in rattus with arthritis compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/2931580/
expansion of Bacteroides fragilis in arthritis rat gut
A host-microbiome interaction where the host is musculus.
YH, HW
mouse-microbiome interaction
An interaction between musculus and gut microbiome.
YH
mouse gut microbiome interaction
A musculus gut-microbiome interaction that is associated with system lupus erythematosus(SLE).
Haihe Wang, Hong Yu, Yongqun He
association of mouse gut microbiota with system lupus erythematosus
SLE mouse-gut microbiome interaction
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.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/25261516/
expansion of Lachnospiraceae in SLE mouse gut
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.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/25261516/
expansion of Ruminococcaceae in SLE mouse gut
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.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/25261516/
expansion of Clostridiales in SLE mouse gut
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.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/25261516/
expansion of Streptococcaceae in SLE mouse gut
An association of rattus gut microbiota with arthritis that shows an expansion of Streptococcus pyogenes in rattus with arthritis compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/1572097/
expansion of Streptococcus pyogenes in arthritis rat gut
A musculus gut-microbiome interaction that is associated with arthritis
Haihe Wang, Hong Yu, Yongqun He
association of mouse gut microbiota with arthritis
arthritis mouse-gut microbiome interaction
An association of musuculus gut microbiota with arthritis that shows an expansion of Prevotella copri in musuculus with arthritis compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/22553482/
https://www.ncbi.nlm.nih.gov/pubmed/27789760/
expansion of Prevotella copri in arthritis mouse gut
An association of musculus gut microbiota with arthritis that shows a depleted quantity of Actinobacteria<class> in musculus with arthritis compared with healty controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/?term=22553482
https://www.ncbi.nlm.nih.gov/pubmed/?term=27789760
Actinobacteria<class> depletion in arthritis mouse gut
An association of musculus gut microbiota with arthritis that shows a depleted quantity of Bacteroides in musculus with arthritis compared with healty controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/?term=22553482
https://www.ncbi.nlm.nih.gov/pubmed/?term=27789760
Bacteroides depletion in arthritis mouse gut
an AS human-gut microbiome interaction that shows an expansion of Dialister in patients with AS compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/27390077/
expansion of Dialister in AS human gut
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.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/25261516/
expansion of Alistipes in SLE mouse gut
a SLE human-gut microbiome interaction that shows an expansion of Bacteroidia in patients with SLE compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/25271284/
expansion of Bacteroidia in SLE human gut
a SLE human-gut microbiome interaction that shows an expansion of Bacteroidales in patients with SLE compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/25271284/
expansion of Bacteroidales in SLE human gut
a SLE human-gut microbiome interaction that shows an decrease of Vibrio in patients with SLEcompared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/?term=25271284
depletion of Clostridia in SLE human gut
a SLE human-gut microbiome interaction that shows an decrease of Clostridiales in patients with SLE compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/?term=25271284
depletion of Clostridiales in SLE human gut
RA human respiratory airway microbiome interaction that shows an decrease of Treponema in patients with RA compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/?term=27855721
depletion of Treponema in RA human respiratory airway
RA human respiratory airway microbiome interaction that shows an decrease of Burkholderia in patients with RA compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/?term=27855721
depletion of Burkholderia in RA human respiratory airway
RA human respiratory airway microbiome interaction that shows an decrease of Actynomyces in patients with RA compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/?term=27855721
depletion of Actynomyces in RA human respiratory airway
RA human respiratory airway microbiome interaction that shows an expansion of Pseudonocardia in patients with RA compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/27855721/
expansion of Pseudonocardia in RA human respiratory airway
RA human respiratory airway microbiome interaction that shows an expansion of Micrococcus in patients with RA compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/27855721/
expansion of Micrococcus in RA human respiratory airway
RA human respiratory airway microbiome interaction that shows an expansion of Methylobacterium in patients with RA compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/27855721
expansion of Methylobacterium in RA human respiratory airway
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.
YH
http://microbiomedb.org/mbio/app/
expansion of Natronobacillus in diarrheal patient gut
a RA human-gut microbiome interaction that shows an expansion of Eggerthella in patients with RA compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/28376066/
expansion of Eggerthella in RA human gut
an AS human oral cavity microbiome interaction that shows an expansion of rare taxa,Treponema denticola in patients with AS compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/26002454/
expansion of Treponema denticola in AS human oral cavity
an AS human-gut microbiome interaction that shows an expansion of Rikenellaceae in patients with AS compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/25417597/
https://www.ncbi.nlm.nih.gov/pubmed/26362730/
expansion of Rikenellaceae in AS human gut
an AS human-gut microbiome interaction that shows an expansion of Porphyromonas macacae in patients with AS compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/25417597/
expansion of Porphyromonas macacae in AS human gut
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.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/?term=25140823
Rikenellaceae depletion in AS rat gut
an AS human-gut microbiome interaction that shows an expansion of Campylobacter in patients with AS compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/25417597/
expansion of Campylobacter in AS human gut
a SLE human-gut microbiome interaction that shows an expansion of Eubacterium in patients with SLE compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/27980687/
expansion of Eubacterium in SLE human gut
a SLE human-gut microbiome interaction that shows an expansion of Flavonifractor in patients with SLE compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/27980687/
expansion of Flavonifractor in SLE human gut
a SLE human-gut microbiome interaction that shows an expansion of Rhodococcus in patients with SLE compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/27980687/
expansion of Rhodococcus in SLE human gut
a RA human oral cavity microbiome interaction that shows an expansion of rare taxa,Atopobium sp. in patients with RA compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/26214836
expansion of Atopobium sp. in RA human oral cavity
a SLE human-gut microbiome interaction that shows an expansion of Eggerthella in patients with SLE compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/27980687/
expansion of Eggerthella in SLE human gut
a SLE human oral cavity microbiome interaction that shows an decrease of Prevotella pleuritidis in patients with SLE compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/?term=28320468
depletion of Prevotella pleuritidis in SLE human oral cavity
a SLE human oral cavity microbiome interaction that shows an decrease of Pseudomonas sp. in patients with SLE compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/?term=28320468
depletion of Pseudomonas sp. in SLE human oral cavity
a SLE human oral cavity microbiome interaction that shows an decrease of Treponema maltophilum in patients with SLE compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/?term=28320468
depletion of Treponema maltophilum in SLE human oral cavity
a SLE human oral cavity microbiome interaction that shows an decrease of Capnocytophaga gingivalis in patients with SLE compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/?term=28320468
depletion of Capnocytophaga gingivalis in SLE human oral cavity
a SLE human oral cavity microbiome interaction that shows an decrease of Streptococcus sanguinis in patients with SLE compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/?term=28320468
depletion of Streptococcus sanguinis in SLE human oral cavity
a SLE human oral cavity microbiome interaction that shows a depletion of Haemophilus parainfluenzae in patients with SLE compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/?term=28320468
depletion of Haemophilus parainfluenzae in SLE human oral cavity
a SLE human oral cavity microbiome interaction that shows an expansion of Prevotella oulorum in patients with SLE compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/28320468
expansion of Prevotella oulorum in SLE human oral cavity
a SLE human oral cavity microbiome interaction that shows an expansion of Fretibacterium fastidiosum in patients with SLE compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/28320468/
expansion of Fretibacterium fastidiosum in SLE human oral cavity
a SLE human oral cavity microbiome interaction that shows an expansion of Fusobacterium in patients with SLE compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/28320468
expansion of Fusobacterium in SLE human oral cavity
a SLE human oral cavity microbiome interaction that shows an expansion of Selenomonas in patients with SLE compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/28320468/
expansion of Selenomonas in SLE human oral cavity
a SLE human oral cavity microbiome interaction that shows an expansion of Treponema in patients with SLE compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/28320468/
expansion of Treponema in SLE human oral cavity
a Gout human-gut microbiome interaction that shows an expansion of Chloroflexi in patients with gout compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/28270806/
expansion of Chloroflexi in gout human gut
a Gout human-gut microbiome interaction that shows an expansion of Anaerolineae in patients with gout compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/28270806/
expansion of Anaerolineae in gout human gut
a Gout human-gut microbiome interaction that shows an expansion of Anaerolineales in patients with gout compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/28270806/
expansion of Anaerolineales in gout human gut
a Gout human-gut microbiome interaction that shows an expansion of Anaerolineaceae in patients with gout compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/28270806/
expansion of Anaerolineaceae in gout human gut
a Gout human-gut microbiome interaction that shows an expansion of Corynebacteriales in patients with gout compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/28270806/
expansion of Corynebacteriales in gout human gut
a Gout human-gut microbiome interaction that shows an expansion of Nocardiaceae in patients with gout compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/28270806/
expansion of Nocardiaceae in gout human gut
a Gout human-gut microbiome interaction that shows an expansion of Rhodococcus in patients with gout compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/28270806/
expansion of Rhodococcus in gout human gut
a Gout human-gut microbiome interaction that shows an expansion of Selenomonadales in patients with gout compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/28270806/
expansion of Selenomonadales in gout human gut
An association of rattus gut microbiota with arthritis that shows an expansion of Desulfovibrionaceae in rattus with arthritis compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/27481047/
expansion of Desulfovibrionaceae in arthritis rat gut
A human gut-microbiome interaction that is associated with juvenile rheumatoid arthritis (ERA).
Haihe Wang, Hong Yu, Yongqun He
ERA human-gut microbiome interaction
an ERA human-gut microbiome interaction that shows an expansion of Bacteroidaceae in patients with ERA compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/27861762
expansion of Bacteroidaceae in ERA human gut
an ERA human-gut microbiome interaction that shows an expansion of Enterobacteriaceae in patients with ERA compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/27861762
expansion of Enterobacteriaceae in ERA human gut
an ERA human-gut microbiome interaction that shows an expansion of Enterococcaceae in patients with ERA compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/27861762
expansion of Enterococcaceae in ERA human gut
an ERA human-gut microbiome interaction that shows an expansion of Bacteroides in patients with ERA compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/?term=25434931
https://www.ncbi.nlm.nih.gov/pubmed/?term=27861762
expansion of Bacteroides in ERA human gut
an ERA human-gut microbiome interaction that shows an expansion of Enterococcus in patients with ERA compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/27861762
expansion of Enterococcus in ERA human gut
an ERA human-gut microbiome interaction that shows an expansion of Klebsiella in patients with ERA compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/27861762
expansion of Klebsiella in ERA human gut
an ERA human-gut microbiome interaction that shows an expansion of Prevotella in patients with ERA compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/27861762
expansion of Prevotella in ERA human gut
an ERA human-gut microbiome interaction that shows an expansion of Badula fragilis in patients with ERA compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/27861762
expansion of Badula fragilis in ERA human gut
an ERA human-gut microbiome interaction that shows an expansion of Bacteroides plebeius in patients with ERA compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/27861762
expansion of Bacteroides plebeius in ERA human gut
an ERA human-gut microbiome interaction that shows an decrease of Prevotellaceae in patients with ERA compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/?term=27861762
depletion of Prevotellaceae in ERA human gut
an ERA human-gut microbiome interaction that shows an decrease of Prevotella copri in patients with ERA compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/?term=27861762
depletion of Prevotella copri in ERA human gut
an ERA human-gut microbiome interaction that shows an expansion of Salmonella in patients with ERA compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/21679096
expansion of Salmonella in ERA human gut
an ERA human-gut microbiome interaction that shows an decrease of Prevotella stercorea in patients with ERA compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/?term=27861762
depletion of Prevotella in ERA human gut
an ERA human-gut microbiome interaction that shows an decrease of Faecalibacterium prausnitzii in patients with ERA compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/?term=25434931
depletion of Faecalibacterium prausnitzii in ERA human gut
an ERA human-gut microbiome interaction that shows an decrease of Lachnospiraceae in patients with ERA compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/?term=25434931
depletion of Lachnospiraceae in ERA human gut
an ERA human-gut microbiome interaction that shows an decrease of [Clostridium] clostridioforme in patients with ERA compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/?term=25434931
depletion of [Clostridium] clostridioforme in ERA human gut
an ERA human-gut microbiome interaction that shows an expansion of Bifidobacterium in patients with ERA compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/25434931
expansion of Bifidobacterium in ERA human gut
an ERA human-gut microbiome interaction that shows an expansion of Akkermansia muciniphila in patients with ERA compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/25434931
expansion of Akkermansia muciniphila in ERA human gut
a PsA human-gut microbiome interaction that shows an decrease of Coprococcus in patients with PsA compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/?term=25319745
depletion of Coprococcus in PsA human gut
A colorectal cancer human-gut microbiome interaction where Parvimonas micra is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/26408641
https://www.ncbi.nlm.nih.gov/pubmed/28912574
expansion of P. micra in colorectal cancer human gut
a PsA human-gut microbiome interaction that shows an expansion of Diutina rugosa in patients with PsA compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/11413927/
expansion of Diutina rugosa in PsA human gut
a PsA human skin microbiome interaction that shows an expansion of Malassezia furfur in patients with PsA compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/14675283/
expansion of Malassezia furfur in PsA human skin
an ERA human-gut microbiome interaction that shows an expansion of Yersinia in patients with ERA compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/21679096
expansion of Yersinia in ERA human gut
A rattus gut-microbiome interaction that is associated with reactive arthritis'.
Haihe Wang, Hong Yu, Yongqun He
reactive arthritis rat-gut microbiome interaction
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.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/7768612/
expansion of Yersinia in reactive arthritis rat gut
An association of rattus gut microbiota with reactive arthritis that shows an expansion of Salmonella in rattus with reactive arthritis compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/7768612/
expansion of Salmonella in reactive arthritis rat gut
A colorectal cancer human-gut microbiome interaction where Solobacterium moorei is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/26408641
expansion of S. moorei in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Fusobacteria is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/26408641
https://www.ncbi.nlm.nih.gov/pubmed/28483840
https://www.ncbi.nlm.nih.gov/pubmed/28827587
https://www.ncbi.nlm.nih.gov/pubmed/28912574
expansion of Fusobacteria in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Basidiomycota is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/26408641
expansion of Basidiomycota in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Parvimonas is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/25758642
https://www.ncbi.nlm.nih.gov/pubmed/26408641
expansion of Parvimonas in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Peptostreptococcus is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/26408641
expansion of Peptostreptococcusi in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Fusobacterium is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/26170900
https://www.ncbi.nlm.nih.gov/pubmed/26408641
https://www.ncbi.nlm.nih.gov/pubmed/18644884
https://www.ncbi.nlm.nih.gov/pubmed/24316595
https://www.ncbi.nlm.nih.gov/pubmed/25104642
https://www.ncbi.nlm.nih.gov/pubmed/25439270
https://www.ncbi.nlm.nih.gov/pubmed/25758642
expansion of Fusobacterium in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Beggiatoa is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/26408641
expansion of Beggiatoa in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Malassezia is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/26408641
expansion of Malassezia in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Leptotrichia is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/26408641
expansion of Leptotrichia in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Filifactor is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/26408641
expansion of Filifactor in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Crenothrix is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/26408641
expansion of Crenothrix in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Solobacterium is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/26408641
expansion of Solobacterium in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Sulfurovum is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/26408641
expansion of Sulfurovum in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Streptobacillus is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/26408641
expansion of Streptobacillus in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Moniliophthora is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/26408641
expansion of Moniliophthora in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Slackia is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/ 21647227
expansion of Slackia in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Collinsella is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/ 21647227
expansion of Collinsella in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Clostridiaceae is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/ 21647227
expansion of Clostridiaceae in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Bacteroidales is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/ 21647227
expansion of Bacteroidales in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Cronobacter is decreased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/21647227
depletion of Cronobacter in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Kluyvera is decreased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/21647227
depletion of Kluyvera in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Serratia is decreased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/21647227
depletion of Serratia in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Salmonella enterica subsp. enterica is decreased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/21647227
depletion of Salmonella enterica subsp. enterica in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Eubacteriaceae is decreased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/21647227
depletion of Eubacteriaceae in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Anaerovorax is decreased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/21647227
depletion of Anaerovorax in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Microbacterium is decreased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/21647227
https://www.ncbi.nlm.nih.gov/pubmed/23497613
depletion of Microbacterium in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Bacteroides finegoldii is decreased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/23940645
depletion of B. finegoldii in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Bacteroides intestinalis is decreased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/23940645
depletion of B.intestinalis in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Prevotella copri is decreased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/23940645
depletion of P.copri in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Prevotella oris is decreased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/23940645
depletion of P. oris in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Dorea formicigenerans is decreased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/23940645
depletion of D.formicigenerans in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Lachnobacterium bovis is decreased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/23940645
depletion of L. bovis in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Lachnospira pectinoschiza is decreased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/23940645
depletion of L.pectinoschiza in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Pseudobutyrivibrio ruminis is decreased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/23940645
depletion of P.ruminis in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Ruminococcus albus is decreased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/23940645
depletion of R.albus in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Dialister invisus is decreased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/23940645
depletion of D. invisus in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Dialister pneumosintes is decreased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/23940645
depletion of D. pneumosintes in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Megamonas hypermegale is decreased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/23940645
depletion of M. hypermegale in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Acidaminobacter is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/ 23940645
expansion of Acidaminobacter in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Phascolarctobacterium is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/ 23940645
expansion of Phascolarctobacterium in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Citrobacter farmeri is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/ 23940645
expansion of C.farmeri in colorectal cancer human gut
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.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/9456020
expansion of Bacteroides fragilis in RA human gut
A colorectal cancer human-gut microbiome interaction where Roseburia is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/21647227
https://www.ncbi.nlm.nih.gov/pubmed/23497613
https://www.ncbi.nlm.nih.gov/pubmed/23733170
expansion of Roseburia in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Anoxybacillus is decreased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/23497613
depletion of Anoxybacillus in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Bacteroides is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/24194538
https://www.ncbi.nlm.nih.gov/pubmed/24967088
https://www.ncbi.nlm.nih.gov/pubmed/25439270
https://www.ncbi.nlm.nih.gov/pubmed/25758642
expansion of Bacteroides in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Odoribacter is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/24194538
expansion of Odoribacter in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Akkermansia muciniphila is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/23940645
https://www.ncbi.nlm.nih.gov/pubmed/24194538
https://www.ncbi.nlm.nih.gov/pubmed/24967088
expansion of A. muciniphila in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Prevotellaceae is decreased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/24194538
depletion of Prevotellaceae in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Porphyromonadaceae is decreased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/24194538
depletion of Porphyromonadaceae in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Clostridiaceae is decreased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/24316595
depletion of Clostridiaceae in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Parabacteroides is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/24967088
https://www.ncbi.nlm.nih.gov/pubmed/25758642
expansion of Parabacteroides in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where ParaAlistipes is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/24967088
expansion of Alistipes in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Bacteroides ovatus is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/24967088
expansion of B. ovatus in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Bacteroides xylanisolvens is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/24967088
expansion of B. xylanisolvens in colorectal cancer human gut
An interaction between human and urine microbiome.
YH
human-urine microbiome interaction
A human urine-microbiome interaction that is associated with rheumatoid arthritis (RA).
YH
RA human-urine microbiome interaction
A colorectal cancer human-gut microbiome interaction where Lachnospiraceae is decreased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/22761885
https://www.ncbi.nlm.nih.gov/pubmed/23397545
https://www.ncbi.nlm.nih.gov/pubmed/25439270
https://www.ncbi.nlm.nih.gov/pubmed/24967088
https://www.ncbi.nlm.nih.gov/pubmed/25104642
https://www.ncbi.nlm.nih.gov/pubmed/26170900
depletion of Lachnospiraceae in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Enterobacteriaceae is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/25104642
expansion of Enterobacteriaceae in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Lactobacillus acidophilus is decreased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/25439270
depletion of L. acidophilus in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Bacteroides is decreased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/25104642
'depletion of Bacteroides in colorectal cancer human gut'
A colorectal cancer human-gut microbiome interaction where Clostridiales is decreased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/24967088
https://www.ncbi.nlm.nih.gov/pubmed/25104642
depletion of Clostridiales in colorectal cancer human gut
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.
YH
http://microbiomedb.org/mbio/app/
expansion of unclassified Proteobacteria in diarrheal patient gut
A colorectal cancer human-gut microbiome interaction where Firmicutes is decreased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/26170900
https://www.ncbi.nlm.nih.gov/pubmed/28912574
depletion of Firmicutes in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Bacteroidetes is decreased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/26170900
depletion of Bacteroidetes in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Bacteroidales is decreased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/26170900
depletion of Bacteroidales in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Rikenellaceae is decreased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/26170900
depletion of Rikenellaceae in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Bacteroides uniformis is decreased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/26170900
depletion of B. uniformis in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Providencia is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/26170900
expansion of Providencia in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Bacteroidaceae is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/ 22761885
https://www.ncbi.nlm.nih.gov/pubmed/ 23397545
https://www.ncbi.nlm.nih.gov/pubmed/25439270
expansion of Bacteroidaceae in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Streptococcaceae is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/ 22761885
https://www.ncbi.nlm.nih.gov/pubmed/ 23397545
https://www.ncbi.nlm.nih.gov/pubmed/25439270
expansion of Streptococcaceae in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Fusobacteriaceae is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/ 22761885
https://www.ncbi.nlm.nih.gov/pubmed/ 23397545
https://www.ncbi.nlm.nih.gov/pubmed/25439270
expansion of Fusobacteriaceae in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Peptostreptococcaceae is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/21647227
https://www.ncbi.nlm.nih.gov/pubmed/22761885
https://www.ncbi.nlm.nih.gov/pubmed/23397545
https://www.ncbi.nlm.nih.gov/pubmed/25439270
expansion of Peptostreptococcaceae in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Veillonellaceae is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/ 22761885
https://www.ncbi.nlm.nih.gov/pubmed/ 23397545
https://www.ncbi.nlm.nih.gov/pubmed/25439270
expansion of Veillonellaceae in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Pasteurellaceae is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/ 22761885
https://www.ncbi.nlm.nih.gov/pubmed/ 23397545
https://www.ncbi.nlm.nih.gov/pubmed/25439270
expansion of Pasteurellaceae in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Porphyromonas is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/24316595
https://www.ncbi.nlm.nih.gov/pubmed/25104642
https://www.ncbi.nlm.nih.gov/pubmed/22761885
https://www.ncbi.nlm.nih.gov/pubmed/23397545
https://www.ncbi.nlm.nih.gov/pubmed/25439270
expansion of Porphyromonas in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Mogibacterium is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/ 22761885
https://www.ncbi.nlm.nih.gov/pubmed/ 23397545
https://www.ncbi.nlm.nih.gov/pubmed/25439270
expansion of Mogibacterium in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Erysipelotrichaceae is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/21647227
https://www.ncbi.nlm.nih.gov/pubmed/22761885
https://www.ncbi.nlm.nih.gov/pubmed/23397545
https://www.ncbi.nlm.nih.gov/pubmed/25439270
expansion of Erysipelotrichaceae in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Prevotellaceae is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/ 22761885
https://www.ncbi.nlm.nih.gov/pubmed/ 23397545
https://www.ncbi.nlm.nih.gov/pubmed/25439270
expansion of Prevotellaceae in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Coriobacteriaceae is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/ 22761885
https://www.ncbi.nlm.nih.gov/pubmed/ 23397545
https://www.ncbi.nlm.nih.gov/pubmed/25439270
expansion of Coriobacteriaceae in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Ruminococcaceae is decreased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/26170900
https://www.ncbi.nlm.nih.gov/pubmed/22761885
https://www.ncbi.nlm.nih.gov/pubmed/23397545
https://www.ncbi.nlm.nih.gov/pubmed/25439270
depletion of Ruminococcaceae in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Lactobacillaceae is decreased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/ 23397545
https://www.ncbi.nlm.nih.gov/pubmed/22761885
https://www.ncbi.nlm.nih.gov/pubmed/25439270
depletion of Lactobacillaceae in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Bifidobacterium longum is decreased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/22761885
https://www.ncbi.nlm.nih.gov/pubmed/23397545
https://www.ncbi.nlm.nih.gov/pubmed/25439270
depletion of B. longum in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Faecalibacterium prausnitzii is decreased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/22009989
https://www.ncbi.nlm.nih.gov/pubmed/24021287
https://www.ncbi.nlm.nih.gov/pubmed/26170900
https://www.ncbi.nlm.nih.gov/pubmed/22761885
https://www.ncbi.nlm.nih.gov/pubmed/23397545
https://www.ncbi.nlm.nih.gov/pubmed/25439270
depletion of F. prausnitzii in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Blautia is decreased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/ 23397545
https://www.ncbi.nlm.nih.gov/pubmed/22761885
https://www.ncbi.nlm.nih.gov/pubmed/25439270
depletion of Blautia in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Lactobacillus rhamnosus is decreased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/25439270
depletion of L. rhamnosus in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Lactobacillus reuteri is decreased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/25439270
'depletion of L. reuteri in colorectal cancer human gut'
a RA human-urine microbiome interaction that shows an expansion of Proteus mirabilis in patients with RA compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/9032817
expansion of Proteus mirabilis in RA human urine
A colorectal cancer human-gut microbiome interaction where Alistipes putredinis is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/25758642
expansion of A. putredinis in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Lachnospiraceae bacterium is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/25758642
expansion of L. bacterium in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Escherichia coli NC101 is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/22903521
https://www.ncbi.nlm.nih.gov/pubmed/25758642
expansion of E. coli NC101 in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Bilophila wadsworthia is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/22009989
https://www.ncbi.nlm.nih.gov/pubmed/25758642
https://www.ncbi.nlm.nih.gov/pubmed/26073561
expansion of B. wadsworthia in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Bifidobacterium animalis is decreased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/25758642
depletion of B. animalis in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Streptococcus thermophilus is decreased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/25758642
depletion of S. thermophilus in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Ruminococcus is decreased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/25758642
depletion of Ruminococcus in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Bifidobacterium is decreased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/25758642
depletion of Bifidobacterium in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Streptococcus is decreased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/25758642
depletion of Streptococcus in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Escherichia is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/25758642
expansion of Escherichia in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Bilophila is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/25758642
expansion of Bilophila in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Bacteroidetes is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/22009989
https://www.ncbi.nlm.nih.gov/pubmed/26073561
expansion of Bacteroidetes in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Streptococcus equinus is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/25439270
https://www.ncbi.nlm.nih.gov/pubmed/19226366
https://www.ncbi.nlm.nih.gov/pubmed/26073561
https://www.ncbi.nlm.nih.gov/pubmed/484953
https://www.ncbi.nlm.nih.gov/pubmed/9282212
expansion of S. equinus in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Enterococcaceae is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/18644884
https://www.ncbi.nlm.nih.gov/pubmed/22009989
https://www.ncbi.nlm.nih.gov/pubmed/23954159
https://www.ncbi.nlm.nih.gov/pubmed/9282212
expansion of Enterococcaceae in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Campylobacter is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/18644884
https://www.ncbi.nlm.nih.gov/pubmed/22009989
https://www.ncbi.nlm.nih.gov/pubmed/23954159
https://www.ncbi.nlm.nih.gov/pubmed/9282212
expansion of Campylobacter in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Salmonella is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/22009989
expansion of Salmonella in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Shigella is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/22009989
expansion of Shigella in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Bifidobacterium animalis subsp. lactis is decreased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/15542102
https://www.ncbi.nlm.nih.gov/pubmed/22009989
depletion of B. animalis subsp. lactis in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Chlamydia is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/22009989
https://www.ncbi.nlm.nih.gov/pubmed/22687960
https://www.ncbi.nlm.nih.gov/pubmed/22687961
expansion of Chlamydia in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Mycobacterium is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/22009989
https://www.ncbi.nlm.nih.gov/pubmed/22687960
https://www.ncbi.nlm.nih.gov/pubmed/22687961
expansion of Mycobacterium in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Clostridia is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/25439270
https://www.ncbi.nlm.nih.gov/pubmed/22009989
https://www.ncbi.nlm.nih.gov/pubmed/22687960
https://www.ncbi.nlm.nih.gov/pubmed/22687961
expansion of Clostridia in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Candidatus Portiera is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/26170900
https://www.ncbi.nlm.nih.gov/pubmed/22009989
https://www.ncbi.nlm.nih.gov/pubmed/22687960
https://www.ncbi.nlm.nih.gov/pubmed/22687961
expansion of C. Portiera in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Proteus mirabilis is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/22009989
https://www.ncbi.nlm.nih.gov/pubmed/22687960
https://www.ncbi.nlm.nih.gov/pubmed/22687961
expansion of P. mirabilis in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Klebsiella pneumoniae is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/22009989
https://www.ncbi.nlm.nih.gov/pubmed/22687960
https://www.ncbi.nlm.nih.gov/pubmed/22687961
expansion of K. pneumoniae in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction whereProteobacteria is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/25439270
https://www.ncbi.nlm.nih.gov/pubmed/26170900
https://www.ncbi.nlm.nih.gov/pubmed/28827587
https://www.ncbi.nlm.nih.gov/pubmed/20740058
https://www.ncbi.nlm.nih.gov/pubmed/22009989
https://www.ncbi.nlm.nih.gov/pubmed/22687960
https://www.ncbi.nlm.nih.gov/pubmed/22687961
expansion of Proteobacteria in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Helicobacter is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/22009989
https://www.ncbi.nlm.nih.gov/pubmed/22687960
https://www.ncbi.nlm.nih.gov/pubmed/22687961
https://www.ncbi.nlm.nih.gov/pubmed/28982615
expansion of Helicobacter in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Roseburia hominis is decreased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/22009989
https://www.ncbi.nlm.nih.gov/pubmed/24021287
depletion of R. hominis in colorectal cancer human gut
a RA human-gut microbiome interaction that shows an decrease of Blautia coccoides in patients with RA compared with fibromyalgia patients.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/18528968
depletion of Blautia coccoides in RA human gut compared to fibromyalgia patients
A colorectal cancer human-gut microbiome interaction where Helicobacter pylori is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/24164483
https://www.ncbi.nlm.nih.gov/pubmed/25834331
https://www.ncbi.nlm.nih.gov/pubmed/28982615
expansion of H. pylori in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Helicobacter hepaticus is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/20944559
https://www.ncbi.nlm.nih.gov/pubmed/28982615
expansion of H. hepaticus in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Fusobacterium nucleatum is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/22009990
https://www.ncbi.nlm.nih.gov/pubmed/26408641
https://www.ncbi.nlm.nih.gov/pubmed/28465070
https://www.ncbi.nlm.nih.gov/pubmed/28483840
https://www.ncbi.nlm.nih.gov/pubmed/28912574
https://www.ncbi.nlm.nih.gov/pubmed/23335968
https://www.ncbi.nlm.nih.gov/pubmed/24385213
https://www.ncbi.nlm.nih.gov/pubmed/25751261
https://www.ncbi.nlm.nih.gov/pubmed/27130618
https://www.ncbi.nlm.nih.gov/pubmed/28982615
expansion of F. nucleatum in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Peptostreptococcus anaerobius is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/28126350
expansion of P. anaerobius in colorectal cancer human gut
a RA human-gut microbiome interaction that shows an decrease of Bacteroides in patients with RA compared with fibromyalgia patients.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/18528968
depletion of Bacteroides in RA human gut compared to fibromyalgia patients
A colorectal cancer human-gut microbiome interaction where Fusobacterium hwasookii is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/28912574
expansion of F. hwasookii in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Porphyromonas gingivalis is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/28912574
expansion of P. gingivalis in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Selenomonas is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/28912574
expansion of Selenomonas in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Prevotella is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/28912574
expansion of Prevotella in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Peptostreptococcus stomatis is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/28912574
expansion of P. stomatis in colorectal cancer human gut
a RA human-gut microbiome interaction that shows an decrease of Bacteroides fragilis in patients with RA compared with fibromyalgia patients.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/18528968
depletion of Bacteroides fragilis in RA human gut compared to fibromyalgia patients
A colorectal cancer human-gut microbiome interaction where Solobacterium sp. S4-A19 is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/28827587
expansion of Solobacterium sp. S4-A19 in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Dolosicoccus paucivorans is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/28827587
expansion of D. paucivorans in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Clostridium sp. cp01.19 is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/28827587
expansion of Clostridium sp. cp01.19 in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Bacteroides sp. is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/28827587
expansion of Bacteroides sp. in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Subdoligranulum sp. 60_17 is decreased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/28827587
depletion of Subdoligranulum sp. 60_17 in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Mycobacterium avium is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/17445316
https://www.ncbi.nlm.nih.gov/pubmed/24334760
https://www.ncbi.nlm.nih.gov/pubmed/28465070
expansion of M. avium in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Escherichia coli B is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/16902142
https://www.ncbi.nlm.nih.gov/pubmed/24334760
https://www.ncbi.nlm.nih.gov/pubmed/27810411
expansion of E. coli B in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Aggregatibacter actinomycetemcomitans is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/22998585
https://www.ncbi.nlm.nih.gov/pubmed/27810411
expansion of A. actinomycetemcomitans in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where [Haemophilus] ducreyi is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/22998585
https://www.ncbi.nlm.nih.gov/pubmed/27810411
expansion of H. ducreyi in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Shigella dysenteriae is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/22998585
https://www.ncbi.nlm.nih.gov/pubmed/27810411
expansion of S. dysenteriae in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Campylobacter jejuni is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/22998585
https://www.ncbi.nlm.nih.gov/pubmed/27810411
expansion of Campylobacter jejuni in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Salmonella enterica is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/22998585
https://www.ncbi.nlm.nih.gov/pubmed/27810411
expansion of S. enterica in colorectal cancer human gut
a RA human-gut microbiome interaction that shows an decrease of Bifidobacterium bifidum in patients with RA compared with fibromyalgia patients.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/18528968
depletion of Bifidobacterium bifidum in RA human gut compared to fibromyalgia patients
A colorectal cancer human-gut microbiome interaction where Pseudomonas is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/22622349
expansion of Pseudomonas in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Acinetobacter is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/24855012
expansion of Acinetobacter in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Blautia obeum is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/20629751
expansion of B.obeum in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Catenisphaera adipataccumulans is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/20629751
expansion of C. adipataccumulans in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Microbacterium is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/23733170
expansion of Microbacterium in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Anoxybacillus is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/23733170
expansion of Anoxybacillus in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Citrobacter rodentium is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/11424022
https://www.ncbi.nlm.nih.gov/pubmed/28951889
expansion of C. rodentium in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Enterococcus faecalis is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/11722738
https://www.ncbi.nlm.nih.gov/pubmed/11895869
https://www.ncbi.nlm.nih.gov/pubmed/12208369
https://www.ncbi.nlm.nih.gov/pubmed/15825073
https://www.ncbi.nlm.nih.gov/pubmed/17258726
https://www.ncbi.nlm.nih.gov/pubmed/19047172
expansion of E. faecalis in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where [Clostridium] scindens is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/16299351
https://www.ncbi.nlm.nih.gov/pubmed/21267546
expansion of C. scindens in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where [Clostridium] hiranonis is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/16299351
https://www.ncbi.nlm.nih.gov/pubmed/21267546
expansion of C. hiranonis in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where [Clostridium] hylemonae is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/16299351
https://www.ncbi.nlm.nih.gov/pubmed/21267546
expansion of C.hylemonae in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Acidovorax is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/16299351
https://www.ncbi.nlm.nih.gov/pubmed/21267546
expansion of Acidovorax in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Streptococcus gallolyticus is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/20846456
https://www.ncbi.nlm.nih.gov/pubmed/24911876
expansion of S. gallolyticus in colorectal cancer human gut
a RA human gut microbiome interaction that shows an decrease of Haemophilus sp in patients with RA compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/?term=26214836
depletion of Haemophilus spp. in RA human gut
A colorectal cancer human-gut microbiome interaction where Fusobacterium nucleatum subsp. nucleatum is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/27607555
https://www.ncbi.nlm.nih.gov/pubmed/28483840
expansion of F. nucleatum subsp. nucleatum in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Fusobacterium nucleatum subsp. polymorphum is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/27607555
https://www.ncbi.nlm.nih.gov/pubmed/28483840
expansion of F. nucleatum subsp. polymorphum in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Fusobacterium nucleatum subsp. vincentii is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/27607555
https://www.ncbi.nlm.nih.gov/pubmed/28483840
expansion of F. nucleatum subsp. vincentii in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Fusobacterium nucleatum subsp. animalis is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/27607555
https://www.ncbi.nlm.nih.gov/pubmed/28483840
expansion of F. nucleatum subsp. animalis in colorectal cancer human gut
a RA human-gut microbiome interaction that shows an expansion of Bacteroides sp in patients with RA compared with healthy controls.
Haihe Wang, Hong Yu, Yongqun He
https://www.ncbi.nlm.nih.gov/pubmed/26214836
expansion of Bacteroides sp. in RA human gut
A RA human-gut microbiome interaction where Lachnospiraceae bacterium is increased.
YH, HW
https://www.ncbi.nlm.nih.gov/pubmed/26214836
expansion of Lachnospiraceae bacterium in RA human gut
An organism or virus or viron that is too small to be viewed by the unaided eye.
Oliver He, Jie Zheng
microbe
OH
https://en.wikipedia.org/wiki/Dysbiosis
An abnormal phenotype that has a microbial imbalance or maladaption on or inside the body.
dysbiosis
A physical object quality that is inhered in a material entity that is too small to be viewed by the unaided eye.
Jie Zheng, Oliver He
invisible to unaided eye
2
A collection of microbial organisms that reside in a particular environment.
Jie Zheng, Oliver He, Anna Maria Masci, Jihad Obeid
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4520061/
microbiota
A measurement datum that is a logarithmic scale used to specify the acidity or basicity of an aqueous solution. It is the negative of the base 10 logarithm of the activity of the hydrogen ion. At 25 °C, solutions with a pH less than 7 are acidic and solutions with a pH greater than 7 are basic.
OH
https://en.wikipedia.org/wiki/PH
pH value
A drug product that has its ability to alter the progression of a rheumatic disease.
Oliver He
disease-modifying antirheumatic drug
https://en.wikipedia.org/wiki/Disease-modifying_antirheumatic_drug
DMARD
A community species diversity that exists in a microbiome ecosystem where different microbial species are found.
microbial species diversity
A quality of ecological community that refers to how common or rare a species is relative to other species in a defined location or community
relative species abundance
A relative species abundance that refers to the microbial species abundance in a host ecosystem
Oliver He
relative abundance of microbe in host
A genome from a microbe
microbial genome
the mean species diversity in sites or habitats at a local scale
α-diversity
https://en.wikipedia.org/wiki/Alpha_diversity
alpha diversity
the ratio between regional and local species diversity
true beta diversity
β-diversity
https://en.wikipedia.org/wiki/Beta_diversity
beta diversity
the total species diversity in a landscape
γ-diversity
https://en.wikipedia.org/wiki/Gamma_diversity
gamma diversity
A biological process that leads to the restoration of microbial community in a host organism
Oliver He
host microbiome restoration
A host microbiome restoration that is due to a treatment
Oliver He
host microbiome restoration by treatment
host microbiome restoration by a DMARD treatment
Oliver He
host microbiome restoration by DMARD
host microbiome restoration by an antibiotics treatment
Oliver He
host microbiome restoration by antibiotics
host microbiome restoration through the transplantation of a microbiota into the host
Oliver He
host microbiome restoration by microbiota transplantation
A microbe that is differentially enriched in a microbiome host and can serve as a marker for a dysbiosis
Oliver He
differentially enriched microbial marker for dysbiosis
A microbe that is differentially enriched in a microbiome host and can serve as a marker for a disease
Oliver He
differentially enriched microbial marker for disease
An host-microbiome interaction that involves the interaction between enteric microbiota on the host and the host brain (esp. the central nervous system), which often leads to a specific nervous phenotype
Oliver He, Kaiyong Liu
microbiome-gut-brain axis
https://www.ncbi.nlm.nih.gov/pubmed/21303428
microbiome-gut-brain interaction
An host-microbiome interaction that is associated with cancer
Oliver He, Jianmin Wu
microbiome-cancer interaction
An interaction between microbiome and host immune system that is associated with cancer
Oliver He, Jianmin Wu
microbiome-immune-cancer axis
https://www.hindawi.com/journals/mi/2019/4107917/
microbiome-immune-cancer interaction
An organism that has 'host role', i.e., a role played by an organism and realized by providing nourishment, shelter or a means of reproduction to another organism.
Oliver He
host
A time quality inhering in a bearer by virtue of how long the bearer has existed.
quality
PATO:0000011
age
An organismal quality inhering in a bearer by virtue of the bearer's ability to undergo sexual reproduction in order to differentiate the individuals or types involved.
quality
PATO:0000047
biological sex
A quality which inheres in a continuant.
PATO:0001237
PATO:0001238
snap:Quality
monadic quality of a continuant
multiply inhering quality of a physical entity
quality of a continuant
quality of a single physical entity
quality of an object
quality of continuant
monadic quality of an object
monadic quality of continuant
quality
PATO:0001241
Relational qualities are qualities that hold between multiple entities. Normal (monadic) qualities such as the shape of a eyeball exist purely as a quality of that eyeball. A relational quality such as sensitivity to light is a quality of that eyeball (and connecting nervous system) as it relates to incoming light waves/particles.
physical object quality
A quality that inheres in an entire organism or part of an organism.
quality
PATO:0001995
organismal quality
A quality that inheres in an entire population or part of a population.
quality
PATO:0002003
population quality
Examples include: population, community, species (meaning the collection of organisms that makes up a species, not the taxonomic rank), and family.
A material entity that consists of two or more organisms, viruses, or viroids.
A material entity that consists of two or more organisms, viruses, or viroids.
group of organism
organism collection
May be of the same or different species.
collection of organisms
collection of organisms
A quality that inheres in a community.
These may not belong under BFO:quality. May be better to call them community characteristics, and classify as specifically dependent continuants. Need to look at process profiles in BFO2.
Includes qualities like diversity, species richness, stability, resilience, community structure, number of trophic levels. A community quality may depend on the qualities of individual organism in the community, but cannot be measured or described for a single individual.
quality of an ecological community
The number of different species represented in an ecological community.
This is a quality of an ecological community (PCO_0000002). If your metric includes the abundances of species (evenness) as well as the number, you should use community species diversity (PCO_0000019).
adapted from http://en.wikipedia.org/wiki/Species_richness
community species richness
The number of different species that are represented in a given community, weighted by their abundance. Community species diversity can be calculated in different ways, but consists of two components: species richness and species evenness.
If your metric does not include the abundances of different species, but rather just the numer of species, you should use community species richness (PCO_0000010). More specific subclasses or instances of this class may be created to describe specific ways of measuring diversity.
adapted from http://en.wikipedia.org/wiki/Species_diversity
The Shannon Index and Simpson Index are examples of ways in which species diversity is quantified.
community species diversity
If there are 40 foxes, and 1000 dogs, the community is not very even, but if there are 40 foxes and 42 dogs, the community is quite even.
A quality of a community that reflects how close in abundance all species in a community are.
adapted from http://en.wikipedia.org/wiki/Species_evenness
community species evenness
protein
antithrombin III is a protein
An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA.
protein
PR:000000001
Proteins descended from a common ancestor can be classified into families and superfamilies composed of products of evolutionarily-related genes. The domain architecture of a protein is described by the order of its constituent domains. Proteins with the same domains in the same order are defined as homeomorphic [PRO:WCB].
protein
A material entity consisting of multiple components that are causally integrated.
May be replaced by a BFO class, as discussed in http://www.jbiomedsem.com/content/4/1/43
Chris Mungall
http://www.jbiomedsem.com/content/4/1/43
system
region
A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids.
primary structure of sequence macromolecule
sequence
region
Any portion of the organ that covers that body and consists of a layer of epidermis and a layer of dermis.
Note the distinction between the entire skin of the body, of which there is only 1 in an organism, and zones of skin, of which there can be many. Examples: skin of knee
(...) it is well-established that neural crest cells contribute to both the dermal skeleton (craniofacial bone, teeth, and the caudal fin rays of teleosts) and the integument, including craniofacial dermis and all pigment cells outside the retina (...).[well established][VHOG]
we assume that mouse, HOG and GAID all mean zone of skin when they say skin. We also choose skin as an exact synonym, as it is more intuitive
EHDAA2:0001844
EHDAA:6530
EMAPA:17525
EV:0100152
FMA:86166
GAID:933
MA:0000151
MAT:0000284
MESH:D012867
MIAA:0000284
OpenCyc:Mx4rvVjX3ZwpEbGdrcN5Y29ycA
VHOG:0000860
portion of skin
region of skin
skin
skin region
skin zone
uberon
UBERON:0000014
zone of skin
A subdivision of the digestive tract that connects the small intestine to the cloaca or anus. Lacks or has few villi[Kardong].
Intestinal surface area also is increased in amphibians and reptiles by internal folds and occasionally by a few villi. The intestine can be divided into a small intestine and a slightly wider large intestine.[well established][VHOG]
AAO:0010396
BTO:0000706
CALOHA:TS-1306
EFO:0000840
EMAPA:19252
EV:0100077
FMA:7201
GAID:306
MA:0000333
MESH:A03.492.411.495
MIAA:0000046
NCIT:C12379
OpenCyc:Mx4rvVkF5pwpEbGdrcN5Y29ycA
UMLS:C0021851
VHOG:0000054
XAO:0000131
galen:LargeIntestine
uberon
intestinum crassum
UBERON:0000059
large intestine
Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome.
AAO:0010825
AEO:0000003
BILA:0000003
CARO:0000003
EHDAA2:0003003
EMAPA:0
FBbt:00007001
FMA:305751
FMA:67135
GAID:781
HAO:0000003
MA:0003000
MESH:D000825
TAO:0000037
TGMA:0001823
VHOG:0001759
XAO:0003000
ZFA:0000037
biological structure
connected biological structure
uberon
UBERON:0000061
anatomical structure
Anatomical structure that performs a specific function or group of functions [WP].
Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions.
CARO v1 does not include a generic 'organ' class, only simple and compound organ. CARO v2 may include organ, see https://github.com/obophenotype/caro/issues/4
CARO:0020004
EFO:0000634
EMAPA:35949
ENVO:01000162
FMA:67498
MA:0003001
NCIT:C13018
OpenCyc:Mx4rv5XMb5wpEbGdrcN5Y29ycA
OpenCyc:Mx4rwP3iWpwpEbGdrcN5Y29ycA
UMLS:C0178784
WBbt:0003760
uberon
anatomical unit
body organ
element
UBERON:0000062
organ
A multicellular structure that is a part of an organ.
currently defined in a very broad sense, may be replaced by more specific classes in the future
AAO:0011124
EFO:0000635
FMA:82472
cardinal organ part
uberon
regional part of organ
UBERON:0000064
organ part
Segment of the alimentary canal extending from the stomach to the anus and, in humans and other mammals, consists of two segments, the small intestine and the large intestine.
This class is probably too inclusive
Portion of the alimentary canal bounded anteriorly by the pyloric sphincter and posteriorly by the cloacal sphincter.[AAO]
The tract of the alimentary canal. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
intestinal
In zebrafish, No stomach, small intestine, or large intestine can be distinguished. However, differences can be found in the morphology of the mucosa columnar epithelial cells and the number of goblet cells, suggesting functional differentiation. The intestine has numerous folds that become progressively shorter in a rostral-to-caudal direction. Proportionally, these folds are significantly larger than the finger-like intestinal villi of mammals and other amniotes (Wallace et al. 2005). Columnar-shaped absorptive enterocytes are the most numerous in the zebrafish intestinal epithelium. Goblet cells are the second most populous epithelial cell type.
AAO:0000246
ANISEED:1235303
BSA:0000093
BTO:0000648
CALOHA:TS-0490
EFO:0000834
EMAPA:32874
EV:0100071
FMA:7199
GAID:295
MA:0000328
MA:0001524
MESH:A03.492.411
MIAA:0000043
NCIT:C12736
TAO:0001338
UMLS:C0021853
VHOG:0000056
WBbt:0005772
XAO:0000129
ZFA:0001338
galen:Intestine
bowel
uberon
intestinal tract
UBERON:0000160
intestine
The proximal portion of the digestive tract, containing the oral cavity and bounded by the oral opening. In vertebrates, this extends to the pharynx and includes gums, lips, tongue and parts of the palate. Typically also includes the teeth, except where these occur elsewhere (e.g. pharyngeal jaws) or protrude from the mouth (tusks).
Cavity in which food is initially ingested and generally contains teeth, tongue and glands.[AAO]
Molecular and developmental cell lineage data suggest that the acoel mouth opening is homologous to the mouth of protostomes and deuterostomes and that the last common ancestor of the Bilateria (the 'urbilaterian') had only this single digestive opening.[well established][VHOG]
oral
some AOs place this as developing from the stomodeum but we weaken this to developmental contribution, as the mouth includes non-ectodermal derivatives
in FMA, the tongue, palate etc are part of the mouth which is itself a subdivision of the face. ZFA includes a separate class 'oral region' which is part of the mouth, but excludes tongue and lips
AAO:0010355
BTO:0001090
BTO:0004698
CALOHA:TS-1315
EFO:0000825
EHDAA2:0001326
EHDAA:542
EMAPA:16262
FBbt:00003126
FMA:49184
GAID:75
MA:0000341
MA:0002474
MAT:0000038
MESH:D009055
MIAA:0000038
OpenCyc:Mx4rvVidh5wpEbGdrcN5Y29ycA
TADS:0000040
TAO:0000547
TAO:0000590
TGMA:0000131
VHOG:0000280
VHOG:0000812
XAO:0003029
ZFA:0000547
ZFA:0000590
galen:Mouth
regio oralis
adult mouth
uberon
cavital oralis
cavitas oris
cavum oris
mouth cavity
oral region
oral vestibule
rima oris
stoma
stomatodaeum
trophic apparatus
vestibule of mouth
vestibulum oris
UBERON:0000165
mouth
Anatomical cavity at the start of the digestive tract that that is enclosed by the mouth. The boundaries and contents vary depending on the species. In vertebrates, the boundaries are the oral opening, the cheeks, the palate and (if present) the palatoglossal arch - if this is not present then the mouth and pharynx form the oropharyngeal cavity. The buccal cavity contains the teeth, tongue and palate (when present)
Anatomical cavity bounded anteriorly by the mouth and posteriorly by the derivatives of the branchial arches.[AAO]
The cavity of the mouth, bounded by the jaw bones and associated structures (muscles and mucosa). [TFD][VHOG]
Echinoderms, hemichordates, and chordates are called deuterostomes because the mouth arises not from the blastopore but from a second invagination at the anterior end of the larva that pushes in to connect with the archenteron.[well established][VHOG]
AAO:0000053
AAO:0000960
BSA:0000107
CALOHA:TS-1315
EFO:0001975
EHDAA2:0001324
EHDAA:6970
EMAPA:17411
EMAPA:18399
EV:0100057
FMA:20292
HAO:0000669
NCIT:C12421
TAO:0001027
TGMA:0000102
UMLS:C0226896
VHOG:0000188
WBbt:0005255
XAO:0000126
ZFA:0001027
buccal cavity
cavity of mouth
uberon
bucca
UBERON:0000167
oral cavity
A portion of organism substance that is the product of an excretion process that will be eliminated from the body. An excretion process is elimination by an organism of the waste products that arise as a result of metabolic activity
UBERON:0000324
UBERON:0007550
AEO:0000184
BTO:0000491
EHDAA2_RETIRED:0003184
ENVO:02000022
FMA:9674
galen:Excretion
excreted substance
portion of excreted substance
waste substance
uberon
excretion
UBERON:0000174
excreta
material anatomical entity
Anatomical entity that has mass.
AAO:0010264
AEO:0000006
BILA:0000006
CARO:0000006
EHDAA2:0003006
FBbt:00007016
FMA:67165
HAO:0000006
TAO:0001836
TGMA:0001826
VHOG:0001721
uberon
UBERON:0000465
material anatomical entity
anatomical cluster
Anatomical group that has its parts adjacent to one another.
anatomical cluster
An expanded region of the vertebrate alimentary tract that serves as a food storage compartment and digestive organ. A stomach is lined, in whole or in part by a glandular epithelium.
Portion of alimentary canal with increased circular and longitudinal smooth muscle. Bounded posteriorly by the pyloric sphincter. Mucosal lining has increased folding.[AAO]
It appears that the stomach has an ancient origin. The stomach first appears in the fish lineage. The prevertebrate chordates do not have a true stomach, whereas the cartilaginous and bony fish do. Although most fish do have a true stomach, some fish species appear to have lost the stomach secondarily. The remaining vertebrate lineages do have a true stomach (at least in the adult animal), although there is great variation in the size and shape of the stomach.[well established][VHOG]
We restrict this to the vertebrate specific structure - see the grouping class 'food storage organ' for analogous structures in other species. Teleosts: Zebrafish is functionally stomach-less, but may retain ontogenic footprint. Although the precise shape and size of the stomach varies widely among different vertebrates, the relative positions of the oesophageal and duodenal openings remain relatively constant. As a result, the organ always curves somewhat to the left before curving back to meet the pyloric sphincter. However, lampreys, hagfishes, chimaeras, lungfishes, and some teleost fish have no stomach at all, with the oesophagus opening directly into the intestine. The gastric lining is usually divided into two regions, an anterior portion lined by fundic glands, and a posterior with pyloric glands. Cardiac glands are unique to mammals, and even then are absent in a number of species. The distributions of these glands vary between species, and do not always correspond with the same regions as in man. Furthermore, in many non-human mammals, a portion of the stomach anterior to the cardiac glands is lined with epithelium essentially identical to that of the oesophagus. Ruminants, in particular, have a complex stomach, the first three chambers of which are all lined with oesophageal mucosa
AAO:0000579
ANISEED:1235297
BTO:0001307
CALOHA:TS-0980
EFO:0000837
EHDAA2:0001915
EHDAA:2993
EMAPA:17021
EV:0100070
FMA:7148
GAID:293
MA:0000353
MAT:0000051
MESH:A03.492.766
MIAA:0000051
NCIT:C12391
OpenCyc:Mx4rvVjlqpwpEbGdrcN5Y29ycA
TAO:0002121
UMLS:C0038351
VHOG:0000408
XAO:0000128
galen:Stomach
stomach chamber
uberon
anterior intestine
gaster
mesenteron
ventriculus
UBERON:0000945
stomach
An airway through which respiratory air passes in organisms.
This class generically groups trachea and analagous structures throughout metazoa. Consider renaming, as the term could be taken to mean lumen of tracheal system (e.g. in SNOMED). As a grouping class this is quite vague, as it is not clear where the airway begins and ends
airway
airways
FMA:265130
uberon
UBERON:0001005
respiratory airway
Anatomical system that has as its parts the organs devoted to the ingestion, digestion, and assimilation of food and the discharge of residual wastes.
An anatomical system consisting of the alimentary canal and digestive glands responsible for intake, absorption, digestion and excretion of food.[AAO]
digestive
many anatomy ontologies consider gastrointestinal system synonymous with digestive system. here we follow MA in dividing digestive system into gastrointestinal and hepatobiliary. hepatobiliary includes the liver and biliary tract. species-specific AO classes are categorized according to whether liver is included. For example, XAO includes liver as part of XAO:0000125 alimentary system, so we assume this class is the more generic class
AAO:0000129
BILA:0000082
BTO:0000058
CALOHA:TS-1293
EFO:0000793
EV:0100056
FBbt:00005055
FMA:7152
GAID:278
MA:0002431
MAT:0000018
MESH:D004064
MIAA:0000018
TADS:0000170
TAO:0000339
WBbt:0005748
XAO:0000125
ZFA:0000339
galen:DigestiveSystem
ncithesaurus:Digestive_System
uberon
alimentary system
alimentary tract
gastrointestinal system
gut
UBERON:0001007
digestive system
Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species.
AAO:0010841
AEO:0000000
BILA:0000000
CARO:0000000
EHDAA2:0002229
FBbt:10000000
FBbt_root:00000000
FMA:62955
HAO:0000000
MA:0000001
NCIT:C12219
TAO:0100000
TGMA:0001822
UMLS:C1515976
WBbt:0000100
XAO:0000000
ZFA:0100000
uberon
UBERON:0001062
anatomical entity
Excretion that is the output of a kidney
kidney excreta from some taxa (e.g. in aves) may not be liquid
BTO:0001419
CALOHA:TS-1092
EFO:0001939
EMAPA:36554
ENVO:00002047
FMA:12274
GAID:1189
MA:0002545
MAT:0000058
MESH:D014556
MIAA:0000058
NCIT:C13283
OpenCyc:Mx4rvVjGppwpEbGdrcN5Y29ycA
UMLS:C0042036
galen:Urine
uberon
UBERON:0001088
urine
Portion of semisolid bodily waste discharged through the anus[MW,modified]
Excretion in semisolid state processed by the intestine.[FMA]
fecal
excreta
BTO:0000440
CALOHA:TS-2345
ENVO:00002003
FMA:64183
GAID:1199
MA:0002509
MAT:0000053
MESH:D005243
MIAA:0000053
NCIT:C13234
OpenCyc:Mx4rvVjJMZwpEbGdrcN5Y29ycA
UMLS:C0015733
galen:Feces
faeces
fecal material
fecal matter
matières fécales@fr
merde@fr
partie de la merde@fr
piece of shit
porción de mierda@es
portion of excrement
portion of faeces
portion of fecal material
portion of fecal matter
portion of feces
portionem cacas
stool
teil der fäkalien@de
cow dung
cow pat
dung
fewmet
frass
guano
portion of dung
portion of guano
portion of scat
scat
spraint
uberon
droppings
excrement
ordure
spoor
UBERON:0001988
feces
Subdivision of digestive tract that connects the stomach to the large intestine and is where much of the digestion and absorption of food takes place (with the exception of ruminants). The mammalian small intestine is long and coiled and can be differentiated histologically into: duodenum, jejunem, ileum[WP,cjm,Kardong].
The terminal region of the mid intestine is comprised of specialized enterocytes that appear to play a role in mucosal immunity. Wallace et al, 2005.[TAO]
Intestinal surface area also is increased in amphibians and reptiles by internal folds and occasionally by a few villi. The intestine can be divided into a small intestine and a slightly wider large intestine.[well established][VHOG]
AAO:0010397
BTO:0000651
CALOHA:TS-0942
EFO:0000841
EMAPA:32834
EV:0100072
FMA:7200
GAID:313
MA:0000337
MAT:0000047
MESH:A03.492.411.620
MIAA:0000047
NCIT:C12386
OpenCyc:Mx4rvVjlIJwpEbGdrcN5Y29ycA
TAO:0001323
UMLS:C0021852
VHOG:0000055
XAO:0000130
ZFA:0001323
galen:SmallIntestine
small bowel
small intestine
uberon
anterior intestine
intestinum tenue
mid intestine
UBERON:0002108
small intestine
The region of the digestive tract extending from the beginning of the intestines to the anus[GO - gut definition].
MA class was moved from here. See https://github.com/obophenotype/uberon/issues/509
WP: small intestine, large intestine, anus. Anal canal not part of LGIT according to FMA, but anus is considered part of LGIT according to WP. Duodenum overlaps both U/L
gut
FMA:49179
NCIT:C33010
UMLS:C0226875
galen:LowerGastrointestinalTract
lower GI tract
lower gastrointestinal tract
uberon
UBERON:0004907
lower digestive tract
The region of the digestive tract extending from the mouth cavity through pharynx esophagus stomach and duodenum.
WP: small intestine, large intestine, anus. Anal canal not part of LGIT according to FMA, but anus is considered part of LGIT according to WP. Duodenum overlaps both U/L. In Galen, entire GI tract excludes esophagus
FMA:49177
NCIT:C33837
UMLS:C0226874
galen:UpperGastrointestinalTract
upper GI tract
upper gastrointestinal tract
uberon
UBERON:0004908
upper digestive tract
A proximal-distal subdivision of the digestive tract.
intended to denote both embryonic and adult structures. Note the FMA grouping here is not quite correct.
FBbt:00100315
FMA:71131
uberon
alimentary system subdivision
intestinal tract
segment of intestinal tract
subdivision of alimentary system
UBERON:0004921
subdivision of digestive tract
An anatomical structure that has more than one cell as a part.
CARO:0010000
FBbt:00100313
multicellular structure
uberon
UBERON:0010000
multicellular anatomical structure
Any of the organs or elements that are part of the digestive system. Examples: tongue, esophagus, spleen, crop, lunge feeding organ, tooth elements.
EMAPA:37843
digestive organ
digestive system organ
uberon
UBERON:0013765
digestive system element
time unit
A unit which is a standard measure of the dimension in which events occur in sequence.
time unit
Phenotype
abnormal phenotype
example to be eventually removed
Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete.
metadata complete
term created to ease viewing/sort terms for development purpose, and will not be included in a release
PERSON:Alan Ruttenberg
organizational term
Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release."
ready for release
Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors.
metadata incomplete
Nothing done yet beyond assigning a unique class ID and proposing a preferred term.
uncurated
All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor.
pending final vetting
Terms with this status should eventually replaced with a term from another ontology.
Alan Ruttenberg
group:OBI
to be replaced with external ontology term
A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues.
Alan Ruttenberg
group:OBI
requires discussion
## Elucidation
This is used when the statement/axiom is assumed to hold true 'eternally'
## How to interpret (informal)
First the "atemporal" FOL is derived from the OWL using the standard
interpretation. This axiom is temporalized by embedding the axiom
within a for-all-times quantified sentence. The t argument is added to
all instantiation predicates and predicates that use this relation.
## Example
Class: nucleus
SubClassOf: part_of some cell
forall t :
forall n :
instance_of(n,Nucleus,t)
implies
exists c :
instance_of(c,Cell,t)
part_of(n,c,t)
## Notes
This interpretation is *not* the same as an at-all-times relation
axiom holds for all times
en
Ontology for Biomedical Investigations
Advisors for this project come from the IFOMIS group, Saarbruecken and from the Co-ODE group in Manchester
Alan Ruttenberg
Allyson Lister
Barry Smith
Bill Bug
Bjoern Peters
Carlo Torniai
Chris Mungall
Chris Stoeckert
Chris Taylor
Christian Bolling
Cristian Cocos
Daniel Rubin
Daniel Schober
Dawn Field
Dirk Derom
Elisabetta Manduchi
Eric Deutsch
Frank Gibson
Gilberto Fragoso
Helen C. Causton
Helen Parkinson
Holger Stenzhorn
James A. Overton
James Malone
Jay Greenbaum
Jeffrey Grethe
Jennifer Fostel
Jessica Turner
Jie Zheng
Joe White
John Westbrook
Kevin Clancy
Larisa Soldatova
Lawrence Hunter
Liju Fan
Luisa Montecchi
Matthew Brush
Matthew Pocock
Melanie Courtot
Melissa Haendel
Mervi Heiskanen
Monnie McGee
Norman Morrison
Philip Lord
Philippe Rocca-Serra
Pierre Grenon
Richard Bruskiewich
Richard Scheuermann
Robert Stevens
Ryan R. Brinkman
Stefan Wiemann
Susanna-Assunta Sansone
Tanya Gray
Tina Hernandez-Boussard
Trish Whetzel
Yongqun He
2009-07-31
The Ontology for Biomedical Investigations (OBI) is build in a collaborative, international effort and will serve as a resource for annotating biomedical investigations, including the study design, protocols and instrumentation used, the data generated and the types of analysis performed on the data. This ontology arose from the Functional Genomics Investigation Ontology (FuGO) and will contain both terms that are common to all biomedical investigations, including functional genomics investigations and those that are more domain specific.
OWL-DL
An ontology for the annotation of biomedical and functional genomics experiments.
http://creativecommons.org/licenses/by/4.0/
Please cite the OBI consortium http://purl.obolibrary.org/obo/obi where traditional citation is called for. However it is adequate that individual terms be attributed simply by use of the identifying PURL for the term, in projects that refer to them.
2018-08-27
2
2
2
OBO Relations Ontology
The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies.
Includes Ontology(OntologyID(Anonymous-21)) [Axioms: 32 Logical Axioms: 0]
https://github.com/oborel/obo-relations/
Includes Ontology(OntologyID(Anonymous-21)) [Axioms: 26 Logical Axioms: 0]