Haihe Wang
Yongqun "Oliver" He (YH)
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
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
BFO CLIF specification label
editor preferred label
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
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.
example of usage
has curation status
PERSON:Alan Ruttenberg
PERSON:Bill Bug
PERSON:Melanie Courtot
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.
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.
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.
definition editor
alternative term
An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)
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
Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
curator note
An administrative note of use for a curator but of no use for a user
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
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
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:Bjoern Peters
PERSON:Chris Mungall
GROUP:OBO Foundry <http://obofoundry.org/>
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
has associated axiom(nl)
Person:Alan Ruttenberg
An axiom associated with a term expressed using natural language
has associated axiom(fol)
An axiom expressed in first order logic using CLIF syntax
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.
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
ISA tools project (http://isa-tools.org)
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:Randi Vita, Jason Greenbaum, Bjoern Peters
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
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
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'
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
Used to annotate object properties representing a causal relationship where the value indicates a direction. Should be "+", "-" or "0"
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.
This annotation property may be replaced with an annotation property from an external ontology such as IAO
Notes on the homology status of this class.
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'.
Notes on the how instances of this class vary across species.
Notes on the ontogenic development of instances of this class.
Notes on how similar or equivalent classes are represented in other ontologies.
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
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
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
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
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
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
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
label
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
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.
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
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
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
accidentally included in BFO 1.2 proposal - should have been BFO_0000062
obsolete preceded by
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
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.
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
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.
Smith, Ceusters, Ruttenberg, 2000 years of philosophy
is about
relates a process to a time-measurement-datum that represents the duration of the process
is duration of
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
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
Alan Ruttenberg
is_specified_input_of
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.
is_specified_output_of
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.
modified according to email thread from 1/23/09 in accordince with DT and PPPB branch
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
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
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.
A relation between an information content entity and a value specification that specifies its value.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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
has microbe population size altered in diseased host
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
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
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
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
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).
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
disposition of
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
A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B.
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.
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.
This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations.
Primitive instance level timing relation between events
before or simultaneous with
t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2)
simultaneous with
t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2)
before
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
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
X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)
ends after
X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)
immediately preceded by
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
starts before
X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)
immediately precedes
X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y))
starts 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
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
Regulation precludes parthood; the regulatory process may not be within the regulated process.
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.
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.
has prototype
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.
A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.
temporal relation
temporally related to
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.
starts with
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.
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.
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.
has output
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
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
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
inheres in part of
A mereological relationship or a topological relationship
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.
This is a grouping relation that collects relations used for the purpose of connecting structure and function
functionally related to
regulated by
negatively regulated by
positively regulated by
has member is a mereological relation between a collection and an item.
has member
input of
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.
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.
causally downstream of
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
directly activates
indirectly activates
directly inhibits
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.
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
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.
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
directly provides input for (process to process)
directly provides input for
transitive form of directly_provides_input_for
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
inverse of causally upstream 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.
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.
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)
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)
causally upstream of or within, negative effect
causally upstream of or within, positive effect
Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison.
has measurement 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.
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.
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
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
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
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
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
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
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
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
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 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
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
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
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
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
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
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.
High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms.
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
A chemical entity constituting the smallest component of an element having the chemical properties of the element.
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.
High molecular weight, linear polymers, composed of nucleotides containing ribose and linked by phosphodiester bonds; RNA is central to the synthesis of proteins.
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
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.
A cell in vitro that is or has been maintained or propagated as part of a cell culture.
A cell in vitro that has undergone physical changes as a consequence of a deliberate and specific experimental procedure.
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.
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.
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.
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.
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.
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.
An intestinal disease characterized by inflammation located_in all parts of digestive tract.
Xref MGI. OMIM mapping confirmed by DO. [SN].
A cancer that is classified based on the organ it starts in.
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.
autoimmune disease of musculoskeletal system
A gastrointestinal system cancer that is located_in the hepatobiliary system
hepatobiliary system cancer
A gastrointestinal system cancer that is located_in the intestine.
A gastrointestinal system cancer that is located_in the stomach.
malignant neoplasm of lesser curve of stomach
malignant tumor of greater curve of stomach
malignant tumor of lesser curve of stomach
An arthritis that has_material_basis_in uric acid crystal deposits located_in joint.
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.
An autoimmune hypersensitivity disease that involves inflammation or pain in the muscles, joints, or fibrous tissue.
A disease of cellular proliferation that is malignant and primary, characterized by uncontrolled cellular proliferation, local cell invasion and metastasis.
A disease of anatomical entity that occurs in the muscular and/or skeletal system.
An organ system cancer located_in endocrine system that is characterized by uncontrolled cellular proliferation of the hormone producing glands of the endocrine system.
An endocrine gland cancer located_in the pancreas.
A large intestine cancer that is located_in the colon.
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.
A disease of anatomical entity that is located_in the immune system.
A cell type cancer that has_material_basis_in abnormally proliferating cells derives_from epithelial cells.
A gastrointestinal system disease that is located_in the liver and/or biliary tract.
An organ system cancer located_in gastrointestinal tract that is manifested in organs of the gastrointestinal system.
A bone disease that results_in inflammation of the located_in bone.
A hepatobiliary system cancer that is located_in the liver.
malignant neoplasm of liver, not specified as primary or secondary
non-resectable primary hepatic malignant neoplasm
resectable malignant neoplasm of the liver
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.
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.
hypersensitivity reaction type II disease
A biliary tract cancer that is located_in the bile duct.
malignant neoplasm of the extrahepatic bile duct
A gastrointestinal system cancer that is located_in the esophagus.
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 the middle Third of the esophagus
A gastrointestinal system disease that is located_in the intestine.
A stomach cancer that is located_in the stomach.
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.
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.
A rheumatoid arthritis that involves an autoimmune disease onset in children under 16 which attacks the healthy cells and tissue of located_in joint.
Pauciarticular onset juvenile chronic arthritis
monarticular juvenile rheumatoid arthritis
A liver carcinoma that has_material_basis_in undifferentiated hepatocytes.
A liver cancer that has_material_basis_in epithelial cells.
Liver and Intrahepatic bile duct carcinoma
A disease that manifests in a defined anatomical structure.
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.
An arthritis that is an autoimmune disease which attacks healthy cells and tissue located_in joint.
A disease of anatomical entity that is located_in the gastrointestinal tract.
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.
A syndrome that occurs in humans with psoriasis who also experience symptoms similar to 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.
A large intestine cancer that is located_in the colon and/or located_in the rectum.
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
drug product
A biome is an ecosystem to which resident ecological communities have evolved adaptations.
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.
A portion of environmental material is a fiat object which forms the medium or part of the medium of an environmental system.
A system which has the disposition to environ one or more material entities.
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.
An environmental system which can sustain and allow the growth of an ecological population.
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
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.
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.
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.
Any process in which an organism has an effect on an organism of a different species.
interspecies interaction with other organisms
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.
A biological process which involves another organism of the same or different species.
physiological interaction between organisms
physiological interaction with other organism
This is the root of the phenotypic abnormality subontology of the HPO.
Accumulation of substantial excess body fat.
Abnormally increased frequency of loose or watery bowel movements.
The presence of chronic diarrhea, which is usually taken to mean diarrhea that has persisted for over 4 weeks.
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: Melanie Courtot
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: Barry Smith
PERSON: Bjoern Peters
PERSON: Jennifer Fostel
goal specification
OBI Plan and Planned Process/Roles Branch
Pour the contents of flask 1 into flask 2
a directive information entity that describes an action the bearer will take
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
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.
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: Chris Stoeckert
PERSON: Jonathan Rees
data
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.
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.
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
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)
data about an ontology part is a data item about a part of an ontology, for example a term
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
2/3/2009 Comment from OBI review. Action specification not well enough specified. Conditional specification not well enough specified. Question whether all plan specifications have objective specifications. Request that IAO either clarify these or change definitions not to use them
measurement datum
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
A scalar measurement datum that is the result of measuring a temporal interval
2009/09/28 Alan Ruttenberg. Fucoidan-use-case
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.
Interaction is a processual entity that has two or more participants (i.e., interactors) that have an effect upon one another.
interact, interacted, interacting, interaction, interaction, interactor, interactors, interacts, participates; plays a role, contribute, contributed, contributes, contributing, engagement, engagements, engages, engaging, involve, involved, involves, involving, act, acted, acting, acts
Enthesitis-related juvenile idiopathic arthritis 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 .
enthesitis-related juvenile idiopathic arthritis
Capnocytophaga gingivalis
purple photosynthetic bacteria and relatives
Micrococcus
Streptococcus sanguinis
Fusobacterium nucleatum subsp. vincentii
Fusibacterium nucleatum subsp. fusiforme
Fusibacterium nucleatum subsp. vincentii
Treponema
Treponema denticola
Rikenellaceae
Eubacterium
Rhodococcus
Pseudonocardia
Campylobacter
Chloroflexi
Prevotella oulorum
Anaerolineae
Anaerolineaceae
Pseudomonas sp.
Burkholderia
Methylobacterium
Prevotella pleuritidis
Treponema maltophilum
Clostridiales Family XIII. Incertae Sedis
Pityriasis (Tinea) versicolor infection agent
Yersinia
Fretibacterium fastidiosum
Haemophilus parainfluenzae
Haemophilus sp.
Fusobacterium nucleatum subsp. nucleatum
Fusibacterium nucleatum subsp. nucleatum
Fusobacterium nucleatum subsp. polymorphum
Fusibacterium nucleatum subsp. polymorphum
Chlamydia trachomatis
Eggerthella
Fusobacterium
Salmonella enterica subsp. enterica serovar Typhi
Salmonella enterica subsp. enterica serovar Typhimurium
Selenomonadales
Flavonifractor
Selenomonas
Porphyromonas macacae
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.
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)
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
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.
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")
Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term.
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
sample preparation for assay
A sample_preparation_for_assay is a protocol_application including material_enrollments and biomaterial_transformations. definition_source: OBI.
study
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
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
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
A cell lysis, production of a cloning vector, creating a buffer.
A planned process which results in physical changes in a specified input material
material transformation
material processing
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.
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.
DNA extraction
A DNA extraction is a nucleic acid extraction where the desired output material is DNA.
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.
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
extracted material
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.
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)
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.
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.
artifact creation objective
material transformation objective
Illumina (Solexa) sequencing is an example of DNA sequencing
A sequencing assay which determines information on the sequence of a DNA molecule.
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.
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.
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/
5/31/2012: This process is not necessarily an acquisition, as specimens may be collected from materials already in posession
a material obtained from an organism in order to be a representative of the whole
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.
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.
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
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.
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
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.
A specimen gathering process with the objective to obtain a specimen that is representative of the input material entity
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
An objective specification maintains some or all of the qualities of a material over time.
a quality of a DNA molecule that inheres in its bearer due to the order of its DNA nucleotide residues.
A ruler, a microarray scanner, a Geiger counter.
A device in which a measure function inheres.
a process with that achieves the objective to maintain some or all of the characteristics of an input material over time
an extract which is the output of an extraction process in which RNA molecules are isolated from a 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.
A tissue sample that has been sliced and stained for a histology study.
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.
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.
sequence data
An extract that is the output of an extraction process in which nucleic acid molecules are isolated from a specimen.
The output of an extraction process in which DNA molecules are purified in order to exclude DNA from organellas.
An device that is used to determine the order of nucleotides in nucleic acid sequences.
An device that is used to determine the order of amino acids in protein sequences.
An transcription profiling assay that determines an RNA sequence by analyzing the transcibed regions of the genome and or to quantitate transcript abundance.
transcription profiling by high throughput sequencing
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
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).
tissue specimen
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
The part of a FASTA file that contains the letters ACTGGGAA
A sequence data item that is about the primary structure of DNA
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.
specimen collection time measurement datum
A time measurement datum that is the measure of the time when the specimens are collected.
collection date
NIAID GSCID-BRC metadata working group
sample preparation for sequencing assay
A sample preparation for assay that preparation of nucleic acids for a sequencing assay
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.
cell freezing medium
A value specification that consists of two parts: a numeral and a unit label
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.
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.
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.
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.
WEB: http://en.wikipedia.org/wiki/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.
GROUP: OBI Biomaterial Branch
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.
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.
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.
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
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
IEDB
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
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
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
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).
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.
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
RNA extraction
A RNA extraction is a nucleic acid extraction where the desired output material is RNA
requested by Helen Parkinson for MO
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
requested by Helen Parkinson for MO. Could be defined class
the detrimental process in which an infectious agent colonizes or replicates in a host environment
infection process
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
disposition to infect an organism
abnormal, harmful processes caused by or associated with a disease
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.
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.
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
host-microbiome interaction
human microbiome
A biome that consists of a collection of microorganisms (i.e., microbiota) and the surrounding environment where the microorganisms reside.
microbiome
mouse microbiome
A microbiome that includes a collective population of bacterial organisms.
bacterial microbiome
A microbiome that includes a collective population of fungal microorganisms.
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
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)
fungal microbiome of mucosal site
A fungal microbiome that is located in a lung of a host organism
fungal microbiome of lung
A host-microbiome interaction where the microbiome interacts with the host immune system
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
interaction between microbiome and adaptive immune system
a human microbiome that is located in a human respiratory system
microbiome in human lung
a human microbiome that is located in a human lung
microbiome in human respiratory system
a human microbiome that is located in a human oral system
microbiome in human oral
a human microbiome that is located in a human gastrointestinal system
microbiome in human gastrointestinal system
a human microbiome that is located in a human cutaneous system
microbiome in human cutaneous system
a human microbiome that is located in a human urogenital system
microbiome in human urogenital system
A host-microbiome interaction where the host is human
human-microbiome interaction
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.
human-gut microbiome interaction
A human-gut microbiome interaction that is associated with bowel syndrome.
human gut microbiome interaction in bowel syndrome
A human-gut microbiome interaction that is associated with Crohn's disease.
human gut microbiome interaction in Crohn's disease
A human-gut microbiome interaction that is associated with colon cancer.
colon cancer human-gut microbiome interaction
A human-gut microbiome interaction that involves in Clostridium difficile
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.
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.
restoring human gut microbiome resistance to CDI by FMT
restoring human gut microbiome resistance to C. difficile infection by fecal microbiota transplantation
An infection process that is caused by Clostridioides difficile.
A human gut-microbiome interaction that is associated with rheumatoid arthritis (RA).
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
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.
increased organism quantity compared with healthy control
A quality with an decreased microbiome organism dirversity in a host microbiome environment (e.g., gut).
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.
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.
decreased organism quantity compared with healthy controls
An interaction between human and oral microbiome.
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.
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.
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.
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.
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.
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.
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.
expansion of [Clostridium] asparagiforme in RA human gut
A colorectal cancer human-gut microbiome interaction where B. fragilis is increased.
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.
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.
decreased organism quantity in acute disease patient compared with chronic disease control
A host-microbiome interaction where the host is rattus.
rat-microbiome interaction
a RA human-gut microbiome interaction that shows an expansion of Bifidobacterium dentium in patients with RA compared with healthy controls.
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.
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.
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.
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.
decreased organism quantity compared with fibromyalgia patients
A human gut-microbiome interaction that is associated with systemic lupus erythematosus (SLE).
SLE human-gut microbiome interaction
A human-gut microbiome interaction that is associated with colorectal cancer.
colorectal cancer human-gut microbiome interaction
A colorectal cancer human-gut microbiome interaction where Fusobacterium sp. is increased.
expansion of Fusobacterium sp. in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Citrobacter is decreased.
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.
https://www.ncbi.nlm.nih.gov/pubmed/20436074 /
expansion of Porphyromonas gingivalis in RA human gut
A colorectal cancer human-gut microbiome interaction where Shigella is decreased.
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.
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.
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.
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.
expansion of Collinsella aerofaciens in RA human gut
A human gut-microbiome interaction that is associated with the diarrhea disease
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.
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.
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.
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.
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.
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.
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.
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
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
depletion of Prevotella in RA human gut compared to fibromyalgia patients
An interaction between human and respiratory airway microbiome.
human respiratory airway microbiome interaction
A human respiratory airway microbiome interaction that is associated with rheumatoid arthritis (RA).
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.
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.
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.
depletion of Pseudobutyrivibrio in SLE human gut
A human oral cavity microbiome interaction that is associated with systemic lupus erythematosus (SLE).
SLE human oral cavity microbiome interaction
A human oral cavity microbiome interaction that is associated with rheumatoid arthritis (RA).
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
expansion of Veillonella in RA human oral cavity
An interaction between rattus and gut microbiome.
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.
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.
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.
depletion of Faecalibacterium in RA human gut
A human gut-microbiome interaction that is associated with ankylosing spondylitis (AS).
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.
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.
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.
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.
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.
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.
expansion of Klebsiella pneumoniae in AS human gut
A human oral cavity microbiome interaction that is associated with ankylosing spondylitis (AS).
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.
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.
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.
expansion of Tannerella forsythia in AS human oral cavity
A rattus gut-microbiome interaction that is associated with ankylosing spondylitis (AS).
association of rat gut microbiota with ankylosing spondylitis
a SLE human oral cavity microbiome interaction that shows an expansion of Prevotella in patients with SLE compared with healthy controls.
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.
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.
expansion of Bacteroidetes in SLE human gut
A human gut-microbiome interaction that is associated with gout.
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.
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.
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.
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.
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.
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.
expansion of Negativicutes in gout human gut
An interaction between human and zone of skin microbiome.
human skin microbiome interaction
A human skin microbiome interaction that is associated with psoriatic arthritis (PsA).
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.
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.
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.
depletion of Vibrio in gout human gut
A colorectal cancer human-gut microbiome interaction where Eubacterium ventriosum is decreased.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
depletion of Propionibacterium acnes 17B in PsA human skin
A human gut-microbiome interaction that is associated with juvenile psoriatic arthritis(PsA).
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
expansion of Candida albicans in PsA human gut
A human oral cavity microbiome interaction that is associated with psoriatic arthritis (PsA).
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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
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.
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.
expansion of Bacteroides vulgatus in AS rat gut
A rattus gut-microbiome interaction that is associated with arthritis.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
expansion of Bacteroides fragilis in arthritis rat gut
A host-microbiome interaction where the host is musculus.
mouse-microbiome interaction
An interaction between musculus and gut microbiome.
mouse gut microbiome interaction
A musculus gut-microbiome interaction that is associated with system lupus erythematosus(SLE).
association of mouse gut microbiota with system lupus erythematosus
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.
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.
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.
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.
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.
expansion of Streptococcus pyogenes in arthritis rat gut
A musculus gut-microbiome interaction that is associated with arthritis
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
expansion of Desulfovibrionaceae in arthritis rat gut
A human gut-microbiome interaction that is associated with juvenile rheumatoid arthritis (ERA).
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
depletion of Coprococcus in PsA human gut
A colorectal cancer human-gut microbiome interaction where Parvimonas micra is increased.
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.
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.
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.
expansion of Yersinia in ERA human gut
A rattus gut-microbiome interaction that is associated with reactive arthritis'.
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.
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.
expansion of Salmonella in reactive arthritis rat gut
A colorectal cancer human-gut microbiome interaction where Solobacterium moorei is increased.
expansion of S. moorei in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Fusobacteria is increased.
expansion of Fusobacteria in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Basidiomycota is increased.
expansion of Basidiomycota in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Parvimonas is increased.
expansion of Parvimonas in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Peptostreptococcus is increased.
expansion of Peptostreptococcusi in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Fusobacterium is increased.
expansion of Fusobacterium in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Beggiatoa is increased.
expansion of Beggiatoa in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Malassezia is increased.
expansion of Malassezia in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Leptotrichia is increased.
expansion of Leptotrichia in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Filifactor is increased.
expansion of Filifactor in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Crenothrix is increased.
expansion of Crenothrix in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Solobacterium is increased.
expansion of Solobacterium in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Sulfurovum is increased.
expansion of Sulfurovum in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Streptobacillus is increased.
expansion of Streptobacillus in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Moniliophthora is increased.
expansion of Moniliophthora in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Slackia is increased.
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.
expansion of Collinsella in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Clostridiaceae is increased.
expansion of Clostridiaceae in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Bacteroidales is increased.
expansion of Bacteroidales in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Cronobacter is decreased.
depletion of Cronobacter in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Kluyvera is decreased.
depletion of Kluyvera in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Serratia is decreased.
depletion of Serratia in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Salmonella enterica subsp. enterica is decreased.
depletion of Salmonella enterica subsp. enterica in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Eubacteriaceae is decreased.
depletion of Eubacteriaceae in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Anaerovorax is decreased.
depletion of Anaerovorax in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Microbacterium is decreased.
depletion of Microbacterium in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Bacteroides finegoldii is decreased.
depletion of B. finegoldii in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Bacteroides intestinalis is decreased.
depletion of B.intestinalis in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Prevotella copri is decreased.
depletion of P.copri in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Prevotella oris is decreased.
depletion of P. oris in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Dorea formicigenerans is decreased.
depletion of D.formicigenerans in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Lachnobacterium bovis is decreased.
depletion of L. bovis in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Lachnospira pectinoschiza is decreased.
depletion of L.pectinoschiza in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Pseudobutyrivibrio ruminis is decreased.
depletion of P.ruminis in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Ruminococcus albus is decreased.
depletion of R.albus in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Dialister invisus is decreased.
depletion of D. invisus in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Dialister pneumosintes is decreased.
depletion of D. pneumosintes in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Megamonas hypermegale is decreased.
depletion of M. hypermegale in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Acidaminobacter is increased.
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.
expansion of Phascolarctobacterium in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Citrobacter farmeri is increased.
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.
expansion of Bacteroides fragilis in RA human gut
A colorectal cancer human-gut microbiome interaction where Roseburia is increased.
expansion of Roseburia in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Anoxybacillus is decreased.
depletion of Anoxybacillus in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Bacteroides is increased.
expansion of Bacteroides in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Odoribacter is increased.
expansion of Odoribacter in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Akkermansia muciniphila is increased.
expansion of A. muciniphila in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Prevotellaceae is decreased.
depletion of Prevotellaceae in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Porphyromonadaceae is decreased.
depletion of Porphyromonadaceae in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Clostridiaceae is decreased.
depletion of Clostridiaceae in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Parabacteroides is increased.
expansion of Parabacteroides in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where ParaAlistipes is increased.
expansion of Alistipes in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Bacteroides ovatus is increased.
expansion of B. ovatus in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Bacteroides xylanisolvens is increased.
expansion of B. xylanisolvens in colorectal cancer human gut
An interaction between human and urine microbiome.
human-urine microbiome interaction
A human urine-microbiome interaction that is associated with rheumatoid arthritis (RA).
RA human-urine microbiome interaction
A colorectal cancer human-gut microbiome interaction where Lachnospiraceae is decreased.
depletion of Lachnospiraceae in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Enterobacteriaceae is increased.
expansion of Enterobacteriaceae in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Lactobacillus acidophilus is decreased.
depletion of L. acidophilus in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Bacteroides is decreased.
'depletion of Bacteroides in colorectal cancer human gut'
A colorectal cancer human-gut microbiome interaction where Clostridiales is decreased.
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.
expansion of unclassified Proteobacteria in diarrheal patient gut
A colorectal cancer human-gut microbiome interaction where Firmicutes is decreased.
depletion of Firmicutes in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Bacteroidetes is decreased.
depletion of Bacteroidetes in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Bacteroidales is decreased.
depletion of Bacteroidales in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Rikenellaceae is decreased.
depletion of Rikenellaceae in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Bacteroides uniformis is decreased.
depletion of B. uniformis in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Providencia is increased.
expansion of Providencia in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Bacteroidaceae is increased.
https://www.ncbi.nlm.nih.gov/pubmed/ 22761885
https://www.ncbi.nlm.nih.gov/pubmed/ 23397545
expansion of Bacteroidaceae in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Streptococcaceae is increased.
expansion of Streptococcaceae in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Fusobacteriaceae is increased.
expansion of Fusobacteriaceae in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Peptostreptococcaceae is increased.
expansion of Peptostreptococcaceae in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Veillonellaceae is increased.
expansion of Veillonellaceae in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Pasteurellaceae is increased.
expansion of Pasteurellaceae in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Porphyromonas is increased.
expansion of Porphyromonas in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Mogibacterium is increased.
expansion of Mogibacterium in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Erysipelotrichaceae is increased.
expansion of Erysipelotrichaceae in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Prevotellaceae is increased.
expansion of Prevotellaceae in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Coriobacteriaceae is increased.
expansion of Coriobacteriaceae in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Ruminococcaceae is decreased.
depletion of Ruminococcaceae in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Lactobacillaceae is decreased.
depletion of Lactobacillaceae in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Bifidobacterium longum is decreased.
depletion of B. longum in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Faecalibacterium prausnitzii is decreased.
depletion of F. prausnitzii in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Blautia is decreased.
depletion of Blautia in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Lactobacillus rhamnosus is decreased.
depletion of L. rhamnosus in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Lactobacillus reuteri is decreased.
'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.
expansion of Proteus mirabilis in RA human urine
A colorectal cancer human-gut microbiome interaction where Alistipes putredinis is increased.
expansion of A. putredinis in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Lachnospiraceae bacterium is increased.
expansion of L. bacterium in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Escherichia coli NC101 is increased.
expansion of E. coli NC101 in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Bilophila wadsworthia is increased.
expansion of B. wadsworthia in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Bifidobacterium animalis is decreased.
depletion of B. animalis in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Streptococcus thermophilus is decreased.
depletion of S. thermophilus in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Ruminococcus is decreased.
depletion of Ruminococcus in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Bifidobacterium is decreased.
depletion of Bifidobacterium in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Streptococcus is decreased.
depletion of Streptococcus in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Escherichia is increased.
expansion of Escherichia in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Bilophila is increased.
expansion of Bilophila in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Bacteroidetes is increased.
expansion of Bacteroidetes in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Streptococcus equinus is increased.
expansion of S. equinus in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Enterococcaceae is increased.
expansion of Enterococcaceae in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Campylobacter is increased.
expansion of Campylobacter in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Salmonella is increased.
expansion of Salmonella in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Shigella is increased.
expansion of Shigella in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Bifidobacterium animalis subsp. lactis is decreased.
depletion of B. animalis subsp. lactis in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Chlamydia is increased.
expansion of Chlamydia in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Mycobacterium is increased.
expansion of Mycobacterium in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Clostridia is increased.
expansion of Clostridia in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Candidatus Portiera is increased.
expansion of C. Portiera in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Proteus mirabilis is increased.
expansion of P. mirabilis in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Klebsiella pneumoniae is increased.
expansion of K. pneumoniae in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction whereProteobacteria is increased.
expansion of Proteobacteria in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Helicobacter is increased.
expansion of Helicobacter in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Roseburia hominis is decreased.
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.
depletion of Blautia coccoides in RA human gut compared to fibromyalgia patients
A colorectal cancer human-gut microbiome interaction where Helicobacter pylori is increased.
expansion of H. pylori in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Helicobacter hepaticus is increased.
expansion of H. hepaticus in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Fusobacterium nucleatum is increased.
expansion of F. nucleatum in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Peptostreptococcus anaerobius is increased.
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.
depletion of Bacteroides in RA human gut compared to fibromyalgia patients
A colorectal cancer human-gut microbiome interaction where Fusobacterium hwasookii is increased.
expansion of F. hwasookii in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Porphyromonas gingivalis is increased.
expansion of P. gingivalis in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Selenomonas is increased.
expansion of Selenomonas in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Prevotella is increased.
expansion of Prevotella in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Peptostreptococcus stomatis is increased.
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.
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.
expansion of Solobacterium sp. S4-A19 in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Dolosicoccus paucivorans is increased.
expansion of D. paucivorans in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Clostridium sp. cp01.19 is increased.
expansion of Clostridium sp. cp01.19 in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Bacteroides sp. is increased.
expansion of Bacteroides sp. in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Subdoligranulum sp. 60_17 is decreased.
depletion of Subdoligranulum sp. 60_17 in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Mycobacterium avium is increased.
expansion of M. avium in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Escherichia coli B is increased.
expansion of E. coli B in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Aggregatibacter actinomycetemcomitans is increased.
expansion of A. actinomycetemcomitans in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where [Haemophilus] ducreyi is increased.
expansion of H. ducreyi in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Shigella dysenteriae is increased.
expansion of S. dysenteriae in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Campylobacter jejuni is increased.
expansion of Campylobacter jejuni in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Salmonella enterica is increased.
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.
depletion of Bifidobacterium bifidum in RA human gut compared to fibromyalgia patients
A colorectal cancer human-gut microbiome interaction where Pseudomonas is increased.
expansion of Pseudomonas in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Acinetobacter is increased.
expansion of Acinetobacter in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Blautia obeum is increased.
expansion of B.obeum in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Catenisphaera adipataccumulans is increased.
expansion of C. adipataccumulans in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Microbacterium is increased.
expansion of Microbacterium in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Anoxybacillus is increased.
expansion of Anoxybacillus in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Citrobacter rodentium is increased.
expansion of C. rodentium in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Enterococcus faecalis is increased.
expansion of E. faecalis in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where [Clostridium] scindens is increased.
expansion of C. scindens in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where [Clostridium] hiranonis is increased.
expansion of C. hiranonis in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where [Clostridium] hylemonae is increased.
expansion of C.hylemonae in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Acidovorax is increased.
expansion of Acidovorax in colorectal cancer human gut
A colorectal cancer human-gut microbiome interaction where Streptococcus gallolyticus is increased.
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.
depletion of Haemophilus spp. in RA human gut
A colorectal cancer human-gut microbiome interaction where Fusobacterium nucleatum subsp. nucleatum is increased.
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.
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.
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.
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.
expansion of Bacteroides sp. in RA human gut
A RA human-gut microbiome interaction where Lachnospiraceae bacterium is increased.
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.
microbe
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.
invisible to unaided eye
A collection of microbial organisms that reside in a particular environment.
Jie Zheng, Oliver He, Anna Maria Masci, Jihad Obeid
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.
pH value
A drug product that has its ability to alter the progression of a rheumatic disease.
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
relative abundance of microbe in host
microbial genome
the mean species diversity in sites or habitats at a local scale
alpha diversity
the ratio between regional and local species diversity
beta diversity
the total species diversity in a landscape
gamma diversity
A biological process that leads to the restoration of microbial community in a host organism
host microbiome restoration
A host microbiome restoration that is due to a treatment
host microbiome restoration by treatment
host microbiome restoration by a DMARD treatment
host microbiome restoration by DMARD
host microbiome restoration by an antibiotics treatment
host microbiome restoration by antibiotics
host microbiome restoration through the transplantation of a microbiota into the host
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
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
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
microbiome-gut-brain interaction
An host-microbiome interaction that is associated with cancer
microbiome-cancer interaction
An interaction between microbiome and host immune system that is associated with cancer
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.
host
A time quality inhering in a bearer by virtue of how long the bearer has existed.
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.
A quality which inheres in a continuant.
multiply inhering quality of a physical entity
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.
A quality that inheres in an entire organism or part of an organism.
A quality that inheres in an entire population or part of a population.
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.
May be of the same or different species.
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
An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA.
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].
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
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
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
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]
Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome.
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
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
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.
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]
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.
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]
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
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]
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
Anatomical group that has its parts adjacent to one another.
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
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
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]
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
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.
Excretion that is the output of a kidney
kidney excreta from some taxa (e.g. in aves) may not be liquid
Portion of semisolid bodily waste discharged through the anus[MW,modified]
Excretion in semisolid state processed by the intestine.[FMA]
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]
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
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
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.
An anatomical structure that has more than one cell as a part.
Any of the organs or elements that are part of the digestive system. Examples: tongue, esophagus, spleen, crop, lunge feeding organ, tooth elements.
A unit which is a standard measure of the dimension in which events occur in sequence.
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
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.
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.
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
Ontology for Biomedical Investigations
Advisors for this project come from the IFOMIS group, Saarbruecken and from the Co-ODE group in Manchester
Allyson Lister
Barry Smith
Bill Bug
Carlo Torniai
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
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
Yongqun He
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.
An ontology for the annotation of biomedical and functional genomics experiments.
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.
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]
Includes Ontology(OntologyID(Anonymous-21)) [Axioms: 26 Logical Axioms: 0]