Bin Zhao
Edison Ong
Yongqun He (Oliver)
Yu Lin (Asiyah)
OHPI is a biomedical ontology in the area of host-pathogen interactions. OHPI is developed by following the OBO Foundry Principles (e.g., openness and collaboration).
OWL-DL
A biomedical ontology in the area of host-pathogen interactions.
OHPI: Ontology of Host-Pathogen Interactions
BFO OWL specification label
BFO OWL规范标签
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.
将本体中的实体关联到用于在代码中表示它的变量的名称，这些代码从lispy规范生成BFO OWL 文件。
Really of interest to developers only
只对开发人员感兴趣
BFO CLIF specification label
BFO CLIF规范标签
Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2
将本体中的实体关联到用于在BFO2 CLIF规范中表示它的术语上。
Person:Alan Ruttenberg
An annotation property that represents an ID used in the NIH LINCS project.
An annotation property that represents an LINCS ID of a cell line.
Oliver He, Jiangan Xie
Cell line LINCS ID
LINCS ID
细胞系LINCS ID
editor preferred label
editor preferred term
editor preferred term~editor preferred label
编辑首选术语
编辑首选标签
The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)
对于一类或属性的简洁的、有意义的、与人类友好的名称由本体开发商首选。 （美国英语）
PERSON:Daniel Schober
example
example of usage
例子
用法示例
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.
短语描述一个类的名字应该如何使用。也可包括其他类型有助于直接理解类的语义的例子，如广为人知的类的原型子类或实例。虽然高水平的术语必不可少，对于低级别术语的示例（例如，Affymetrix HU133阵列）不
has curation status
有管理状态
PERSON:Alan Ruttenberg
PERSON:Bill Bug
PERSON:Melanie Courtot
definition
textual definition
定义
OBI的官方定义，解释类或属性的含义。应该是亚里士多德式的，形式化和规范化的。 可以通过口语定义进行扩充。
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.
官方的定义，解释类或属性的含义。应该是亚里士多德式的，形式化和规范化的。 可以通过口语定义进行扩充。
2012-04-05: Barry Smith OBI的官方定义解释了一个类或属性的含义：'应该是亚里士多德式的，形式化和规范化的。可以用口语定义'是糟糕的。 您能解决这样的问题吗？ 解释关于类或属性的表达含义的必要和充分条件的陈述。 Alan Ruttenberg 您提出的定义是一个合理的备选，除非它很常见，没有给出必要和充分的条件。大多数情况下它们是必要的，偶尔是必要的，充分的或者仅仅仅充分的。它们通常使用不是自己定义的术语，因此它们实际上不能通过这些标准进行评估。 关于拟议定义的具体内容： 我们没有“含义”，或“表达”或“属性”的定义。对于在预期意义上的“参考”，我认为我们使用术语“指示”。对于'表达'，我认为我们和你的意思是符号，或标识符。对于“含义”，它不同于类和属性。对于类，我们希望文档能够让读者确定一个实体是否是该类的实例。对于属性，让我们的目标读者决定，给定一对潜在的关系，判断关系成立的断言正确与否。 “目标读者”部分表明我们也指定了我们期望的能够理解定义的人，并且概括了人类和计算机读者以包含文本和逻辑定义。 就我个人而言，我更愿意削弱对文档的定义，并指出什么是可取的。 我们还有一个悬而未决的问题，就是如何针对不同的受众定位不同的定义。临床读者阅读chebi需要来自受过化学训练的受众的不同类型的定义文档/定义，同样需要一个适合本体工作者的定义。
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.
文本定义
editor note
编者注
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.
管理者注释用于其编辑器。它可能不包含在本体的出版版本中，所以它应该不包含最终用户了解本体所需的信息。
uberon
editor_note
编辑_注释
definition editor
term editor
术语编辑者
Name of editor entering the definition in the file. The definition editor is a point of contact for information regarding the term. The definition editor may be, but is not always, the author of the definition, which may have been worked upon by several people
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
输入文件中术语编辑者的名称。术语编辑者是有关术语的信息交汇点。术语编辑者可以是，但并不总是，定义的作者，这可能是由几个人完成
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.
20110707，MC：术语编辑和定义进行相应的修改。见http://code.google.com/p/information-artifact-ontology/issues/detail?id=115。
alternative term
替代术语
An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)
一类或属性的替代名称，这意味着与所述首选名称同样的事物（语义上等价）
definition source
定义来源
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.
正式引用，例如在外部数据库中的标识符，用于表示/定义的属性源（S）。自由文本表示/为定义属性源（S）。实例：在2007年1月31日的作者姓名，URI，MeSH术语C04，PUBMEDID，维基uri
Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
论OBO-讨论邮件-列表，请参阅http://bit.ly/hgm99w
has obsolescence reason
Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification.
curator note
管理者注释
An administrative note of use for a curator but of no use for a user
管理者注释对管理者有用对用户无用
curator_notes
管理者_注释
curator notes
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
The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition.
The 'term requester' can credit the person, organization or project who request the ontology term.
ontology term requester
expand expression to
ObjectProperty: RO_0002104 Label: has plasma membrane part Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)"
A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones
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
说明
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
在最高级别的本体中的原始术语如BFO是对我们理解现实最基本，以至于无法以非循环的方式来定义它们的术语。对于这些，因此，我们只能提供说明，通过例子和公理进行补充
has associated axiom(nl)
具有相关联的公理（nl）
An axiom associated with a term expressed using natural language
与一个使用自然语言表达的术语相关的公理
has associated axiom(fol)
具有相关联的公理（fol）
An axiom expressed in first order logic using CLIF syntax
使用CLIF语法在第一逻辑进行表达的公理
has axiom id
A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI
has axiom label
term replaced by
Add as annotation triples in the granting ontology
Use on obsolete terms, relating the term to another term that can be used as a substitute
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
the symbol assigned by the nomenclature authority
symbol from nomenclature authority
the full name assigned by the nomenclature authority
full name from nomenclature authority
NCBI GeneID
NCBI LocusTag
gene map location
modification date
The NCBITaxon ontology ID of an organism.
organism NCBITaxon ID
A chromosome ID where a gene is located.
chromosome ID of gene
an annotation property that specifies the type of a gene
type of gene
an annotation property that specifies a nomenclature status
nomenclature status
an annotation property that shows the GO information associated with a specific gene.
YH: use the convention: GO_ID (EC: xx; Qualifier: xx; PMID: xxxxx;) where GO_ID is a GO ID, EC is the Evidence Code, Qualifier is a specific association type, and PMID is a PubMed ID of a paper that supports the gene-GO association.
has GO association
An annotation property that represents a gene's association with PubMed publication(s).
YH: use the format: PMID: pmid1, pmid2, ... where pmid1 and pmid2 are specfic PubMed IDs (PMIDs).
has PubMed association
The annotation of the gene as a virulence factor stored in the Victors database (http://www.phidias.us/victors/).
has Victors annotation
The idenfier of the entity stored in the Victors database (http://www.phidias.us/victors/).
has Victors id
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
S dubious_for_taxon T if it is probably the case that no instances of S can be found in any instance of T.
This relation lacks a strong logical interpretation, but can be used in place of never_in_taxon where it is desirable to state that the definition of the class is too strict for the taxon under consideration, but placing a never_in_taxon link would result in a chain of inconsistencies that will take ongoing coordinated effort to resolve. Example: metencephalon in teleost
this relation lacks a strong logical interpretation, but can be used in place of never_in_taxon where it is desirable to state that the definition of the class is too strict for the taxon under consideration, but placing a never_in_taxon link would result in a chain of inconsistencies that will take time to resolve. Example: metencephalon in teleost
dubious for taxon
S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S
present in taxon
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'
If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL
If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R.
is a defining property chain axiom where second argument is reflexive
part-of is homeomorphic for independent continuants.
R is homemorphic for C iff (1) there exists some x,y such that x R y, and x and y instantiate C and (2) for all x, if x is an instance of C, and there exists some y some such that x R y, then it follows that y is an instance of C.
R homeomorphic-for C expands to: C SubClassOf R only C. Additionally, for any class D that is disjoint with C, we can also expand to C DisjointWith R some D, D DisjointWith R some C.
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
A textual description of an axiom loss in this ontology compared to an external ontology.
Notes on the homology status of this class.
An alternate comment for a class taken unmodified from an external source. Note that obo format only allows a single comment for a class, and does not provide a structured means of adding provenance info.
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 evolved function of instances of this class.
Notes on the structure, composition or histology of instances of this class.
Notes on the ontogenic development of instances of this class.
Notes on how similar or equivalent classes are represented in other ontologies.
Notes on how lexical conventions regarding this class, in particular any issues that may arise due to homonyny or synonymy.
A property used in conjunction with repeated_element_number to indicate an axis and directionality along that axis. If P preceding_element_is R, and P is_count_of S, and X P N, and X' P N+1, then it follows that every X R some X', and the class expression [S and R some X' and inv(R) some X] is empty (i.e. X is followed by X', with no intermediates)
x pharyngeal_arch_number N if and only if (i) x is a pharyngeal arch, and (ii) x is ancestrally pharyngeal arch number N in a series of pharyngeal arches repeated along a antero-posterior axis, with arch_number 1 being the mandibular arch.
gill arch N = PA N-2. the term branchial_arch is ambiguous.
FMA has terms like 'set of X'. In general we do not include set-of terms in uberon, but provide a mapping between the singular form and the FMA set term
Term not to be used for direct annotation
Term not to be used for direct manual annotation
A metadata relation between a class and its taxonomic rank (eg species, family)
Label appended to organism-specific terms in place of scientific name
Unique short label for PRO terms for display purposes; based on orthology
A historic synonym, no longer encouraged
preferred term when talking about an instance of this class in Homo sapiens
indicates that a synonym is used in an inconsistent or confusing way, typically between species
expert consultation and attribution required
A class that represents an early developmental structure, like a blastocyst. This part of the ontology is undergoing review to remove inappropriate grouping classes.
derived from the union of EHDAA2 and EMAPA - still to be checked
Subset consisting of classes creating for grouping purposes
A grouping class that depends on an assumption of homology between subclasses
classes that have some inconsistency with FMA
somewhat fuzzy grouping for analysis purposes, currently composed of something like: liver, heart, skeletal, kidney, bladder, brain, skin, mouth, esophagus, stomach, small intestine, large intestines, trachea nose, lungs, brain, spinal cord, peripheral nerves, kidneys, ureters, bladder, urethra, gonads
abstract class brought in to group ontology classes but not informative
organs, excluding individual muscles and skeletal elements
A subset specifically created for the 2012 Phenotype RCN meeting. Includes some human-specific terms that may eventually be removed when they are adequately represented with part of relationships in FMA
Uberon slim - subset that excludes obscure terms and deep compositional terms
abstract upper-level terms not directly useful for analysis
core classes typically found across vertebrates. one purpose is to create a rough set of terms that could be used to start a new vertebrate AO
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
Typically, a Title will be a name by which the resource is formally known.
A name given to the resource.
Title
Type includes terms describing general categories, functions, genres, or aggregation levels for content. Recommended best practice is to select a value from a controlled vocabulary (for example, the DCMI Type Vocabulary [DCMITYPE]). To describe the physical or digital manifestation of the resource, use the Format element.
The nature or genre of the content of the resource.
Resource Type
database_cross_reference
数据库_交叉_引用
has_obo_namespace
有_obo_命名空间
shorthand
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
b inheres_in c at t =Def. b is a dependent continuant & c is an independent continuant that is not a spatial region & b s-depends_on c at t. (axiom label in BFO2 Reference: [051-002])
Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'inheres in at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'inheres in@en(x,y,t)'.
BFO 2 Reference: Inherence is a subrelation of s-depends_on which holds between a dependent continuant and an independent continuant that is not a spatial region. Since dependent continuants cannot migrate from one independent continuant bearer to another, it follows that if b s-depends_on independent continuant c at some time, then b s-depends_on c at all times at which a exists. Inherence is in this sense redundantly time-indexed.For example, consider the particular instance of openness inhering in my mouth at t as I prepare to take a bite out of a donut, followed by a closedness at t+1 when I bite the donut and start chewing. The openness instance is then shortlived, and to say that it s-depends_on my mouth at all times at which this openness exists, means: at all times during this short life. Every time you make a fist, you make a new (instance of the universal) fist. (Every time your hand has the fist-shaped quality, there is created a new instance of the universal fist-shaped quality.)
BFO2 Reference: independent continuant that is not a spatial region
BFO2 Reference: specifically dependent continuant
(iff (inheresInAt a b t) (and (DependentContinuant a) (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))) // axiom label in BFO2 CLIF: [051-002]
inheres in at all times
b bearer_of c at t =Def. c s-depends_on b at t & b is an independent continuant that is not a spatial region. (axiom label in BFO2 Reference: [053-004])
Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'bearer of at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'bearer of@en'(x,y,t)
(iff (bearerOfAt a b t) (and (specificallyDependsOnAt b a t) (IndependentContinuant a) (not (SpatialRegion a)) (existsAt b t))) // axiom label in BFO2 CLIF: [053-004]
bearer of at some time
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])
if a realizable entity b is realized in a process p, then p stands in the has_participant relation to the bearer of b. (axiom label in BFO2 Reference: [106-002])
(forall (x y z t) (if (and (RealizableEntity x) (Process y) (realizesAt y x t) (bearerOfAt z x t)) (hasParticipantAt y z t))) // axiom label in BFO2 CLIF: [106-002]
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])
(forall (x y t) (if (realizesAt x y t) (and (Process x) (or (Disposition y) (Role y)) (exists (z) (and (MaterialEntity z) (hasParticipantAt x z t) (bearerOfAt z y t)))))) // axiom label in BFO2 CLIF: [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
[copied from inverse property 'has participant at some time'] Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'has participant at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'has participant@en'(x,y,t)
[copied from inverse property 'has participant at some time'] BFO 2 Reference: Spatial regions do not participate in processes.
[copied from inverse property 'has participant at some time'] BFO2 Reference: independent continuant that is not a spatial region, specifically dependent continuant, generically dependent continuant
[copied from inverse property 'has participant at some time'] BFO2 Reference: process
[copied from inverse property 'has participant at some time'] has_participant is an instance-level relation between a process, a continuant, and a temporal region at which the continuant participates in some way in the process. (axiom label in BFO2 Reference: [086-003])
participates in at some time
preceded by
X preceded_by Y iff: end(Y) before_or_simultaneous_with start(X)
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
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 [XXX-001
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
[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 [XXX-001
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
A pain s-depends_on the organism that is experiencing the pain
a gait s-depends_on the walking object. (All at some specific time.)
a shape s-depends_on the shaped object
one-sided s-dependence of a dependent continuant on an independent continuant: an instance of headache s-depends_on some head
one-sided s-dependence of a dependent continuant on an independent continuant: an instance of temperature s-depends_on some organism
one-sided s-dependence of a process on something: a process of cell death s-depends_on a cell
one-sided s-dependence of a process on something: an instance of seeing (a relational process) s-depends_on some organism and on some seen entity, which may be an occurrent or a continuant
one-sided s-dependence of one occurrent on another: a process of answering a question is dependent on a prior process of asking a question
one-sided s-dependence of one occurrent on another: a process of obeying a command is dependent on a prior process of issuing a command
one-sided s-dependence of one occurrent on multiple independent continuants: a relational process of hitting a ball with a cricket bat
one-sided s-dependence of one occurrent on multiple independent continuants: a relational process of paying cash to a merchant in exchange for a bag of figs
reciprocal s-dependence between occurrents: a process of buying and the associated process of selling
reciprocal s-dependence between occurrents: a process of increasing the volume of a portion of gas while temperature remains constant and the associated process of decreasing the pressure exerted by the gas
reciprocal s-dependence between occurrents: in a game of chess the process of playing with the white pieces is mutually dependent on the process of playing with the black pieces
the one-sided dependence of an occurrent on an independent continuant: football match on the players, the ground, the ball
the one-sided dependence of an occurrent on an independent continuant: handwave on a hand
the three-sided reciprocal s-dependence of the hue, saturation and brightness of a color [45
the three-sided reciprocal s-dependence of the pitch, timbre and volume of a tone [45
the two-sided reciprocal s-dependence of the roles of husband and wife [20
Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'specifically depends on at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'specifically depends on@en(x,y,t)'.
BFO 2 Reference: An entity – for example an act of communication or a game of football – can s-depends_on more than one entity. Complex phenomena for example in the psychological and social realms (such as inferring, commanding and requesting) or in the realm of multi-organismal biological processes (such as infection and resistance), will involve multiple families of dependence relations, involving both continuants and occurrents [1, 4, 28
BFO 2 Reference: S-dependence is just one type of dependence among many; it is what, in the literature, is referred to as ‘existential dependence’ [87, 46, 65, 20
BFO 2 Reference: the relation of s-depends_on does not in every case require simultaneous existence of its relata. Note the difference between such cases and the cases of continuant universals defined historically: the act of answering depends existentially on the prior act of questioning; the human being who was baptized or who answered a question does not himself depend existentially on the prior act of baptism or answering. He would still exist even if these acts had never taken place.
BFO2 Reference: specifically dependent continuant\; process; process boundary
To say that b s-depends_on a at t is to say that b and c do not share common parts & b is of its nature such that it cannot exist unless c exists & b is not a boundary of c and b is not a site of which c is the host [64
If b is s-depends_on something at some time, then b is not a material entity. (axiom label in BFO2 Reference: [052-001])
If b s-depends_on something at t, then there is some c, which is an independent continuant and not a spatial region, such that b s-depends_on c at t. (axiom label in BFO2 Reference: [136-001])
If occurrent b s-depends_on some independent continuant c at t, then b s-depends_on c at every time at which b exists. (axiom label in BFO2 Reference: [015-002])
an entity does not s-depend_on any of its (continuant or occurrent) parts or on anything it is part of. (axiom label in BFO2 Reference: [013-002])
if b s-depends_on c at t & c s-depends_on d at t then b s-depends_on d at t. (axiom label in BFO2 Reference: [054-002])
(forall (x y t) (if (and (Entity x) (or (continuantPartOfAt y x t) (continuantPartOfAt x y t) (occurrentPartOf x y) (occurrentPartOf y x))) (not (specificallyDependsOnAt x y t)))) // axiom label in BFO2 CLIF: [013-002]
(forall (x y t) (if (and (Occurrent x) (IndependentContinuant y) (specificallyDependsOnAt x y t)) (forall (t_1) (if (existsAt x t_1) (specificallyDependsOnAt x y t_1))))) // axiom label in BFO2 CLIF: [015-002]
(forall (x y t) (if (specificallyDependsOnAt x y t) (exists (z) (and (IndependentContinuant z) (not (SpatialRegion z)) (specificallyDependsOnAt x z t))))) // axiom label in BFO2 CLIF: [136-001]
(forall (x y z t) (if (and (specificallyDependsOnAt x y t) (specificallyDependsOnAt y z t)) (specificallyDependsOnAt x z t))) // axiom label in BFO2 CLIF: [054-002]
(forall (x) (if (exists (y t) (specificallyDependsOnAt x y t)) (not (MaterialEntity x)))) // axiom label in BFO2 CLIF: [052-001]
specifically depends on at all times
a function_of b at t =Def. a is a function and a inheres_in b at t. (axiom label in BFO2 Reference: [067-001])
Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'function of at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'function of@en(x,y,t)'.
(iff (functionOf a b t) (and (Function a) (inheresInAt a b t))) // axiom label in BFO2 CLIF: [067-001]
function of at all times
b quality_of c at t = Def. b is a quality & c is an independent continuant that is not a spatial region & b s-depends_on c at t. (axiom label in BFO2 Reference: [056-002])
Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'quality of at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'quality of@en(x,y,t)'.
(iff (qualityOfAt a b t) (and (Quality a) (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))) // axiom label in BFO2 CLIF: [056-002]
quality of at all times
a role_of b at t =Def. a is a role and a inheres_in b at t. (axiom label in BFO2 Reference: [065-001])
Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'role of at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'role of@en(x,y,t)'.
(iff (roleOfAt a b t) (and (Role a) (inheresInAt a b t))) // axiom label in BFO2 CLIF: [065-001]
role of at all times
Mary located_in Salzburg
the Empire State Building located_in New York.
this portion of cocaine located_in this portion of blood
this stem cell located_in this portion of bone marrow
your arm located_in your body
b located_in c at t = Def. b and c are independent continuants, and the region at which b is located at t is a (proper or improper) continuant_part_of the region at which c is located at t. (axiom label in BFO2 Reference: [045-001])
Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'located in at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'located in@en(x,y,t)'.
Located_in is transitive. (axiom label in BFO2 Reference: [046-001])
for all independent continuants b, c, and d: if b continuant_part_of c at t & c located_in d at t, then b located_in d at t. (axiom label in BFO2 Reference: [048-001])
for all independent continuants b, c, and d: if b located_in c at t & c continuant_part_of d at t, then b located_in d at t. (axiom label in BFO2 Reference: [049-001])
(forall (x y z t) (if (and (IndependentContinuant x) (IndependentContinuant y) (IndependentContinuant z) (continuantPartOfAt x y t) (locatedInAt y z t)) (locatedInAt x z t))) // axiom label in BFO2 CLIF: [048-001]
(forall (x y z t) (if (and (IndependentContinuant x) (IndependentContinuant y) (IndependentContinuant z) (locatedInAt x y t) (continuantPartOfAt y z t)) (locatedInAt x z t))) // axiom label in BFO2 CLIF: [049-001]
(forall (x y z t) (if (and (locatedInAt x y t) (locatedInAt y z t)) (locatedInAt x z t))) // axiom label in BFO2 CLIF: [046-001]
(iff (locatedInAt a b t) (and (IndependentContinuant a) (IndependentContinuant b) (exists (r_1 r_2) (and (occupiesSpatialRegionAt a r_1 t) (occupiesSpatialRegionAt b r_2 t) (continuantPartOfAt r_1 r_2 t))))) // axiom label in BFO2 CLIF: [045-001]
located in at all times
Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'occupies spatial region at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'occupies spatial region@en'(x,y,t)
b occupies_spatial_region r at t means that r is a spatial region in which independent continuant b is exactly located (axiom label in BFO2 Reference: [041-002])
every region r is occupies_spatial_region r at all times. (axiom label in BFO2 Reference: [042-002])
if b occupies_spatial_region r at t & b continuant_part_of b at t, then there is some r which is continuant_part_of r at t such that b occupies_spatial_region r at t. (axiom label in BFO2 Reference: [043-001])
(forall (r t) (if (Region r) (occupiesSpatialRegionAt r r t))) // axiom label in BFO2 CLIF: [042-002]
(forall (x r t) (if (occupiesSpatialRegionAt x r t) (and (SpatialRegion r) (IndependentContinuant x)))) // axiom label in BFO2 CLIF: [041-002]
(forall (x y r_1 t) (if (and (occupiesSpatialRegionAt x r_1 t) (continuantPartOfAt y x t)) (exists (r_2) (and (continuantPartOfAt r_2 r_1 t) (occupiesSpatialRegionAt y r_2 t))))) // axiom label in BFO2 CLIF: [043-001]
occupies spatial region at some time
a has_function b at t =Def. b function_of a at t. (axiom label in BFO2 Reference: [070-001])
Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'has function at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'has function@en'(x,y,t)
(iff (hasFunctionAt a b t) (functionOf b a t)) // axiom label in BFO2 CLIF: [070-001]
has function at some time
has quality at some time
a has_role b at t =Def. b role_of a at t. (axiom label in BFO2 Reference: [068-001])
Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'has role at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'has role@en'(x,y,t)
(iff (hasRoleAt a b t) (roleOfAt b a t)) // axiom label in BFO2 CLIF: [068-001]
has role at some time
[copied from inverse property 'generically depends on at some time'] Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'generically depends on at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'generically depends on@en'(x,y,t)
[copied from inverse property 'generically depends on at some time'] BFO2 Reference: generically dependent continuant
[copied from inverse property 'generically depends on at some time'] BFO2 Reference: independent continuant
[copied from inverse property 'generically depends on at some time'] b g-depends on c at t1 means: b exists at t1 and c exists at t1 & for some type B it holds that (c instantiates B at t1) & necessarily, for all t (if b exists at t then some instance_of B exists at t) & not (b s-depends_on c at t1). (axiom label in BFO2 Reference: [072-002])
has generic dependent at some time
a disposition_of b at t =Def. a is a disposition and a inheres_in b at t. (axiom label in BFO2 Reference: [066-001])
Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'disposition of at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'disposition of@en(x,y,t)'.
(iff (dispositionOf a b t) (and (Disposition a) (inheresInAt a b t))) // axiom label in BFO2 CLIF: [066-001]
disposition of at all times
b exists_at t means: b is an entity which exists at some temporal region t. (axiom label in BFO2 Reference: [118-002])
exists at
a has_disposition b at t =Def. b disposition_of a at t. (axiom label in BFO2 Reference: [069-001])
Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'has disposition at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'has disposition@en'(x,y,t)
(iff (hasDispositionAt a b t) (dispositionOf b a t)) // axiom label in BFO2 CLIF: [069-001]
has disposition at some time
the material basis of John’s disposition to cough is the viral infection in John’s upper respiratory tract
the material basis of the disposition to wear unevenly of John’s tires is the worn suspension of his car.
Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'has material basis at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'has material basis@en(x,y,t)'.
b has_material_basis c at t means: b is a disposition & c is a material entity & there is some d bearer_of b at t& c continuant_part_of d at t& d has_disposition b at t because c continuant_part_of d at t. (axiom label in BFO2 Reference: [071-002])
(forall (x y t) (if (hasMaterialBasisAt x y t) (and (Disposition x) (MaterialEntity y) (exists (z) (and (bearerOfAt z x t) (continuantPartOfAt y z t) (exists (w) (and (Disposition w) (if (hasDisposition z w) (continuantPartOfAt y z t))))))))) // axiom label in BFO2 CLIF: [071-002]
has material basis at all times
[copied from inverse property 'part of occurrent'] Mary’s 5th birthday occurrent_part_of Mary’s life
[copied from inverse property 'part of occurrent'] The process of a footballer’s heart beating once is an occurrent part but not a temporal_part of a game of football.
[copied from inverse property 'part of occurrent'] the first set of the tennis match occurrent_part_of the tennis match.
b has_occurrent_part c = Def. c occurrent_part_of b. (axiom label in BFO2 Reference: [007-001])
[copied from inverse property 'part of occurrent'] BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion.
[copied from inverse property 'part of occurrent'] BFO2 Reference: occurrent
[copied from inverse property 'part of occurrent'] b occurrent_part_of c =Def. b is a part of c & b and c are occurrents. (axiom label in BFO2 Reference: [003-002])
(iff (hasOccurrentPart a b) (occurrentPartOf b a)) // axiom label in BFO2 CLIF: [007-001]
has occurrent part
[copied from inverse property 'proper part of occurrent'] b proper_occurrent_part_of c =Def. b occurrent_part_of c & b and c are not identical. (axiom label in BFO2 Reference: [005-001])
b has_proper_occurrent_part c = Def. c proper_occurrent_part_of b. [XXX-001
has proper occurrent part
has profile
[copied from inverse property 'temporal part of'] the 4th year of your life is a temporal part of your life\. The first quarter of a game of football is a temporal part of the whole game\. The process of your heart beating from 4pm to 5pm today is a temporal part of the entire process of your heart beating.\ The 4th year of your life is a temporal part of your life
[copied from inverse property 'temporal part of'] the process boundary which separates the 3rd and 4th years of your life.
[copied from inverse property 'temporal part of'] your heart beating from 4pm to 5pm today is a temporal part of the process of your heart beating
[copied from inverse property 'temporal part of'] b proper_temporal_part_of c =Def. b temporal_part_of c & not (b = c). (axiom label in BFO2 Reference: [116-001])
[copied from inverse property 'temporal part of'] b temporal_part_of c =Def.b occurrent_part_of c & & for some temporal region t, b occupies_temporal_region t & for all occurrents d, t (if d occupies_temporal_region t & t? occurrent_part_of t then (d occurrent_part_of a iff d occurrent_part_of b)). (axiom label in BFO2 Reference: [078-003])
has temporal part
[copied from inverse property 'occupies spatial region at some time'] Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'occupies spatial region at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'occupies spatial region@en'(x,y,t)
[copied from inverse property 'occupies spatial region at some time'] BFO2 Reference: independent continuant
[copied from inverse property 'occupies spatial region at some time'] BFO2 Reference: spatial region
[copied from inverse property 'occupies spatial region at some time'] b occupies_spatial_region r at t means that r is a spatial region in which independent continuant b is exactly located (axiom label in BFO2 Reference: [041-002])
has spatial occupant at some time
[copied from inverse property 'specifically depends on at some time'] A pain s-depends_on the organism that is experiencing the pain
[copied from inverse property 'specifically depends on at some time'] a gait s-depends_on the walking object. (All at some specific time.)
[copied from inverse property 'specifically depends on at some time'] a shape s-depends_on the shaped object
[copied from inverse property 'specifically depends on at some time'] one-sided s-dependence of a dependent continuant on an independent continuant: an instance of headache s-depends_on some head
[copied from inverse property 'specifically depends on at some time'] one-sided s-dependence of a dependent continuant on an independent continuant: an instance of temperature s-depends_on some organism
[copied from inverse property 'specifically depends on at some time'] one-sided s-dependence of a process on something: a process of cell death s-depends_on a cell
[copied from inverse property 'specifically depends on at some time'] one-sided s-dependence of a process on something: an instance of seeing (a relational process) s-depends_on some organism and on some seen entity, which may be an occurrent or a continuant
[copied from inverse property 'specifically depends on at some time'] one-sided s-dependence of one occurrent on another: a process of answering a question is dependent on a prior process of asking a question
[copied from inverse property 'specifically depends on at some time'] one-sided s-dependence of one occurrent on another: a process of obeying a command is dependent on a prior process of issuing a command
[copied from inverse property 'specifically depends on at some time'] one-sided s-dependence of one occurrent on multiple independent continuants: a relational process of hitting a ball with a cricket bat
[copied from inverse property 'specifically depends on at some time'] one-sided s-dependence of one occurrent on multiple independent continuants: a relational process of paying cash to a merchant in exchange for a bag of figs
[copied from inverse property 'specifically depends on at some time'] reciprocal s-dependence between occurrents: a process of buying and the associated process of selling
[copied from inverse property 'specifically depends on at some time'] reciprocal s-dependence between occurrents: a process of increasing the volume of a portion of gas while temperature remains constant and the associated process of decreasing the pressure exerted by the gas
[copied from inverse property 'specifically depends on at some time'] reciprocal s-dependence between occurrents: in a game of chess the process of playing with the white pieces is mutually dependent on the process of playing with the black pieces
[copied from inverse property 'specifically depends on at some time'] the one-sided dependence of an occurrent on an independent continuant: football match on the players, the ground, the ball
[copied from inverse property 'specifically depends on at some time'] the one-sided dependence of an occurrent on an independent continuant: handwave on a hand
[copied from inverse property 'specifically depends on at some time'] the three-sided reciprocal s-dependence of the hue, saturation and brightness of a color [45
[copied from inverse property 'specifically depends on at some time'] the three-sided reciprocal s-dependence of the pitch, timbre and volume of a tone [45
[copied from inverse property 'specifically depends on at some time'] the two-sided reciprocal s-dependence of the roles of husband and wife [20
[copied from inverse property 'specifically depends on at some time'] Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'specifically depends on at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'specifically depends on@en'(x,y,t)
[copied from inverse property 'specifically depends on at some time'] BFO 2 Reference: An entity – for example an act of communication or a game of football – can s-depends_on more than one entity. Complex phenomena for example in the psychological and social realms (such as inferring, commanding and requesting) or in the realm of multi-organismal biological processes (such as infection and resistance), will involve multiple families of dependence relations, involving both continuants and occurrents [1, 4, 28
[copied from inverse property 'specifically depends on at some time'] BFO 2 Reference: S-dependence is just one type of dependence among many; it is what, in the literature, is referred to as ‘existential dependence’ [87, 46, 65, 20
[copied from inverse property 'specifically depends on at some time'] BFO 2 Reference: the relation of s-depends_on does not in every case require simultaneous existence of its relata. Note the difference between such cases and the cases of continuant universals defined historically: the act of answering depends existentially on the prior act of questioning; the human being who was baptized or who answered a question does not himself depend existentially on the prior act of baptism or answering. He would still exist even if these acts had never taken place.
[copied from inverse property 'specifically depends on at some time'] BFO2 Reference: specifically dependent continuant\; process; process boundary
[copied from inverse property 'specifically depends on at some time'] To say that b s-depends_on a at t is to say that b and c do not share common parts & b is of its nature such that it cannot exist unless c exists & b is not a boundary of c and b is not a site of which c is the host [64
has specific dependent at some time
[copied from inverse property 'occupies spatiotemporal region'] BFO 2 Reference: The occupies_spatiotemporal_region and occupies_temporal_region relations are the counterpart, on the occurrent side, of the relation occupies_spatial_region.
[copied from inverse property 'occupies spatiotemporal region'] p occupies_spatiotemporal_region s. This is a primitive relation between an occurrent p and the spatiotemporal region s which is its spatiotemporal extent. (axiom label in BFO2 Reference: [082-003])
has spatiotemporal occupant
material basis of at some time
each piece in a chess set is a member part of the chess set; each Beatle in the collection called The Beatles is a member part of The Beatles.
each tree in a forest is a member_part of the forest
b member_part_of c at t =Def. b is an object & there is at t a mutually exhaustive and pairwise disjoint partition of c into objects x1, …, xn (for some n > 1) with b = xi for some 1 ? i ? n. (axiom label in BFO2 Reference: [026-004])
Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'member part of at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'member part of@en'(x,y,t)
if b member_part_of c at t then b continuant_part_of c at t. (axiom label in BFO2 Reference: [104-001])
(forall (x y t) (if (memberPartOfAt x y t) (continuantPartOfAt x y t))) // axiom label in BFO2 CLIF: [104-001]
member part of at some time
BFO 2 Reference: The occupies_spatiotemporal_region and occupies_temporal_region relations are the counterpart, on the occurrent side, of the relation occupies_spatial_region.
p occupies_spatiotemporal_region s. This is a primitive relation between an occurrent p and the spatiotemporal region s which is its spatiotemporal extent. (axiom label in BFO2 Reference: [082-003])
occupies spatiotemporal region
Mary’s 5th birthday occurrent_part_of Mary’s life
The process of a footballer’s heart beating once is an occurrent part but not a temporal_part of a game of football.
the first set of the tennis match occurrent_part_of the tennis match.
[copied from inverse property 'has occurrent part'] b has_occurrent_part c = Def. c occurrent_part_of b. (axiom label in BFO2 Reference: [007-001])
BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion.
b occurrent_part_of c =Def. b is a part of c & b and c are occurrents. (axiom label in BFO2 Reference: [003-002])
occurrent_part_of is antisymmetric. (axiom label in BFO2 Reference: [123-001])
occurrent_part_of is reflexive (every occurrent entity is an occurrent_part_of itself). (axiom label in BFO2 Reference: [113-002])
occurrent_part_of is transitive. (axiom label in BFO2 Reference: [112-001])
occurrent_part_of satisfies unique product. (axiom label in BFO2 Reference: [125-001])
occurrent_part_of satisfies weak supplementation. (axiom label in BFO2 Reference: [124-001])
(forall (x y t) (if (and (occurrentPartOf x y t) (not (= x y))) (exists (z) (and (occurrentPartOf z y t) (not (exists (w) (and (occurrentPartOf w x t) (occurrentPartOf w z t)))))))) // axiom label in BFO2 CLIF: [124-001]
(forall (x y t) (if (and (occurrentPartOf x y t) (occurrentPartOf y x t)) (= x y))) // axiom label in BFO2 CLIF: [123-001]
(forall (x y t) (if (exists (v) (and (occurrentPartOf v x t) (occurrentPartOf v y t))) (exists (z) (forall (u w) (iff (iff (occurrentPartOf w u t) (and (occurrentPartOf w x t) (occurrentPartOf w y t))) (= z u)))))) // axiom label in BFO2 CLIF: [125-001]
(forall (x y z) (if (and (occurrentPartOf x y) (occurrentPartOf y z)) (occurrentPartOf x z))) // axiom label in BFO2 CLIF: [112-001]
(forall (x) (if (Occurrent x) (occurrentPartOf x x))) // axiom label in BFO2 CLIF: [113-002]
part of occurrent
process profile of
proper temporal part of
b proper_continuant_part_of c at t =Def. b continuant_part_of c at t & b and c are not identical. (axiom label in BFO2 Reference: [004-001])
Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'proper part of continuant at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'proper part of continuant@en(x,y,t)'.
(iff (properContinuantPartOfAt a b t) (and (continuantPartOfAt a b t) (not (= a b)))) // axiom label in BFO2 CLIF: [004-001]
proper part of continuant at all times
[copied from inverse property 'has proper occurrent part'] b has_proper_occurrent_part c = Def. c proper_occurrent_part_of b. [XXX-001
b proper_occurrent_part_of c =Def. b occurrent_part_of c & b and c are not identical. (axiom label in BFO2 Reference: [005-001])
(iff (properOccurrentPartOf a b) (and (occurrentPartOf a b) (not (= a b)))) // axiom label in BFO2 CLIF: [005-001]
proper part of occurrent
the 4th year of your life is a temporal part of your life\. The first quarter of a game of football is a temporal part of the whole game\. The process of your heart beating from 4pm to 5pm today is a temporal part of the entire process of your heart beating.\ The 4th year of your life is a temporal part of your life
the process boundary which separates the 3rd and 4th years of your life.
your heart beating from 4pm to 5pm today is a temporal part of the process of your heart beating
b proper_temporal_part_of c =Def. b temporal_part_of c & not (b = c). (axiom label in BFO2 Reference: [116-001])
b temporal_part_of c =Def.b occurrent_part_of c & & for some temporal region t, b occupies_temporal_region t & for all occurrents d, t (if d occupies_temporal_region t & t? occurrent_part_of t then (d occurrent_part_of a iff d occurrent_part_of b)). (axiom label in BFO2 Reference: [078-003])
if b proper_temporal_part_of c, then there is some d which is a proper_temporal_part_of c and which shares no parts with b. (axiom label in BFO2 Reference: [117-002])
(forall (x y) (if (properTemporalPartOf x y) (exists (z) (and (properTemporalPartOf z y) (not (exists (w) (and (temporalPartOf w x) (temporalPartOf w z)))))))) // axiom label in BFO2 CLIF: [117-002]
(iff (properTemporalPartOf a b) (and (temporalPartOf a b) (not (= a b)))) // axiom label in BFO2 CLIF: [116-001]
(iff (temporalPartOf a b) (and (occurrentPartOf a b) (exists (t) (and (TemporalRegion t) (occupiesSpatioTemporalRegion a t))) (forall (c t_1) (if (and (Occurrent c) (occupiesSpatioTemporalRegion c t_1) (occurrentPartOf t_1 r)) (iff (occurrentPartOf c a) (occurrentPartOf c b)))))) // axiom label in BFO2 CLIF: [078-003]
temporal part of
projects onto spatial region at some time
spatial projection of spatiotemporal at some time
projects onto temporal region
temporal projection of spatiotemporal
p occupies_temporal_region t. This is a primitive relation between an occurrent p and the temporal region t upon which the spatiotemporal region p occupies_spatiotemporal_region projects. (axiom label in BFO2 Reference: [132-001])
occupies temporal region
[copied from inverse property 'occupies temporal region'] p occupies_temporal_region t. This is a primitive relation between an occurrent p and the temporal region t upon which the spatiotemporal region p occupies_spatiotemporal_region projects. (axiom label in BFO2 Reference: [132-001])
has temporal occupant
[copied from inverse property 'exists at'] BFO2 Reference: entity
[copied from inverse property 'exists at'] BFO2 Reference: temporal region
[copied from inverse property 'exists at'] b exists_at t means: b is an entity which exists at some temporal region t. (axiom label in BFO2 Reference: [118-002])
during which exists
Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'bearer of at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'bearer of@en(x,y,t)'.
bearer of at all times
has quality at all times
Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'has function at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'has function@en(x,y,t)'.
has function at all times
Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'has role at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'has role@en(x,y,t)'.
has role at all times
Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'has disposition at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'has disposition@en(x,y,t)'.
has disposition at all times
material basis of at all times
participates in at all times
has specific dependent at all times
Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'specifically depends on at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'specifically depends on@en'(x,y,t)
specifically depends on at some time
Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'located in at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'located in@en'(x,y,t)
located in at some time
Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'member part of at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'member part of@en(x,y,t)'.
member part of at all times
[copied from inverse property 'has proper continuant part at some time'] b has_proper_continuant_part c at t = Def. c proper_continuant_part_of b at t. [XXX-001
Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'proper part of continuant at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'proper part of continuant@en'(x,y,t)
[copied from inverse property 'has proper continuant part at some time'] Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'has proper continuant part at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'has proper continuant part@en'(x,y,t)
proper part of continuant at some time
Mary’s arm continuant_part_of Mary in the time of her life prior to her operation
the Northern hemisphere of the planet Earth is a part of the planet Earth at all times at which the planet Earth exists.
[copied from inverse property 'has continuant part at some time'] b has_continuant_part c at t = Def. c continuant_part_of b at t. (axiom label in BFO2 Reference: [006-001])
Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'part of continuant at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'part of continuant@en'(x,y,t)
BFO 2 Reference: Immaterial entities are in some cases continuant parts of their material hosts. Thus the hold of a ship, for example, is a part of the ship; it may itself have parts, which may have names (used for example by ship stow planners, customs inspectors, and the like). Immaterial entities under both 1. and 2. can be of zero, one, two or three dimensions. We define:a(immaterial entity)[Definition: a is an immaterial entity = Def. a is an independent continuant that has no material entities as parts. (axiom label in BFO2 Reference: [028-001])
BFO2 Reference: continuantThe range for ‘t’ (as in all cases throughout this document unless otherwise specified) is: temporal region.
[copied from inverse property 'has continuant part at some time'] Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'has continuant part at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'has continuant part@en'(x,y,t)
b continuant_part_of c at t =Def. b is a part of c at t & t is a time & b and c are continuants. (axiom label in BFO2 Reference: [002-001])
continuant_part_of is antisymmetric. (axiom label in BFO2 Reference: [120-001])
continuant_part_of is reflexive (every continuant entity is a continuant_part_of itself). (axiom label in BFO2 Reference: [111-002])
continuant_part_of is transitive. (axiom label in BFO2 Reference: [110-001])
continuant_part_of satisfies unique product. (axiom label in BFO2 Reference: [122-001])
continuant_part_of satisfies weak supplementation. (axiom label in BFO2 Reference: [121-001])
if b continuant_part_of c at t and b is an independent continuant, then b is located_in c at t. (axiom label in BFO2 Reference: [047-002])
(forall (x t) (if (Continuant x) (continuantPartOfAt x x t))) // axiom label in BFO2 CLIF: [111-002]
(forall (x y t) (if (and (continuantPartOfAt x y t) (IndependentContinuant x)) (locatedInAt x y t))) // axiom label in BFO2 CLIF: [047-002]
(forall (x y t) (if (and (continuantPartOfAt x y t) (continuantPartOfAt y x t)) (= x y))) // axiom label in BFO2 CLIF: [120-001]
(forall (x y t) (if (and (continuantPartOfAt x y t) (not (= x y))) (exists (z) (and (continuantPartOfAt z y t) (not (exists (w) (and (continuantPartOfAt w x t) (continuantPartOfAt w z t)))))))) // axiom label in BFO2 CLIF: [121-001]
(forall (x y t) (if (exists (v) (and (continuantPartOfAt v x t) (continuantPartOfAt v y t))) (exists (z) (forall (u w) (iff (iff (continuantPartOfAt w u t) (and (continuantPartOfAt w x t) (continuantPartOfAt w y t))) (= z u)))))) // axiom label in BFO2 CLIF: [122-001]
(forall (x y z t) (if (and (continuantPartOfAt x y t) (continuantPartOfAt y z t)) (continuantPartOfAt x z t))) // axiom label in BFO2 CLIF: [110-001]
(iff (ImmaterialEntity a) (and (IndependentContinuant a) (not (exists (b t) (and (MaterialEntity b) (continuantPartOfAt b a t)))))) // axiom label in BFO2 CLIF: [028-001]
part of continuant at some time
[copied from inverse property 'has continuant part at all times that part exists'] forall(t) exists_at(y,t) -> exists_at(x,t) and 'has continuant part'(x,y,t)
Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'part of continuant at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'part of continuant@en(x,y,t)'.
[copied from inverse property 'has continuant part at all times that part exists'] This is a binary version of a ternary time-indexed, instance level, relation. Unlike the rest of the temporalized relations which temporally quantify over existence of the subject of the relation, this relation temporally quantifies over the existence of the object of the relation. The relation is provided tentatively, to assess whether the GO needs such a relation. It is inverse of 'part of continuant at all times'
part of continuant at all times
has proper temporal part
[copied from inverse property 'has history'] b has_history c iff c history_of b [XXX-001
b history_of c if c is a material entity or site and b is a history that is the unique history of cAxiom: if b history_of c and b history_of d then c=d [XXX-001
history of
b has_history c iff c history_of b [XXX-001
[copied from inverse property 'history of'] b history_of c if c is a material entity or site and b is a history that is the unique history of cAxiom: if b history_of c and b history_of d then c=d [XXX-001
has history
[copied from inverse property 'has continuant part at all times'] b has_continuant_part c at t = Def. c continuant_part_of b at t. (axiom label in BFO2 Reference: [006-001])
forall(t) exists_at(y,t) -> exists_at(x,t) and 'part of continuant'(x,y,t)
This is a binary version of a ternary time-indexed, instance level, relation. Unlike the rest of the temporalized relations which temporally quantify over existence of the subject of the relation, this relation temporally quantifies over the existence of the object of the relation. The relation is provided tentatively, to assess whether the GO needs such a relation. It is inverse of 'has continuant part at all times'
[copied from inverse property 'has continuant part at all times'] Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'has continuant part at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'has continuant part@en(x,y,t)'.
part of continuant at all times that whole exists
x anterior_to y iff x is further along the antero-posterior axis than y, towards the head. An antero-posterior axis is an axis that bisects an organism from head end to opposite end of body or tail: bearer
x distal_to y iff x is further along the proximo-distal axis than y, towards the appendage tip. A proximo-distal axis extends from tip of an appendage (distal) to where it joins the body (proximal).
x dorsal_to y iff x is further along the dorso-ventral axis than y, towards the back. A dorso-ventral axis is an axis that bisects an organism from back (e.g. spinal column) to front (e.g. belly).
x posterior_to y iff x is further along the antero-posterior axis than y, towards the body/tail. An antero-posterior axis is an axis that bisects an organism from head end to opposite end of body or tail.
x proximal_to y iff x is closer to the point of attachment with the body than y.
x ventral_to y iff x is further along the dorso-ventral axis than y, towards the front. A dorso-ventral axis is an axis that bisects an organism from back (e.g. spinal column) to front (e.g. belly).
Further away from the surface of the organism. Thus, the muscular layer is deep to the skin, but superficial to the intestines.
Near the outer surface of the organism. Thus, skin is superficial to the muscle layer.
X in_left_side_of Y <=> if Y is subdivided into left and right portions, X is part_of the left portion.
X in_right_side_of Y <=> if Y is subdivided into left and right portions, X is part_of the right portion.
X posterior_side_of Y <=> if Y is subdivided into two anterior and posterior portions, X is part_of the posterior portion.
X anterior_side_of Y <=> if Y is subdivided into two anterior and posterior portions, X is part_of the anterior portion.
X proximal_side_of Y <=> if Y is subdivided into distal and proximal portions, X is part_of the proximal portion.
X distal_side_of Y <=> if Y is subdivided into distal and proximal portions, X is part_of the distal portion.
X in_lateral_side_of Y <=> if X is in_left_side_of Y or X is in_right_side_of Y. X is often, but not always a paired structure
X proximalmost_part_of Y <=> X is part_of Y and X is adjacent_to the proximal boundary of Y
This relation holds when both the deep_to and ajdacent_to relationship similarly hold.
X distalmost_part_of Y <=> X is part_of Y and X is adjacent_to the distal boundary of Y
derives from patient having disease
has disease
is in cell line repository
is disease model for
derived from anatomic part
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
A person's name denotes the person. A variable name in a computer program denotes some piece of memory. Lexically equivalent strings can denote different things, for instance "Alan" can denote different people. In each case of use, there is a case of the denotation relation obtaining, between "Alan" and the person that is being named.
denotes is a primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically
2009-11-10 Alan Ruttenberg. Old definition said the following to emphasize the generic nature of this relation. We no longer have 'specifically denotes', which would have been primitive, so make this relation primitive. g denotes r =def r is a portion of reality there is some c that is a concretization of g every c that is a concretization of g specifically denotes r
Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan
denotes
inverse of the relation 'denotes'
Person: Jie Zheng, Chris Stoeckert, Mike Conlon
denoted by
some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay
A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of.
Alan Ruttenberg
is_specified_input_of
is_specified_output_of
A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.
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
PERSON: Alan Ruttenberg
PAPER: Granularity, scale and collectivity: When size does and does not matter, Alan Rector, Jeremy Rogers, Thomas Bittner, Journal of Biomedical Informatics 39 (2006) 333-349
This relation obtains between an objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process.
a 'part of continuant at some time' relation that incides a genome belongs to a organism.
is genome of organism
a relation between a gene and the organism where this gene belongs to the organism in nature. It does not include a foreign gene that is transferred to an organism by a genetic engineering method.
is gene of organism
An object property that represents a relation between a gene and an organism, where the gene comes from a pathogen and the organism is a host, and the mutant of the gene for the pathogen is attenuated in the host organism.
gene mutant attenuated in host organism
An object property that represents a relation between a gene and an organism, where the gene is a virulence factor and the organism is a pathogen, and the mutant of the gene for the pathogen is attenuated in the host.
gene as virulence factor in pathogen
An object property that represents a relation between a gene and a cell line cell, where the gene comes from a pathogen and the cell line cell comes from a host, and the mutant of the gene for the pathogen is attenuated inside the cell line cell.
gene mutant attenuated in host cell line cell
An object property that represents a relation between a gene and a cell, where the gene comes from a pathogen and the cell comes from a host, and the mutant of the gene for the pathogen is attenuated inside the cell.
gene mutant attenuated in host cell
An object property that represents a relation between a gene and a host, where the gene comes from a pathogen, and the mutant of the gene for the pathogen is attenuated in the host.
gene mutant attenuated in host
has microbe mutated gene
An object property that represents a relation between a host-pathogen interaction process and an organism (or tissue or cell as part of the organism, or cell line cell derived from organism) which serves as the host that participates in the process.
has HPI host
An object property that represents a relation between a host-pathogen interaction process and an organism (or virus) which serves as the pathgen that participates in the process.
has HPI pathogen
has HPI host organism
has HPI host cell
has HPI host cell line cell
gene encoding antigen
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
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
This relation is taken from the RO2005 version of RO. It may be obsoleted and replaced by relations with different definitions. See also the 'develops from' family of relations.
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
is location of
my head is the location of my brain
this cage is the location of this rat
a relation between two independent continuants, the location and the target, in which the target is entirely within the location
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
location_of
location of
contained in
Containment is location not involving parthood, and arises only where some immaterial continuant is involved.
Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition):
Intended meaning: domain: material entity range: spatial region or site (immaterial continuant)
contained_in
contains
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
located_in
This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation.
the surface of my skin is a 2D boundary of my body
a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity
A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts.
Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape.
2D_boundary_of
boundary of
is 2D boundary of
is boundary of
2D boundary of
my body has 2D boundary the surface of my skin
a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity
has boundary
has_2D_boundary
has 2D boundary
innervated_by
X outer_layer_of Y iff: . X :continuant that bearer_of some PATO:laminar . X part_of Y . exists Z :surface . X has_boundary Z . Z boundary_of Y has_boundary: http://purl.obolibrary.org/obo/RO_0002002 boundary_of: http://purl.obolibrary.org/obo/RO_0002000
A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane.
bounding layer of
A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B.
A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B.
By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'.
has negative regulatory component activity
A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B.
By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'.
has positive regulatory component activity
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 relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function.
Process(P2) is directly regulated by process(P1) 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(P2) is directly negatively regulated by process(P1) 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 P2 directly negatively regulated by P1.
Process(P2) is directly postively regulated by process(P1) 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 P2 is directly postively regulated by P1.
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.
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)
A non-transitive temporal relation in which one process immediately precedes another process, such that there is no interval of time between the two processes[SIO:000251].
immediately preceded by
X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)
immediately precedes
A overlaps B if they share some part in common.
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
Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input. T innervates some R Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.
David Osumi-Sutherland
<http://purl.obolibrary.org/obo/RO_0002132> some (<http://purl.obolibrary.org/obo/GO_0043005> that (<http://purl.obolibrary.org/obo/RO_0002131> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?)))
innervates
X continuous_with Y if and only if X and Y share a fiat boundary.
The label for this relation was previously connected to. I relabeled this to "continuous with". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)
continuous with
A is spatially_disjoint_from B if and only if they have no parts in common
There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom.
Chris Mungall
Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy
a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones).
Binary relationship: x connected_to y if and only if there exists some z such that z connects x and y in a ternary connected_to(x,y,z) relationship.
a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b
connected to
Binary relationship: z connects x if and only if there exists some y such that z connects x and y in a ternary connected_to(x,y,z) relationship.
c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system.
this is currently used for both structural relationships (such as between a valve and the chamber it connects) and abstract relationships (anatomical lines and the entities they connect)
connects
a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b.
attached to part of (anatomical structure to anatomical structure)
attached to part of
Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy.
relation between an artery and the structure is supplies with blood.
Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure
supplies
Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure.
Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure
drains
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
x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y
Terry Meehan
This is the transitive form of the develops from relation
develops from
develops into
Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y.
directly develops from
directly develops into
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.
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
mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)
osteoclast SubClassOf 'capable of' some 'bone resorption'
A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process.
For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)".
capable of
c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p.
capable of part of
x actively participates in y if and only if x participates in y and x realizes some active role
actively participates in
'heart development' has active participant some Shh protein
x has participant y if and only if x realizes some active role that inheres in y
This may be obsoleted and replaced by the original 'has agent' relation
x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x
x surrounded_by y if and only if x is adjacent to y and for every region r that is adjacent to x, r overlaps y
x surrounded_by y iff: x is adjacent to y and for every region r adjacent to x, r overlaps y
surrounded by
A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts.
The epidermis layer of a vertebrate is adjacent to the dermis.
The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies.
The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used.
x adjacent to y if and only if x and y share a boundary.
x adjacent_to y iff: x and y share a boundary
This relation acts as a join point with BSPO
adjacent to
surrounds
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
Relation between occurrents, shares a start boundary with.
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
x develops from part of y if and only if there exists some z such that x develops from z and z is part of y
develops from part of
x develops_in y if x is located in y whilst x is developing
This relation take from EHDAA2 - precise semantics yet to be defined
develops in
Relation between occurrents, shares an end boundary 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
x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y
has start location
x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y
has end location
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
Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]
x has developmental contribution from y iff x has some part z such that z develops from y
has developmental contribution from
inverse of has developmental contribution from
developmentally contributes to
t1 developmentally_induced_by t2 if there is a process of organ induction (GO:0001759) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor tissue type T to T', where T' develops_from T.
t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor anatomical structure type T to T', where T' develops_from T
Developmental Biology, Gilbert, 8th edition, figure 6.5(F)
We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm]
sources for developmentally_induced_by relationships in Uberon: Developmental Biology, Gilbert, 8th edition, figure 6.5(F)
developmentally induced by
Inverse of developmentally induced by
developmentally induces
Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p
In general you should not use this relation to make assertions - use one of the more specific relations below this one
This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from
developmentally preceded by
A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision.
c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes.
A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway.
c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process.
x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else
This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage
developmentally replaces
developmentally succeeded by
'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue
part of developmental precursor of
p results in the developmental progression of s iff p is a developmental process and s is an anatomical structure and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss).
This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint.
results in developmental progression of
an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists.
every "endocardial cushion formation" (GO:0003272) results_in_formation_of some "endocardial cushion" (UBERON:0002062)
results in formation of
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 relationship that holds between entities participating in some developmental process (GO:0032502)
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development
developmentally related to
a particular instances of akt-2 enables some instance of protein kinase activity
This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized.
This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time.
enables
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
this relation holds between c and p when c is part of some c', and c' is capable of p.
part of structure that is capable of
c involved_in p if and only if c enables some process p', and p' is part of p
involved in
enabled by
regulated by
negatively regulated by
positively regulated by
An organism that is a member of a population of organisms
is member of is a mereological relation between a item and a collection.
member of
has member is a mereological relation between a collection and an item.
has member
input of
output of
formed as result of
a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a
attached to (anatomical structure to anatomical structure)
attached to
m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone.
The insertion is the point of attachment of a muscle that moves the most when the muscle shortens, or the most distal end of limb muscles
has muscle insertion
We need to import uberon muscle into RO to use as a stricter domain constraint
A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network.
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships
This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves)
in branching relationship with
Deschutes River tributary_of Columbia River
inferior epigastric vein tributary_of external iliac vein
x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein.
tributary of
x spatially_coextensive_with y if and inly if x and y have the same location
This relation is added for formal completeness. It is unlikely to be used in many practical scenarios
spatially coextensive with
x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y
we need to check if FMA branch_of implies part_of. the relation we intend to use here should - for example, see vestibulocochlear nerve
branching part of
x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction).
has developmental potential involving
x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y
has potential to developmentally contribute to
x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y
has potential to developmentally induce
x has the potential to develop into y iff x develops into y or if x is capable of developing into y
has potential to develop into
x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y
has potential to directly develop into
causally downstream of
immediately causally downstream of
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
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
c involved in regulation of p if c is involved in some p' and p' regulates some p
c involved in regulation of p if c is involved in some p' and p' positively regulates some p
c involved in regulation of p if c is involved in some p' and p' negatively regulates some p
c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p
OWL does not allow defining object properties via a Union
involved in or involved in regulation of
A protein that enables activity in a cytosol.
c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.
p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm.
A relationship that holds between two entities in which the processes executed by the two entities are causally connected.
This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact.
Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules.
An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other.
An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y.
Holds between molecular entities A and B where A can physically interact with B and in doing so regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B.
Holds between molecular entities A and B where A can physically interact with B and in doing so negatively regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B.
activity directly negatively regulates activity of
Holds between molecular entities A and B where A can physically interact with B and in doing so positively regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B.
activity directly positively regulates activity of
This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning.
helper property (not for use in curation)
'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'
x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y.
x composed_primarily_of y iff: more than half of the mass of x is made from parts of y
p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c.
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage.
Relation between continuant c and occurrent s, such that every instance of c comes into existing during some s.
x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y).
existence starts during
Relation between continuant and occurrent, such that c comes into existence at the start of p.
x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y).
x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y))
The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.
Relation between continuant c and occurrent s, such that every instance of c ceases to exist during some s, if it does not die prematurely.
x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y).
Relation between continuant and occurrent, such that c ceases to exist at the end of p.
x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y).
x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships
x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t
x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y).
x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends.
A relationship between a material entity and a process where the material entity has some causal role that influences the process
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.
The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch
causal relation between material entities
Forelimb SubClassOf has_skeleton some 'Forelimb skeleton'
A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision.
A relation between a subdivision of an organism and the single subdivision of skeleton that provides structural support for that subdivision.
The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell).
This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional.
causally influenced by (material entity to material entity)
molecular interaction relation helper property
Holds between materal entities a and b if the activity of a is causally upstream of the activity of b, or causally upstream of a an activity that modifies b
causally influences (material entity to material entity)
A relation that holds between elements of a musculoskeletal system or its analogs.
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes.
x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull.
s is luminal space of x iff s is lumen_of x and s is an immaterial entity
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.
gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'
s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p
A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity.
causal relation between material entity and a process
Holds between c and p if and only if c is capable of some activity a, and a regulates p.
Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p.
renin -> arteriolar smooth muscle contraction
Holds between c and p if and only if c is capable of some activity a, and a positively regulates p.
A relationship that holds between two entities, where the relationship holds based on the presence or absence of statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes.
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)
a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix.
Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue.
produces
a produced_by b iff some process that occurs_in b has_output a.
produced by
A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M.
Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P.
acts upstream of or within, positive effect
acts upstream of or within, negative effect
c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive
c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative
causally upstream of or within, negative effect
causally upstream of or within, positive effect
A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions.
An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut)
Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph.
r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r.
realized in response to
Genetic information generically depend on molecules of DNA.
The novel *War and Peace* generically depends on this copy of the novel.
The pattern shared by chess boards generically depends on any chess board.
The score of a symphony g-depends on a copy of the score.
This pdf file generically depends on this server.
A generically dependent continuant *b* generically depends on an independent continuant *c* at time *t* means: there inheres in *c* a specifically deendent continuant which concretizes *b* at *t*.
Molecules of DNA are carriers of genetic information.
This copy of *War and Peace* is carrier of the novel written by Tolstoy.
This hard drive is carrier of these data items.
*b* is carrier of *c* at time *t* if and only if *c* *g-depends on* *b* at *t*
is carrier of
Type of tissue or cell/the source of the material.
x anteriorly_connected_to y iff the anterior part of x is connected to y. i.e. x connected_to y and x posterior_to y.
x is a conduit for y iff y passes through the lumen of x.
x distally_connected_to y iff the distal part of x is connected to y. i.e. x connected_to y and x proximal_to y.
Relationship between a fluid and a material entity, where the fluid is the output of a realization of a filtration role that inheres in the material entity.
Relationship between a fluid and a filtration barrier, where the portion of fluid arises as a transformation of another portion of fluid on the other side of the barrier, with larger particles removed
a indirectly_supplies s iff a has a branch and the branch supplies or indirectly supplies s
x posteriorly_connected_to y iff the posterior part of x is connected to y. i.e. x connected_to y and x anterior_to y.
x proximally_connected_to y iff the proximal part of x is connected to y. i.e. x connected_to y and x distal_to y.
placeholder relation. X = 'subdivision of A' and subdivision_of some B means that X is the mereological sum of A and B
has_disease_location
entity
Entity
实体
Julius Caesar
Verdi’s Requiem
the Second World War
your body mass index
你的身体质量指数
凯撒大帝
威尔第年代安魂曲
第二次世界大战
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
BFO 2参考：在经验性总结分析的所有领域，我们遇到两种一般术语。首先是指共相或类型的一般术语：animaltuberculosissurgical proceduredisease其次，是用来指以下实例组的一般术语，这些实例组实例化一个给定共性但对应于该共相的任何子共相的扩展，因为没有实体的内在本质讨论因为他们-只有他们-被视为属于给定的群体。例子是：对斯德哥尔摩病人进行的周三手术过程中诊断出结核分枝杆菌而购买的动物，被确定为临床试验的候选人＃2056-555根据莱昂纳多·达·芬奇（Leonardo da Vinci）条款制定的656-PPV表格的签名人。这些术语代表所谓的“专业化'[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
实体不具有闭合公理，因为子类不一定丧失所有可能性。例如，Werner Ceusters的“现实的部分”包括4类，实体（当BFO构造它们时）、普遍性、配置和关系。这是一个开放性的问题，即在BFO中所解释的实体是否会在某个时候也包含这些其他的现实部分。参见，例如“如何完全追踪所有事物”在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])
一个实体是存在或已经存在或将存在的任何事物。 （BFO2公理标签参考：[001-001]）
continuant
Continuant
常体
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.
一个在任何时候都存在的实体，它持续存在，在维持其特性的同时且没有暂时的部分。
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
BFO 2参考：持续实体是可以被分割的实体，只能沿着空间维度分割成部分，例如产生您的桌子的部分，我们称之为它的腿、顶部、指甲。 “我的桌子从窗户延伸到门口。它有空间部分，可以在空间切成两半。不过，就时间而言，一个事物是连续的。“[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
常体不具有闭合公理，因为子类不一定丧失所有可能性。例如，在涉及引入一些Ceuster的实体的其他部分的扩展中，提出了普遍性是否是连续性的问题
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])
一个常体是一个持续、持久或持续存在且同时保持其身份的实体。 （BFO2中的公理标签参考：[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])
如果b是一个常体，并且如果对于某个t，c在t时刻具有_常体_部分b，则c是一个常体。 （BFO2公理标签参考：[126-001]）
如果b是一个常体，并且如果，对于某个t，c是在t时刻的b的常体_部分，则c是一个常体。 （BFO2公理标签参考：[009-002]）
如果b是物质实体，则在b存在期间有一些时间间隔（以下称为一维时间区域）。 （BFO2公理标签：[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]
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
独立常体
BFO 2 Reference: Spatial regions do not participate in processes.
Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional.
A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001])
All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001])
(forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001]
(forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001]
spatial region
Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional
A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001])
All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001])
Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002])
(forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002]
(forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001]
(forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001]
temporal region
an infinitely thin plane in space.
the surface of a sphere-shaped part of space
A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001])
(forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001]
two-dimensional spatial region
the spatiotemporal region occupied by a human life
the spatiotemporal region occupied by a process of cellular meiosis.
the spatiotemporal region occupied by the development of a cancer tumor
A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001])
All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001])
Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001])
Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001])
Every spatiotemporal region occupies_spatiotemporal_region itself.
Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002])
(forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002]
(forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001]
(forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001]
(forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001]
(forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001]
spatiotemporal 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
realizable
RealizableEntity
realizable entity
可实现实体
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
作为医生的角色
你的生殖器官的功能
你的血液的凝结倾向
这个边界角色描绘了犹他州和科罗拉多州的交汇点
这块金属的导电倾向。
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.
一个特定依赖性常体，在常体实体中存在，并且在每个实体或一组实体中都不会全部展现出来。可实现实体的展示或实现是在特定情况下发生的特定表现、功能或过程。
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])
要说b是一个可实现实体，就是说b是一个特定依赖性常体，它存在于某些依赖常体中，这个连续体不是一个空间区域，而是一个在相关类型的过程中实现的类型实例。 （BFO2公理标签参考：[058-002]）
All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])
所有可实现依赖常体都有独立常体，这些独立常体不是空间区域作为承载。 （BFO2公理标签参考：[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]
A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001])
(forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001]
zero-dimensional spatial region
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
性质
sdc
SpecificallyDependentContinuant
specifically dependent continuant
特定依赖性常体
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
交互特定依赖性常体：这个键的功能打开这个锁和这个锁的相互依赖的配置：被这个键打开
关系独立常体（对个载体）：约翰对玛丽的爱，约翰与这座雕像之间的所有关系，以及约翰与他的下属之间的权力关系。
在它中心的一块四分熟烤菲力牛排的粉色
局部特定依赖性常体：这个番茄的性质
捕食者角色和猎物角色的相互依赖由两个生物体在给定的相互作用中扮演
质子供体和受体在化学反应中的相互依赖[79
这个洞的形状。
这条鱼的腐烂倾向
这部分马苏里拉奶酪的气味
这颗心的功能：抽血
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])
b是一个关系特定依赖性常体 = Def. b是特定依赖性常体并且有n >1个独立常体c1，... cn不是空间区域且是这样的，即对于全部1个 i<j n，ci和cj没有共同的部分，对于每个1 i n，在b存在的过程中每个时间t，b s-依赖_于 ci（BFO2中的公理标号：[131-004]）
b是一个特定依赖性常体 = Def. b是一个常体& 存在一些独立常体c，c不是一个空间区域且是这样的，在b的存在过程地每个时间t，b s-依赖_于c。 （BFO2公理标签参考：[050-003]）
一个在其他实体中存在或由其他实体承担的常体。 A的每个实例都需要一些特定的B实例，这些B实例必须始终相同。
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.
具体而言，相关常体不具有闭合公理，因为子类不一定丧失所有可能性。我们不确定在这里会发生什么，但是会有如什么是承诺，义务等等的问题。
(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]
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
角色
or with divisions drawn by cognitive subjects for practical reasons, such as the division of a cake (before slicing) into (what will become) slices (and thus member parts of an object aggregate). However, this does not mean that fiat object parts are dependent for their existence on divisions or delineations effected by cognitive subjects. If, for example, it is correct to conceive geological layers of the Earth as fiat object parts of the Earth, then even though these layers were first delineated in recent times, still existed long before such delineation and what holds of these layers (for example that the oldest layers are also the lowest layers) did not begin to hold because of our acts of delineation.Treatment of material entity in BFOExamples viewed by some as problematic cases for the trichotomy of fiat object part, object, and object aggregate include: a mussel on (and attached to) a rock, a slime mold, a pizza, a cloud, a galaxy, a railway train with engine and multiple carriages, a clonal stand of quaking aspen, a bacterial community (biofilm), a broken femur. Note that, as Aristotle already clearly recognized, such problematic cases – which lie at or near the penumbra of instances defined by the categories in question – need not invalidate these categories. The existence of grey objects does not prove that there are not objects which are black and objects which are white; the existence of mules does not prove that there are not objects which are donkeys and objects which are horses. It does, however, show that the examples in question need to be addressed carefully in order to show how they can be fitted into the proposed scheme, for example by recognizing additional subdivisions [29
the FMA:regional parts of an intact human body.
the Western hemisphere of the Earth
the division of the brain into regions
the division of the planet into hemispheres
the dorsal and ventral surfaces of the body
the upper and lower lobes of the left lung
BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisions
b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004])
(forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004]
fiat object
fiat object part
an edge of a cube-shaped portion of space.
A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001])
(forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001]
one-dimensional spatial region
a collection of cells in a blood biobank.
a swarm of bees is an aggregate of members who are linked together through natural bonds
a symphony orchestra
an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team)
defined by fiat: the aggregate of members of an organization
defined through physical attachment: the aggregate of atoms in a lump of granite
defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container
defined via attributive delimitations such as: the patients in this hospital
the aggregate of bearings in a constant velocity axle joint
the aggregate of blood cells in your body
the nitrogen atoms in the atmosphere
the restaurants in Palo Alto
your collection of Meissen ceramic plates.
An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects
BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee).
ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158.
b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004])
(forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004]
object aggregate
a cube-shaped region of space
a sphere-shaped region of space,
A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001])
(forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001]
three-dimensional spatial region
Manhattan Canyon)
a hole in the interior of a portion of cheese
a rabbit hole
an air traffic control region defined in the airspace above an airport
the Grand Canyon
the Piazza San Marco
the cockpit of an aircraft
the hold of a ship
the interior of a kangaroo pouch
the interior of the trunk of your car
the interior of your bedroom
the interior of your office
the interior of your refrigerator
the lumen of your gut
your left nostril (a fiat part – the opening – of your left nasal cavity)
b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002])
(forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002]
site
atom
cell
cells and organisms
engineered artifacts
grain of sand
molecule
organelle
organism
planet
solid portions of matter
star
BFO 2 Reference: BFO rests on the presupposition that at multiple micro-, meso- and macroscopic scales reality exhibits certain stable, spatially separated or separable material units, combined or combinable into aggregates of various sorts (for example organisms into what are called ‘populations’). Such units play a central role in almost all domains of natural science from particle physics to cosmology. Many scientific laws govern the units in question, employing general terms (such as ‘molecule’ or ‘planet’) referring to the types and subtypes of units, and also to the types and subtypes of the processes through which such units develop and interact. The division of reality into such natural units is at the heart of biological science, as also is the fact that these units may form higher-level units (as cells form multicellular organisms) and that they may also form aggregates of units, for example as cells form portions of tissue and organs form families, herds, breeds, species, and so on. At the same time, the division of certain portions of reality into engineered units (manufactured artifacts) is the basis of modern industrial technology, which rests on the distributed mass production of engineered parts through division of labor and on their assembly into larger, compound units such as cars and laptops. The division of portions of reality into units is one starting point for the phenomenon of counting.
BFO 2 Reference: Each object is such that there are entities of which we can assert unproblematically that they lie in its interior, and other entities of which we can assert unproblematically that they lie in its exterior. This may not be so for entities lying at or near the boundary between the interior and exterior. This means that two objects – for example the two cells depicted in Figure 3 – may be such that there are material entities crossing their boundaries which belong determinately to neither cell. Something similar obtains in certain cases of conjoined twins (see below).
BFO 2 Reference: To say that b is causally unified means: b is a material entity which is such that its material parts are tied together in such a way that, in environments typical for entities of the type in question,if c, a continuant part of b that is in the interior of b at t, is larger than a certain threshold size (which will be determined differently from case to case, depending on factors such as porosity of external cover) and is moved in space to be at t at a location on the exterior of the spatial region that had been occupied by b at t, then either b’s other parts will be moved in coordinated fashion or b will be damaged (be affected, for example, by breakage or tearing) in the interval between t and t.causal changes in one part of b can have consequences for other parts of b without the mediation of any entity that lies on the exterior of b. Material entities with no proper material parts would satisfy these conditions trivially. Candidate examples of types of causal unity for material entities of more complex sorts are as follows (this is not intended to be an exhaustive list):CU1: Causal unity via physical coveringHere the parts in the interior of the unified entity are combined together causally through a common membrane or other physical covering\. The latter points outwards toward and may serve a protective function in relation to what lies on the exterior of the entity [13, 47
BFO 2 Reference: an object is a maximal causally unified material entity
BFO 2 Reference: ‘objects’ are sometimes referred to as ‘grains’ [74
b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001])
object
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
普遍依赖性常体
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
the temporal region during which a process occurs.
BFO 2 Reference: A temporal interval is a special kind of one-dimensional temporal region, namely one that is self-connected (is without gaps or breaks).
A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001])
(forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001]
one-dimensional temporal region
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
b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001])
BFO 2 Reference: In BFO 1.1 the assumption was made that the external surface of a material entity such as a cell could be treated as if it were a boundary in the mathematical sense. The new document propounds the view that when we talk about external surfaces of material objects in this way then we are talking about something fiat. To be dealt with in a future version: fiat boundaries at different levels of granularity.More generally, the focus in discussion of boundaries in BFO 2.0 is now on fiat boundaries, which means: boundaries for which there is no assumption that they coincide with physical discontinuities. The ontology of boundaries becomes more closely allied with the ontology of regions.
BFO 2 Reference: a continuant fiat boundary is a boundary of some material entity (for example: the plane separating the Northern and Southern hemispheres; the North Pole), or it is a boundary of some immaterial entity (for example of some portion of airspace). Three basic kinds of continuant fiat boundary can be distinguished (together with various combination kinds [29
Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions.
Every continuant fiat boundary is located at some spatial region at every time at which it exists
(iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001]
continuant fiat boundary
BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10
immaterial entity
The Equator
all geopolitical boundaries
all lines of latitude and longitude
the line separating the outer surface of the mucosa of the lower lip from the outer surface of the skin of the chin.
the median sulcus of your tongue
a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001])
(iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001]
one-dimensional continuant fiat boundary
On a somewhat higher level of complexity are what we shall call rate process profiles, which are the targets of selective abstraction focused not on determinate quality magnitudes plotted over time, but rather on certain ratios between these magnitudes and elapsed times. A speed process profile, for example, is represented by a graph plotting against time the ratio of distance covered per unit of time. Since rates may change, and since such changes, too, may have rates of change, we have to deal here with a hierarchy of process profile universals at successive levels
One important sub-family of rate process profiles is illustrated by the beat or frequency profiles of cyclical processes, illustrated by the 60 beats per minute beating process of John’s heart, or the 120 beats per minute drumming process involved in one of John’s performances in a rock band, and so on. Each such process includes what we shall call a beat process profile instance as part, a subtype of rate process profile in which the salient ratio is not distance covered but rather number of beat cycles per unit of time. Each beat process profile instance instantiates the determinable universal beat process profile. But it also instantiates multiple more specialized universals at lower levels of generality, selected from rate process profilebeat process profileregular beat process profile3 bpm beat process profile4 bpm beat process profileirregular beat process profileincreasing beat process profileand so on.In the case of a regular beat process profile, a rate can be assigned in the simplest possible fashion by dividing the number of cycles by the length of the temporal region occupied by the beating process profile as a whole. Irregular process profiles of this sort, for example as identified in the clinic, or in the readings on an aircraft instrument panel, are often of diagnostic significance.
The simplest type of process profiles are what we shall call ‘quality process profiles’, which are the process profiles which serve as the foci of the sort of selective abstraction that is involved when measurements are made of changes in single qualities, as illustrated, for example, by process profiles of mass, temperature, aortic pressure, and so on.
b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002])
b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005])
(forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005]
(iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002]
process profile
a marriage bond, an instance of love, an obligation between one person and another.
a marriage bond, an instance of requited love, an obligation between one person and another.
b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001])
(iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001]
relational quality
a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001])
(iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001]
two-dimensional continuant fiat boundary
the geographic North Pole
the point of origin of some spatial coordinate system.
the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet
zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona.
a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001])
(iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001]
zero-dimensional continuant fiat boundary
a temporal region that is occupied by a process boundary
right now
the moment at which a child is born
the moment at which a finger is detached in an industrial accident
the moment of death.
temporal instant.
A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001])
(forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001]
zero-dimensional temporal region
A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001])
history
anatomical entity
connected anatomical structure
material anatomical entity
multi-cell-part structure
neuron projection bundle
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 is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances.
a maintaining cell culture process that keeps cell line cell alive and actively cultured.
维持细胞株存活和活跃培养的细胞培养过程。
cell line cell culturing
细胞系细胞培养
cell line cell
细胞系细胞
A cultured cell that is part of a cell line - a stable and homogeneous population of cells with a common biological origin and propagation history in culture
一个培养细胞，它是一个细胞株（一个稳定的，同质的细胞群，具有共同的生物学起源和增殖史）的一部分
Yongqun He, Matthew Brush, Sirarat Sarntivijai, Alexander Diehl, Jie Zheng, Yu Lin, Bjoern Peters
A 'cell line cell' is a part of a cell line established through the passaging/selection of a primary cultured cells or the experimental modification of an existing cell line. New types of cell line cells are established after sufficient passaging of a primary culture to establish a stable and homogenous population that qualifies as a line (typically 1-20 passages), or following some spontaneous or experimental modification that confers novel characteristics to an existing line. A cell line cell typically has mutations of five or more genes compared to the original cell that derives the cell line cell. Some gene mutations may turn on some oncogenes. Cell line cells can be in active culture, stored in a quiescent state for future use (e.g. frozen in liquid nitrogen), or applied in experimental procedures.
“细胞系细胞”是通过原代培养细胞的传代/选择或现有细胞系的实验性修饰而建立的细胞系的一部分。新类型的细胞系细胞的建立过程是原代培养物充分传代后以建立符合条件（典型地1-20代）的稳定且同质的群体，或者在某些自发或实验性修饰之后赋予现有细胞系新的特征。与产生细胞系细胞的原始细胞相比，细胞系细胞通常具有5个或更多个基因的突变。 一些基因突变可能会开启一些致癌基因。 细胞系细胞可处于活性培养物中，以静止状态储存以供将来使用（例如在液氮中冷冻），或者在实验程序使用。
suspension cell line culturing is a cell line culturing method where cells do not require a surface for growth and differentiation. This method is appropriate for cells that are adapted to suspension culture or cells that are non-adhesive (e.g. hematopoietic cells)
悬浮细胞系培养是其中细胞不需要生长和分化表面的细胞系培养方法。 该方法适用于适合悬浮培养的细胞或非贴壁细胞（如造血细胞）
suspension cell line culturing
悬浮细胞培养
adherent cell line culturing is a cell line culturing method where cells require a surface for growth and differentiation.
贴壁细胞系培养是一种细胞系培养方法，其中细胞需要一个表面进行生长和分化。
adherent cell line culturing
贴壁细胞系培养
a role that inheres in a cell line repository organization.
一个细胞系资源组织中所起的作用
SS, YH
cell line repository role
细胞库角色
an organization that serves as a repository of cell lines.
cell line repository
细胞库
adherent on coated surface cell line culturing is an adherent cell line culturing method that the surface is coated with extracellular matrix component to increase adhesion properties and provide other signals needed for growth and differentiation.
adherent on coated surface cell line culturing
adherent on feeder cells cell line culturing
在饲养细胞上贴壁培养细胞系
adherent-patchy cell line culturing
贴壁斑片状细胞培养
loosely adherent cell line culturing
松散贴壁细胞培养
immortal cell line cell
永生细胞系细胞
A cell line cell that is expected to be capable of an unlimited number of divisions, and is thus able to support indefinite propagation in vitro as part of an immortal cell line.
预期能够进行无限次分裂的细胞系细胞，作为永生细胞系一部分，能够支持体外无限增殖。
Yongqun He, Matthew Brush, Allen Xiang, Asiyah Yu Lin, Sirarat Sarntivijai, James Malone, Jie Zheng, Tomasz Adamusiak
continuous cell line cell
permanent cell line cell
a cell culture growth mode that indicates a cell needs to adhere to a cell culture plate to grow.
一种细胞培养生长模式：细胞需要粘附在细胞培养板上生长
adherent cell culture growth mode
贴壁细胞培养生长模式
a cell culture growth mode that indicates a cell can grow when the cell is suspended in cell culture medium.
一种细胞培养生长模式：当细胞悬浮在细胞培养基中时，细胞可以生长
suspension cell culture growth mode
悬浮细胞培养生长模式
a disposition that represents a mode of cell culture growth, i.e., the cell will grow at a specific cell culture mode. For example, an adherent cell culture growh mode means that the cell will grow when the cell is adhere to a cell culture plate.
一种代表细胞培养生长模式的配置，即细胞将以特定细胞培养模式生长。 例如，贴壁细胞培养生长模式意味着当细胞粘附于细胞培养板时细胞将生长。
cell culture growth mode
细胞培养生长模式
cell line
A cultured cell population that represents a genetically stable and homogenous population of cultured cells that shares a common propagation history (i.e. has been successively passaged together in culture).
细胞系
mixed adherent and suspension cell line culturing
混合贴壁悬浮细胞培养
clusters in suspension cell line culturing
在悬浮细胞系培养中的成簇细胞
suspension with feeder cells cell line culturing
suspension-multicell aggregates cell line culturing
a immortal cell line that is dervied from mouse tissue.
从老鼠组织中得到的一种永生细胞系。
Yue Liu, Yongqun He
immortal mouse cell line
永生的小鼠细胞系
immortal mouse cell line cell
永生的小鼠细胞系细胞
a immortal cell line that is dervied from mouse macrophage.
immortal mouse macrophage cell line
a cell line that is derived from motile cell
源自运动细胞的细胞系
ZX, YH
immortal motile cell line
永生的游动细胞系
immortal motile cell line cell
永生的游动细胞系细胞
a immortal motile cell line that is derived from leukocyte
源自白细胞的永生游动细胞系
immortal leukocyte cell line
永生的白细胞系
immortal leukocyte cell line cell
永生的白细胞系细胞
a immortal leukocyte cell line that is derived from myeloid leukocyte
源自髓系白细胞的永生白细胞系
immortal myeloid leukocyte cell line
永生的髓样白血球细胞系
immortal myeloid leukocyte cell line cell
永生的髓样白血球细胞系细胞
a immortal myeloid leukocyte cell line that is derived from monocyte
源自单核细胞的永生髓系白细胞系
immortal monocyte cell line
永生的单核细胞系
immortal monocyte cell line cell
永生的单核细胞系细胞
a immortal leukocyte cell line that is derived from nongranular leukocyte
源自无粒白细胞的永生白细胞细胞系
immortal nongranular leukocyte cell line
永生的无颗粒白细胞细胞系
immortal nongranular leukocyte cell line cell
永生的无颗粒白细胞细胞系细胞
a immortal cell line cell that is derived from eukaryotic cell
源自真核细胞的永生细胞系细胞
immortal eukaryotic cell line cell
永生的真核细胞系细胞
a immortal eukaryotic cell line that is derived from animal cell
源自动物细胞的永生真核细胞系
immortal animal cell line
永生的动物细胞系
immortal animal cell line cell
永生的动物细胞系细胞
a immortal animal cell line that is derived from epithelial cell
源自上皮细胞的永生动物细胞系
immortal epithelial cell line cell
永生的上皮细胞系细胞
a immortal animal cell line that is derived from hematopoietic cell
源自造血细胞的永生动物细胞系
immortal hematopoietic cell line
永生的造血细胞系
immortal hematopoietic cell line cell
永生的造血细胞系细胞
a immortal hematopoietic cell line that is derived from myeloid cell
源自骨髓细胞的永生造血细胞系
immortal myeloid cell line
永生的骨髓细胞系
immortal myeloid cell line cell
永生的骨髓细胞系细胞
a cell line that is derived from somatic cell
源自体细胞的细胞系
immortal somatic cell line cell
永生的体细胞系细胞
An immortal cell line cell that derives from pair of lungs.
源自一对肺的永生细胞系细胞。
immortal lung-derived cell line cell
永生化的肺衍生细胞系细胞
An immortal cell line cell that derives from kidney.
源自肾的永生细胞系细胞。
immortal kidney-derived cell line cell
永生化的肾衍生细胞系细胞
An immortal cell line cell that derives from colon.
源自结肠的永生细胞系细胞。
immortal colon-derived cell line cell
永生的结肠衍生细胞系细胞
An immortal cell line cell that derives from female gonad.
源自雌性性腺的永生细胞系细胞。
immortal female gonad-derived cell line cell
永生的雌性性腺衍生细胞系细胞
An immortal cell line cell that derives from stomach.
源自胃的永生细胞系细胞。
immortal stomach-derived cell line cell
永生化的胃衍生细胞系细胞
An immortal epithelial cell line cell that derives from uterine cervix.
源自子宫颈的永生上皮细胞系细胞。
immortal uterine cervix-derived epithelial cell line cell
永生的宫颈衍生上皮细胞系细胞
An immortal lung-derived cell line cell that derives from human.
源自人的永生肺衍生细胞系细胞。
immortal human lung-derived cell line cell
永生的人肺衍生细胞系细胞
An immortal cell line cell that derives from human.
源自人的永生细胞系细胞。
immortal human cell line cell
永生的人细胞系细胞
An immortal colon-derived cell line cell that derives from human.
源自人的永生结肠衍生细胞系细胞。
immortal human colon-derived cell line cell
永生化的人结肠衍生细胞系细胞
An immortal kidney-derived cell line cell that derives from vervet monkey.
源自黑长尾猴的永生肾衍生细胞系细胞。
immortal vervet monkey kidney-derived cell line cell
永生的黑长尾猴肾衍生细胞系细胞
An immortal stomach-derived cell line cell that derives from human.
源自人的永生胃衍生细胞系细胞。
immortal human stomach-derived cell line cell
永生的人胃衍生细胞系细胞
An immortal epithelial cell line cell that derives from human.
源自人的永生上皮细胞系细胞。
immortal human epithelial cell line cell
永生的人上皮细胞系细胞
An immortal uterine cervix-derived epithelial cell line cell that derives from human.
源自人的永生子宫颈衍生上皮细胞系细胞。
immortal human uterine cervix-derived epithelial cell line cell
永生的人宫颈衍生上皮细胞系细胞
An immortal monocyte cell line cell that derives from human.
源自人的永生单核细胞系细胞。
immortal human monocyte cell line cell
永生的人单核细胞系细胞
LCL-1601
A549 cell
A549 细胞
ATCC: CCL-185
CHEMBL: CHEMBL3307651
CVCL: CVCL_0023
EFO: EFO_0001086
HyperCLDB: cl207
LCL-1893
AGS
AGS cell
AGS 细胞
ATCC: CRL-1739
CHEMBL: CHEMBL3308078
CVCL: CVCL_0139
EFO: EFO_0002109
LCL-1170
Caco-2
disease: colorectal adenocarcinoma
Caco-2 cell
Caco-2 细胞
ATCC: HTB-37
CHEMBL: CHEMBL3307519
CVCL: CVCL_0025
EFO: EFO_0001099
HyperCLDB: cl618
MeSH: D018938
CHO
Chinese Hamster Ovary cell
CHO cell
CHO 细胞
HyperCLDB: cl721
MeSH: D016466
LCL-1512
HeLa
WEB: http://en.wikipedia.org/wiki/HeLa
WEB: http://www.atcc.org/products/all/CCL-2.aspx
WEB: https://www.ncbi.nlm.nih.gov/pubmed/12001993
1951年2月8日从一位于1951年10月4日因癌症死亡的病人Henrietta Lacks中获取的宫颈腺癌癌细胞衍生的永生人类子宫颈衍生上皮细胞系。
an immortal human uterine cervix-derived epithelial cell line that was derived from cervical adenocarcinoma cancer cells taken on February 8, 1951 from Henrietta Lacks, a patient who died of her cancer on October 4, 1951.
HeLa cell
HeLa 细胞
ATCC: CCL-2
CHEMBL: CHEMBL3308376
EFO: EFO_0001185
HyperCLDB: cl1601
MeSH: D006367
J774A.1 cell
J774A.1 细胞
ATCC: TIB-67
HyperCLDB: cl2928
LS 174T
LS 174T cell
LS 174T 细胞
ATCC: CL-188
NCI-H292
disease: mucoepidermoid pulmonary carcinoma
NCI-H292 cell
NCI-H292 细胞
ATCC: CRL-1848
LCL-1072
THP-1
THP1
THP-1 cell
THP-1 细胞
ATCC: TIB-202
CHEMBL: CHEMBL3307574
CVCL: CVCL_0006
EFO: EFO_0001253
HyperCLDB: cl4514
Vero
Vero cell
Vero 细胞
ATCC: CCL-81
HyperCLDB: cl4644
MeSH: D014709
A immortal human cell line cell that has the characteristics: Lung carcinoma, refer to ATCC CCL185
Derived from tissue: lung in animal: human.
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.
The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one).
cell type
细胞
细胞类型
A cultured cell that is freshly isolated from a organismal source, or derives in culture from such a cell prior to the culture being passaged.
primary cultured cell
原代培养细胞
A cell that is found in a natural setting, which includes multicellular organism cells 'in vivo' (i.e. part of an organism), and unicellular organisms 'in environment' (i.e. part of a natural environment).
To accommodate unicellular organisms better, 'cell in vivo' has been re-labeled 'native cell' to better represent its intended meaning - that is, that it is a cell in the context of a multicellular organism or in a natural environment. 'Native' is intended to contrast with 'in vitro', which refers to cells or other biological entities that have been intentionally placed in a controlled, non-natural setting for the purpose of study or manipulation. (MAH 1.12.12).
A cell in vitro that is or has been maintained or propagated as part of a cell culture.
Note that this class was re-labeled to 'cultured cell' instead of 'cell line cell', as it intent was clarified to cover any cultured cells of multicellular and unicellular organisms. This includes cells actively being cultured, or cells that have been cultured but are stored in a quiescent state for future use. In having been cultured, cells must establish homeostasis and often replicate in a foreign environment. Accomodation of this stress initiates a selection of cells fit for such challenges, wherein necessary adaptive biochemical and.or genetic changes can occur. These changes can set them apart from the in vivo cells from which they derive, and such changes will typically accumulate and change over increasing time in culture.
A cell that is usually found in a two-dimensional sheet with a free surface. The cell has a cytoskeleton that allows for tight cell to cell contact and for cell polarity where apical part is directed towards the lumen and the basal part to the basal lamina.
epithelial cell
上皮细胞
A cell found predominately in the blood.
blood cell
血细胞
An endothelial cell comprises the outermost layer or lining of anatomical structures and can be squamous or cuboidal. In mammals, endothelial cell has vimentin filaments and is derived from the mesoderm.
From FMA: 9.07.2001: Endothelial cell has always been classified as a kind of epithelial cell, specifically a squamous cell but that is not true. First, endothelial cell can either be squamous or cuboidal (e.g. high-endothelial cell) and secondly, it has different embryological derivation (mesodermal) than a true epithelial cell (ectodermal and endodermal). The basis for present classification is the fact that it comprises the outermost layer or lining of anatomical structures (location-based) but a better structural basis for the differentia is the cytoskeleton of the cell. Endothelial cell has vimentin filaments while an epithelial cell has keratin filaments. [Onard].
A cell that moves by its own activities.
motile cell
游动细胞
A mononuclear phagocyte present in variety of tissues, typically differentiated from monocytes, capable of phagocytosing a variety of extracellular particulate material, including immune complexes, microorganisms, and dead cells.
Morphology: Diameter 30_M-80 _M, abundant cytoplasm, low N/C ratio, eccentric nucleus. Irregular shape with pseudopods, highly adhesive. Contain vacuoles and phagosomes, may contain azurophilic granules; markers: Mouse & Human: CD68, in most cases CD11b. Mouse: in most cases F4/80+; role or process: immune, antigen presentation, & tissue remodelling; lineage: hematopoietic, myeloid.
macrophage
巨噬细胞
A lymphocyte of B lineage with the phenotype CD19-positive, CD20-positive, and capable of B cell mediated immunity.
eukaryotic cell
真核细胞
A lymphocyte is a leukocyte commonly found in the blood and lymph that has the characteristics of a large nucleus, a neutral staining cytoplasm, and prominent heterochromatin.
Editors note: consider adding taxon constraint to vertebrata (PMID:18025161)
animal cell
动物细胞
Myeloid mononuclear recirculating leukocyte that can act as a precursor of tissue macrophages, osteoclasts and some populations of tissue dendritic cells.
Morphology: Mononuclear cell, diameter, 14 to 20 _M, N/C ratio 2:1-1:1. Nucleus may appear in variety of shapes: round, kidney, lobulated, or convoluted. Fine azurophilic granules present; markers: CD11b (shared with other myeloid cells), human: CD14, mouse: F4/80-mid,GR1-low; location: Blood, but can be recruited into tissues; role or process: immune & tissue remodelling; lineage: hematopoietic, myeloid.
monocyte
单核细胞
A cell in vitro that has undergone physical changes as a consequence of a deliberate and specific experimental procedure.
An achromatic cell of the myeloid or lymphoid lineages capable of ameboid movement, found in blood or other tissue.
leukocyte
白血球
A cell of the monocyte, granulocyte, mast cell, megakaryocyte, or erythroid lineage.
myeloid cell
骨髓细胞
A cell of the monocyte, granulocyte, or mast cell lineage.
myeloid leukocyte
骨髓白细胞
A leukocyte with a single non-segmented nucleus in the mature form.
hematopoietic cell
造血干细胞
nongranular leukocyte
无颗粒白细胞
A large nucleated basophilic erythrocyte found in mammalian embryos. This cell type arises from the blood islands of yolk sacs and expresses different types of hemoglobins (beta-H1, gamma-1 and zeta) than adult erythrocytes. Considered a type of erythroblast as this cell type can enucleate in circulation.
A cell of an organism that does not pass on its genetic material to the organism's offspring (i.e. a non-germ line cell).
somatic cell
体细胞
nasopharynx respiratory epithelial cells
Any blood vessel endothelial cell that is part of a microvascular endothelium.
A nervous system disease which is located in a part of the nervous system responsible for processing sensory information that consists of sensory receptors, neural pathways, and parts of the brain involved in sensory perception. Commonly recognized sensory systems are those for vision, hearing, somatic sensation (touch), taste and olfaction (smell).
A respiratory system disease which involves the lower respiratory tract.
An organ system cancer located_in the respiratory system that is characterized by uncontrolled cellular proliferation in the respiratory tract.
A cancer that is classified based on the organ it starts in.
A cancer that is classified by the type of cell from which it is derived.
A large intestine cancer that is located_in the terminal part of the large intestine.
An eye and adnexa disease that is located_in the adnexa of the eye.
A heart disease that is located_in the innermost layer of tissue that lines the chambers of the heart.
A vascular disease that is located_in an artery.
An organ system cancer located_in the muscular and skeletal organs and characterized by uncontrolled cellular proliferation of the musculoskeletal organs.
A connective tissue tumor that can be a benign chondroma or a maligannt chondrosarcoma.
A nervous system cancer that is located in the sensory system.
A disease of anatomical entity that is located_in the thoracic cavity.
A gastrointestinal system cancer that is located_in the pharynx.
An organ system cancer that is located_in the skin, hair and nails.
A musculoskeletal system disease that affects the muscles.
A connective tissue disease that affects the structure or development of bone or causes an impairment of normal bone function.
An eye disease that affects the cornea, which is the transparent surface of the eye that assists in light refraction.
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 eye disease that affects the lens of the eye, which is the transparent disc that focuses light to the photosensors in the back of the eye.
A female reproductive system disease that is located_in the ovary.
An urinary system cancer that results_in malignant growth located_in the urinary bladder.
A cardiovascular system disease that involves the heart.
A female reproductive system disease characterized by the growth of endometrial tissue that is located_in the fallopian tube.
A female reproductive system disease characterized by the growth of endometrial tissue that is located_in the intestine.
A female reproductive system disease characterized by the growth of endometrial tissue that is located_in the ovary.
A cardiovascular cancer located_in the heart.
malignant neoplasm of urinary bladder neck
A urinary system cancer that is located_in the ureter.
A female reproductive system cancer that is located_in the vagina.
A respiratory system cancer that is located_in the trachea.
An organ system cancer that arises in the head or neck region. This region includes the nasal cavity, sinuses, lips, mouth, salivary glands, throat, or larynx.
A reproductive organ cancer that is manifested in the female genitals. This includes organs such as the ovaries, fallopian tubes, uterus, cervix, vagina and vulva.
malignant neoplasm of female genital organ
A female reproductive system disease that is located_in the vagina.
A cancer that affects the blood or bone marrow characterized by an abnormal proliferation of blood cells.
An eye disease that involves the globe of the eye.
A vascular disease that is located_in the capillaries.
A disease of anatomical entity which occurs in the blood, heart, blood vessels or the lymphatic system that passes nutrients (such as amino acids and electrolytes), gases, hormones, blood cells or lymph to and from cells in the body to help fight diseases and help stabilize body temperature and pH to maintain homeostasis.
disease of subdivision of hemolymphoid system
A hematologic cancer located_in the central nervous system.
A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain.
A respiratory system cancer that is located_in the lung.
A uterine cancer that is located_in tissues lining the uterus.
primary malignant neoplasm of endometrium
A large intestine cancer that is located_in the anus.
A urinary system disease that is located_in the ureter.
A disease that is characterized by abnormally rapid cell division.
A sensory system disease that is located_in the eye or the adnexa of the eye.
A disease of anatomical entity that is located_in reproductive system organs.
A colon cancer that has_material_basis_in abnormally proliferating cells derives_from epithelial cells.
A disease of anatomical entity that located_in the respiratory system which extends from the nasal sinuses to the diaphragm.
A disease of anatomical entity that is located_in the integumentary system comprising the skin and its appendages.
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.
A cardiovascular cancer that is located_in blood vessels.
An organ system cancer that located_in the heart and blood vessels.
A cardiovascular system disease that primarily affects the blood vessels which includes the arteries, veins and capillaries that carry blood to and from the heart.
A disease of anatomical entity that is located_in kidney, ureter, bladder and urethra.
A connective tissue cancer that is located_in bone and is characterized by uncontrolled cellular proliferation that destroys normal bone tissue.
A bone cancer and jaw disease that is located in the jaw and results in a swollen jaw, results in numbness or a tingling sensation in jaw, and results in an abnormal growth of the jaw bone.
An organ system cancer that is manifested in the reproductive organs.
A female reproductive system disease that is located_in the fallopian tube.
A female reproductive organ cancer that is located_in fallopian tube.
A colorectal cancer that is located_in the rectum.
A musculoskeletal system cancer that is located_in connective tissue.
A sensory system cancer located_in the eye that is characterized by uncontrolled cellular proliferation in the eye.
A colorectal cancer that is located_in the colon.
A uterine disease that is located_in the cervix.
An endocrine system disease that is located_in the gonads.
A reproductive system disease that impairs the ability to reproduce and is located in the uterus, vagina, cervix, ovaries or fallopian tubes.
A colon carcinoma that derives_from epithelial cells of glandular origin.
colon adenocarcinoma
结肠腺癌
A female reproductive organ cancer that is located_in the ovary.
Xref MGI. OMIM mapping confirmed by DO. [SN].
An organ system cancer located in the hematological system that is characterized by uncontrolled cellular proliferation in blood, bone marrow and lymph nodes.
A urinary system cancer that is located_in the kidney.
malignant neoplasm of kidney except pelvis
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 female reproductive system disease characterized by the growth of endometrial tissue outside the uterine body.
A cervical cancer that is located_in the cervix uteri or located_in the cervical area and that has_material_basis_in abnormally proliferating cells derives_from epithelial cells.
A carcinoma that has_material_basis_in abnormally proliferating cells, derives_from epithelial cells, which originate in glandular tissue.
adenocarcinoma
腺癌
An adenocarcinoma that derives_from epithelial cells originating in glandular tissue, which produce mucin.
Pseudomyxoma peritonei with unknown primary site
A cell type cancer that has_material_basis_in abnormally proliferating cells derives_from epithelial cells.
carcinoma
An organ system cancer located_in the nervous system that affects the central or peripheral nervous system.
An organ system cancer located_in gastrointestinal tract that is manifested in organs of the gastrointestinal system.
A nervous system disease that affects either the spinal cord (myelopathy) or brain (encephalopathy) of the central nervous system.
A female reproductive system disease that is located_in the uterus.
An eye disease affecting the uvea, which are the pigmented layers of the eye consisting of the iris, ciliary body, and choroid.
A skin disease where there is a diffuse infection of connective tissue with severe inflammation of dermal and subcutaneous layers of the skin. Cellulitis can be caused by normal skin flora or by exogenous bacteria, and often occurs where the skin has previously been broken: cracks in the skin, cuts, blisters, burns, insect bites, surgical wounds, or sites of intravenous catheter insertion.
A nervous system cancer that is located_in the central nervous system.
malignant neoplasm of central nervous system
A female reproductive organ cancer that is located_in the uterus.
A urinary system disease that is located_in the bladder.
An integumentary system disease that is located_in skin.
A cervix carcinoma that derives_from epithelial cells of glandular origin.
cervical adenocarcinoma
子宫颈腺癌
A stomach carcinoma that derives_from epithelial cells of glandular origin.
gastric adenocarcinoma
胃腺癌
A lung cancer that has_material_basis_in abnormally proliferating cells derives_from epithelial cells and is located_in the lungs and has_symptom cough and has_symptom chest discomfort or pain and has_symptom weight loss and has_symptom hemoptysis.
A lung carcinoma that is characterized as any type of epithelial lung cancer other than small cell lung carcinoma.
non-small cell lung carcinoma
非小细胞肺癌
An organ system cancer that is located_in the kidneys, ureteres, bladder or urethra.
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.
A gastrointestinal system disease that is located_in the mouth.
A musculoskeletal system cancer that is located_in muscle.
An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells.
A female reproductive organ cancer that is located_in the cervix.
A brain cancer that is located_in the infratentorial region.
An organ system cancer located_in the thoracic cavity that develops in the different types of cells within the lungs, as well as less common cancers of the esophagus, the trachea, or the chest wall.
An artery disease that is characterized by degeneration of the cells composing the aortic wall.
A gastrointestinal system disease that is located_in the intestine.
A stomach cancer that is located_in the stomach.
A urinary system disease that is located_in the kidney.
A central nervous system cancer that is located_in the spinal cord. It is mostly formed from metastases from primary cancers elsewhere (commonly breast, prostate, and lung cancer).
An eye and adnexa disease that is located_in the eye.
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 eye disease that is located_in the retina.
A nervous system disease that affects the peripheral nervous system.
A hematologic cancer and central nervous system neoplasm that is located_in the central nervous system.
hematopoietic neoplasm of central nervous system
central nervous system hematologic cancer
An artery disease that is located in the lungs.
A musculoskeletal system disease that affects tissues such as skin, tendons, and cartilage.
An vascular disease that is characterized by dysfunction of the blood vessels supplying the brain.
A disease that manifests in a defined anatomical structure.
A urinary system disease that is located_in the urethra.
An urinary tract cancer that derives_from the tissues of the urethra.
A disease of anatomical entity that has_material_basis_in hematopoietic cells.
DISEASE OF THE BLOOD AND BLOOD-FORMING ORGANS
A gastrointestinal system disease that is located_in the stomach.
A disease of anatomical entity that is located_in the gastrointestinal tract.
A lower respiratory tract disease in which the function of the lungs is adversely affected by narrowing or blockage of the airways resulting in poor air flow, a loss of elasticity in the lungs that produces a decrease in the total volume of air that the lungs are able to hold, and clotting, scarring, or inflammation of the blood vessels that affect the ability of the lungs to take up oxygen and to release carbon dioxide.
Updating out dated CUI and removing lung abscess as a synonym.
A myeloid leukemia that is characterized by a dominance of monocytes in the marrow.
malignant neoplasm of external Lip, not specified as upper or lower
malignant neoplasm of labial commissure of lip
malignant neoplasm of lip, vermilion border
malignant neoplasm of lower lip, buccal aspect
malignant neoplasm of lower lip, inner aspect
malignant neoplasm of lower lip, oral aspect
malignant neoplasm of oral aspect of lip, not specified whether upper or lower
malignant neoplasm of other sites of lip
malignant neoplasm of vermilion border of lip
A gastrointestinal system cancer that is located_in the oral cavity.
malignant neoplasm of anterior portion of floor of mouth
malignant neoplasm of lateral floor of mouth
malignant neoplasm of lateral portion of floor of mouth
malignant tumor of anterior floor of mouth
malignant tumor of lateral floor of mouth
malignant tumor of the Floor of the Mouth
A disease of anatomical entity that is located_in the central nervous system or located_in the peripheral nervous system.
A vascular disease that is located_in a vein.
A leukemia that is located_in myeloid tissue.
A monocytic leukemia where the majority of monocytic cells are promonocytes.
acute Monoblastic Leukemia and acute Monocytic Leukemia
acute monocytic leukemia without mention of remission
acute monocytic leukemia
急性单核细胞性白血病
A large intestine cancer that is located_in the colon and/or located_in the rectum.
An adnexa disease that is located_in the eye socket.
A central nervous system disease that is located_in the brain.
A hematopoietic system disease that is located_in white blood cells.
A respiratory system disease which involves the upper respiratory tract.
Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
Note that this term is a direct child of 'biological_process ; GO:0008150' because some immune system processes are types of cellular process (GO:0009987), whereas others are types of multicellular organism process (GO:0032501). This term was added by GO_REF:0000022.
Any process that modulates the frequency, rate, or extent of an immune system process.
Any process that stops, prevents, or reduces the frequency, rate, or extent of an immune system process.
down regulation of immune system process
down-regulation of immune system process
negative regulation of immune system process
Any process that activates or increases the frequency, rate, or extent of an immune system process.
positive regulation of immune system process
A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process.
Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code "no data" (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex.
Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
Where appropriate, also consider annotating to 'receptor agonist activity ; GO:0048018'.
The selective, non-covalent, often stoichiometric, interaction of a molecule with one or more specific sites on another molecule.
Note that this term is in the subset of terms that should not be used for direct, manual gene product annotation. Please choose a more specific child term, or request a new one if no suitable term is available. For ligands that bind to signal transducing receptors, consider the molecular function term 'receptor binding ; GO:0005102' and its children.
Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
An anchoring protein, ZFYVE9 (SARA), recruits SMAD2/3
The chemical reactions and pathways involving the nonmetallic element phosphorus or compounds that contain phosphorus, usually in the form of a phosphate group (PO4).
The chemical reactions and pathways involving the phosphate group, the anion or salt of any phosphoric acid.
phosphate-containing compound metabolic process
Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
This term was improved by GO_REF:0000022. It was redefined and moved.
Any process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment.
The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
Note that signal transduction is defined broadly to include a ligand interacting with a receptor, downstream signaling steps and a response being triggered. A change in form of the signal in every step is not necessary. Note that in many cases the end of this process is regulation of the initiation of transcription. Note that specific transcription factors may be annotated to this term, but core/general transcription machinery such as RNA polymerase should not.
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.
Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
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 chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
metabolic process resulting in cell growth
multicellular organism metabolic process
Note that metabolic processes do not include single functions or processes such as protein-protein interactions, protein-nucleic acids, nor receptor-ligand interactions.
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism.
negative regulation of organismal metabolism
inhibition of organismal metabolic process
negative regulation of multicellular organismal metabolic process
negative regulation of metabolic process
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism.
positive regulation of multicellular organismal metabolic process
positive regulation of organismal metabolism
stimulation of organismal metabolic process
up-regulation of organismal metabolic process
positive regulation of metabolic process
Any process that modulates the frequency, rate or extent of signal transduction.
Any process that activates or increases the frequency, rate or extent of signal transduction.
positive regulation of signaling pathway
positive regulation of signalling pathway
positive regulation of signal transduction
Any process that stops, prevents, or reduces the frequency, rate or extent of signal transduction.
negative regulation of signaling pathway
negative regulation of signalling pathway
negative regulation of signal transduction
Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level.
Any process that modulates the frequency, rate or extent of a signaling receptor activity. Receptor activity is when a molecule combines with an extracellular or intracellular messenger to initiate a change in cell activity.
regulation of signaling receptor activity
Any process that increases the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus.
positive regulation of phosphorus metabolic process
Any process that decreases the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus.
negative regulation of phosphorus metabolic process
Any process that modulates the frequency, rate or extent of cell communication. Cell communication is the process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment.
Any process that increases the frequency, rate or extent of cell communication. Cell communication is the process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment.
positive regulation of cell communication
Any process that decreases the frequency, rate or extent of cell communication. Cell communication is the process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment.
negative regulation of cell communication
Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
Note that this term encompasses all activities that transfer a single phosphate group; although ATP is by far the most common phosphate donor, reactions using other phosphate donors are included in this term.
The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
TRAF2 ubiquitinates cIAP1,2 in cIAP1,2:TRAF1:TRAF2:TRAF3:NIK
GTPBP3 and MTO1 transform uridine-34 yielding 5-taurinomethyluridine-34 in tRNA
TSR3 transfers aminocarboxypropyl group from S-adenosylmethionine to N(1)-methylpseudouridine-1248 of 18SE rRNA yielding N(1)-methyl-N(3)-aminocarboxypropylpseudouridine-1248
Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor).
Note that this term encompasses all kinase activities, as well as activities that transfer other phosphorus-containing groups such as diphosphate or nucleotides.
transferase activity, transferring phosphorus-containing groups
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving phosphates.
regulation of phosphate metabolic process
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism.
regulation of multicellular organismal metabolic process
regulation of organismal metabolic process
The attachment of a cell or organism to a substrate, another cell, or other organism. Biological adhesion includes intracellular attachment between membrane regions.
Any process that modulates the frequency, rate or extent of a signaling process.
The entirety of a process in which information is transmitted within a biological system. This process begins with an active signal and ends when a cellular response has been triggered.
Note that a signal is any variable property or parameter that serves to convey information, and may be a physical entity such as a gene product or small molecule, a photon, or a change in state such as movement or voltage change.
Any process that activates, maintains or increases the frequency, rate or extent of a signaling process.
positive regulation of signalling process
positive regulation of signaling process
Any process that stops, prevents, or reduces the frequency, rate or extent of a signaling process.
negative regulation of signaling process
negative regulation of signalling process
The function of interacting (directly or indirectly) with receptors such that the proportion of receptors in the active form is changed.
The function of interacting (directly or indirectly) with receptors such that the proportion of receptors in the active form is increased.
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances.
regulation of cellular metabolic process
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances.
down regulation of cellular metabolic process
down-regulation of cellular metabolic process
downregulation of cellular metabolic process
negative regulation of cellular metabolism
inhibition of cellular metabolic process
negative regulation of cellular metabolic process
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances.
positive regulation of cellular metabolism
up regulation of cellular metabolic process
up-regulation of cellular metabolic process
upregulation of cellular metabolic process
activation of cellular metabolic process
stimulation of cellular metabolic process
positive regulation of cellular metabolic process
Any process that stops, prevents, or reduces the frequency, rate or extent of protein binding.
Any process that activates or increases the frequency, rate or extent of protein binding.
Any process that modulates the frequency, rate or extent of any process in which a cell, a substance, or a cellular entity is transported to, or maintained in, a specific location.
Any process that stops, prevents, or reduces the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
Any process that activates or increases the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
Receiving a signal and transmitting it in the cell to initiate a change in cell activity. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response.
receptor activity involved in signal transduction
Any process that modulates the frequency, rate or extent of addition of phosphate groups into a molecule.
Any process that stops, prevents or decreases the rate of addition of phosphate groups to a molecule.
Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to a molecule.
Any process that activates or increases the activity of an enzyme.
positive regulation of metalloenzyme activity
positive regulation of catalytic activity
Any process that stops or reduces the activity of an enzyme.
down-regulation of metalloenzyme activity
down regulation of metalloenzyme activity
downregulation of metalloenzyme activity
negative regulation of metalloenzyme activity
negative regulation of catalytic activity
Any process that modulates the frequency, rate or extent of protein binding.
Any process that modulates the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
Any process that modulates the frequency, rate or extent of a multi-organism process, a process in which an organism has an effect on another organism of the same or different species.
Any process that stops, prevents, or reduces the frequency, rate or extent of a multi-organism process, a process in which an organism has an effect on another organism of the same or different species.
negative regulation of multi-organism process
Any process that activates or increases the frequency, rate or extent of a multi-organism process, a process in which an organism has an effect on another organism of the same or different species.
positive regulation of multi-organism process
Any process that modulates the frequency, rate or extent of symbiosis, an interaction between two organisms living together in more or less intimate association.
regulation of symbiosis, encompassing mutualism through parasitism
Any process that stops or reduces the rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding.
negative regulation of molecular function
Any process that activates or increases the rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding.
positive regulation of molecular function
The chemical reactions and pathways by which individual cells transform chemical substances.
A process carried out by symbiont gene products that enables the interaction between two organisms living together in more or less intimate association. The various forms of symbiosis include parasitism, in which the association is disadvantageous or destructive to one of the organisms; mutualism, in which the association is advantageous, or often necessary to one or both and not harmful to either; and commensalism, in which one member of the association benefits while the other is not affected. However, mutualism, parasitism, and commensalism are often not discrete categories of interactions and should rather be perceived as a continuum of interaction ranging from parasitism to mutualism. In fact, the direction of a symbiotic interaction can change during the lifetime of the symbionts due to developmental changes as well as changes in the biotic/abiotic environment in which the interaction occurs. Microscopic symbionts are often referred to as endosymbionts.
symbiosis, encompassing mutualism through parasitism
symbiotic interaction between host and organism
Changed term, definition see https://github.com/geneontology/go-ontology/issues/14807
The attachment of a symbiont to its host via adhesion molecules, general stickiness etc., either directly or indirectly. The host is defined as the larger of the organisms involved in a symbiotic interaction.
adhesion to other organism involved in symbiotic interaction
adhesion to other organism during symbiotic interaction
This term can be used to annotate both symbiont and host organisms. Consider also annotating to interaction with host ; GO:0051702, or interaction with symbiont ; GO:0051702.
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
Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving phosphates.
down regulation of phosphate metabolic process
down-regulation of phosphate metabolic process
downregulation of phosphate metabolic process
negative regulation of phosphate metabolism
inhibition of phosphate metabolic process
negative regulation of phosphate metabolic process
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving phosphates.
positive regulation of phosphate metabolism
up regulation of phosphate metabolic process
up-regulation of phosphate metabolic process
upregulation of phosphate metabolic process
activation of phosphate metabolic process
stimulation of phosphate metabolic process
positive regulation of phosphate metabolic process
The activity of a gene product that interacts with a receptor to effect a change in the activity of the receptor. Ligands may be produced by the same, or different, cell that expresses the receptor. Ligands may diffuse extracellularly from their point of origin to the receiving cell, or remain attached to an adjacent cell surface (e.g. Notch ligands).
Definition discussed in https://github.com/geneontology/go-ontology/issues/14220
Any process that activates or increases the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule.
positive regulation of physiological process
positive regulation of biological process
Any process that stops, prevents, or reduces the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule.
negative regulation of physiological process
negative regulation of biological process
Any process that activates or increases the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level.
positive regulation of cellular physiological process
Any process that stops, prevents, or reduces the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level.
negative regulation of cellular physiological process
Any process that modulates the frequency, rate or extent of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus.
Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.
Any process that activates, maintains or increases the rate of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus.
positive regulation of response to stimulus
Any process that stops, prevents, or reduces the frequency, rate or extent of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus.
negative regulation of response to stimulus
Any process that modulates the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus.
Any process that stops, prevents, or reduces the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus.
Any process that activates or increases the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus.
Any process that modulates the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule.
Any process that modulates the activity of an enzyme.
Any process that modulates the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level.
regulation of cellular physiological process
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism.
Any process that modulates the frequency, rate or extent of binding, the selective interaction of a molecule with one or more specific sites on another molecule.
Any process that activates or increases the rate or extent of binding, the selective interaction of a molecule with one or more specific sites on another molecule.
Any process that stops or reduces the rate or extent of binding, the selective interaction of a molecule with one or more specific sites on another molecule.
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus.
regulation of phosphorus metabolic process
Any process in which a cell, a substance, or a cellular entity, such as a protein complex or organelle, is transported, tethered to or otherwise maintained in a specific location. In the case of substances, localization may also be achieved via selective degradation.
establishment and maintenance of localization
establishment and maintenance of position
establishment and maintenance of cellular component location
establishment and maintenance of substance location
establishment and maintenance of substrate location
Any process that localizes a substance or cellular component. This may occur via movement, tethering or selective degradation.
Gene Ontology: http://purl.obolibrary.org/obo/go.owl
Any process that modulates the frequency, rate or extent of transferase activity, the catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
This term is useful for grouping, but is too general for manual annotation. Please use a child term instead.
Any process that activates or increases the frequency, rate or extent of transferase activity, the catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from a donor compound to an acceptor.
positive regulation of transferase activity
Any process that stops or reduces the rate of transferase activity, the catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from a donor compound to an acceptor.
negative regulation of transferase activity
A biological process which involves another organism of the same or different species.
physiological interaction between organisms
physiological interaction with other organism
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus by a cell and ends with a change in state or activity or the cell.
A compound molecular function in which an effector function is controlled by one or more regulatory components.
Any process that modulates a measurable attribute of any biological process, quality or function.
Any process that modulates the frequency, rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding.
A molecular function that modulates the activity of a gene product or complex. Examples include enzyme regulators and channel regulators.
Any process that modulates the frequency, rate or extent of a protein or other molecule binding to a receptor.
Any process that stops, prevents or reduces the frequency, rate or extent of a protein or other molecule binding to a receptor.
down regulation of receptor-associated protein activity
Any process that activates or increases the frequency, rate or extent of a protein or other molecule binding to a receptor.
Any process that stops, prevents or reduces the frequency, rate or extent of a signaling receptor activity.
negative regulation of receptor activity
negative regulation of signaling receptor activity
Any process that activates or increases the frequency, rate or extent of signaling receptor activity.
positive regulation of signaling receptor activity
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.
software
Software is a plan specification composed of a series of instructions that can be interpreted by or directly executed by a processing unit.
see sourceforge tracker discussion at http://sourceforge.net/tracker/index.php?func=detail&aid=1958818&group_id=177891&atid=886178
PERSON: Chris Stoeckert
GROUP: OBI
information carrier
In the case of a printed paperback novel the physicality of the ink and of the paper form part of the information bearer. The qualities of appearing black and having a certain pattern for the ink and appearing white for the paper form part of the information carrier in this case.
A quality of an information bearer that imparts the information content
12/15/09: There is a concern that some ways that carry information may be processes rather than qualities, such as in a 'delayed wave carrier'.
2014-03-10: We are not certain that all information carriers are qualities. There was a discussion of dropping it.
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: 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.
An information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity
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.
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 content entity
directive information entity
dot plot
Dot plot of SSC-H and FSC-H.
A dot plot is a report graph which is a graphical representation of data where each data point is represented by a single dot placed on coordinates corresponding to data point values in particular dimensions.
person:Allyson Lister
person:Chris Stoeckert
graph
A diagram that presents one or more tuples of information by mapping those tuples in to a two dimensional space in a non arbitrary way.
PERSON: Lawrence Hunter
algorithm
PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies.
A plan specification which describes the inputs and output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata.
Philippe Rocca-Serra
PlanAndPlannedProcess Branch
adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg)
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 format specification
A data format specification is the information content borne by the document published defining the specification. Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file
2009-03-16: provenance: term imported from OBI_0000187, which had original definition "A data format specification is a plan which organizes information. Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file"
OBI branch derived
data set
Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves).
A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets.
2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type
2014-05-05: Data sets are aggregates and thus must include two or more data items. We have chosen not to add logical axioms to make this restriction.
image
An image is an affine projection to a two dimensional surface, of measurements of some quality of an entity or entities repeated at regular intervals across a spatial range, where the measurements are represented as color and luminosity on the projected on surface.
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
material information bearer
A page of a paperback novel with writing on it. The paper itself is a material information bearer, the pattern of ink is the information carrier.
a brain
a hard drive
A material entity in which a concretization of an information content entity inheres.
histogram
A histogram is a report graph which is a statistical description of a distribution in terms of occurrence frequencies of different event classes.
PERSON:Chris Stoeckert
PERSON:James Malone
heatmap
A heatmap is a report graph which is a graphical representation of data where the values taken by a variable(s) are shown as colors in a two-dimensional map.
dendrogram
Dendrograms are often used in computational biology to illustrate the clustering of genes.
A dendrogram is a report graph which is a tree diagram frequently used to illustrate the arrangement of the clusters produced by a clustering algorithm.
WEB: http://en.wikipedia.org/wiki/Dendrogram
scatter plot
Comparison of gene expression values in two samples can be displayed in a scatter plot
A scatterplot is a graph which uses Cartesian coordinates to display values for two variables for a set of data. The data is displayed as a collection of points, each having the value of one variable determining the position on the horizontal axis and the value of the other variable determining the position on the vertical axis.
scattergraph
WEB: http://en.wikipedia.org/wiki/Scatterplot
obsolescence reason specification
The reason for which a term has been deprecated. 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.
The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology.
figure
Any picture, diagram or table
An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something.
diagram
A molecular structure ribbon cartoon showing helices, turns and sheets and their relations to each other in space.
A figure that expresses one or more propositions
document
A journal article, patent application, laboratory notebook, or a book
A collection of information content entities intended to be understood together as a whole
The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities.
A denotator type indicates how a term should be interpreted from an ontological perspective.
A role borne by an infectious agent when contained in a host in which its infectious disposition can be realized.
infectious agent role
A role borne by pathogen in virtue of the fact that it or one of its products is sufficiently close to an organism towards which it has the pathogenic disposition to allow realization of the pathogenic disposition.
Clostridium botulinum is an example of an entity with the capability to bear the pathogen role but that does not have the capability to bear the infectious agent role or the parasite role. The influenza viruses are examples of organisms that can bear both the infectious agent and pathogen roles.
pathogen role
A disposition borne by a biological macromolecule produced by a pathogen that is a disposition to undergo processes that increase the pathogen's virulence.
The virulence factor disposition is typically realized in processes that improve survival of the pathogen in a host, increase the likelihood of transmission to a host, or cause pathological processes in a host.
virulence factor disposition
A role borne by an infectious disorder in virtue of the fact that (1) the host has at least two distinct infectious disorders, where neither arose from the other through metastasis, (2) at the time the infectious disorder was established in the host, the host had no infectious disorder, and (3) the infectious disorder increases the host's susceptibility to infectious disorders.
The role is realized in a process by which the infectious disorder is established in the host.
primary infection role
A role borne by an infectious disorder in virtue of the fact that (1) the host has at least two distinct infectious disorders, where neither arose from the other through metastasis, (2) at the time the infectious disorder was established in the host, the host had a primary infectious disorder, and (3) establishment of the infectious disorder occurs because of increased susceptibility to infectious disorders conferred by the primary infectious disorder.
secondary infection role
A disease whose physical basis is an infectious disorder.
tranmissible disease
The disposition is realized in an infectious disease course.
infectious disease
A disposition borne by a biological macromolecule that is the disposition to participate in adherence to a host.
The disposition is realized in an adherence to host process.
adhesion disposition
A disposition to initiate processes that result in a disorder.
pathogenicity
A pathogenic disposition is realized in processes that create a disorder.
The use of 'initiates' is intended to convey that a pathogenic disposition is realized when processes resulting in a disorder begin because of some action on the part of the bearer of the disposition. By this interpretation of 'initiates', disorder-causing entities such as glass, UV light, and toxins do not have a pathogenic disposition.
pathogenic disposition
A pathogenic disposition that inheres in an organism and is a disposition for that organism (1) to be transmitted to a host, (2) to establish itself in the host, (3) to initiate processes that result in a disorder in the host, and (4) to become part of that disorder.
The disposition is realized in a process that has as part a transmission process, an establishment in host process, a process that results in a disorder, and a process in which the bearer of the disposition becomes part of that disorder. The infectious disposition has a complementary disposition that inheres in an organism and is the capability to be host to an organism with an infectious disposition and to undergo processes initiated by that infectious organism that result in a disorder.
infectious disposition
A quality that inheres in an entity and is the degree to which it can be harmed by another entity.
Low susceptibility is often referred to as resistance. In this sense, resistance is a quality.
susceptibility
A susceptibility that inheres in an organism and is the degree to which it can be harmed by an infectious agent.
susceptibility to infectious agent
An infection comprised of infectious organisms from different Species.
mixed infection
polymicrobial infection
complex infection
An infection for which the infectious agents that are part of the infection persist in the extracellular space of the host.
extracellular infection
An infection for which the infectious agents that are part of the infection persist inside host cells.
intracellular infection
An infection for which the infectious agents that are part of the infection are distributed throughout the host.
systemic infection
An infection for which the infectious agents that are part of the infection are limited to a relatively small area of the host's body.
local infection
A local infection for which symptoms are observed in parts of the host's extended organism that are distant from the infection.
focal infection
An infectious disease course that begins soon after infection is established and progresses rapidly to severe stages.
acute infectious disease course
A disease course that is the realization of an infectious disease.
infectious disease course
An infection that is clinically abnormal.
infectious disorder
An infection that has as part virus particles located in the blood.
viremia
An infection that has as part bacteria located in the blood.
bacteremia
A material entity with a pathogenic disposition.
pathogen
An organism bearing a host role.
host
A biological macromolecule produced by a pathogen and that has a virulence factor disposition.
virulence factor
A biological macromolecule that has an adhesion disposition.
adhesin
adhesion molecule
adhesion factor
An infection bearing the primary infection role.
primary infection
An infection bearing the secondary infection role.
secondary infection
An infection that is part of an asymptomatic host.
subclinical infection
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.
The organism corresponding to the extended organism is host to the infectious agents. By this definition, parts of the host can be considered part of the infection.
An organism that has an infectious disposition.
infectious agent
An establishment of localization process in which a material entity reaches a site in an organism in which it can survive, grow, multiply, or mature.
Requested addition of this term to the GO.
An organism begins bearing a particular host role as soon as the extended organism contains the relevant material entity, regardless of that entity's location in the extended organism. An establishment process is any process by which the entity reaches a location in the extended organism in which it can persist and continue its lifecycle. For example, an organism is host to a virus as soon as any part of the extended organism is occupied by virus particles. During an establishment process, virus particles enter host cells of the relevant type, and viral DNA is integrated into host DNA.
establishment of localization in host
A process by which a disorder comes into existence.
appearance of disorder
An infectious disorder that is the physical basis for an unfolding acute infectious disease course.
acute infection
An infection that persists for an extended period of time.
persistent infection
chronic infection
A role borne by an organism in virtue of the fact that it's extended organism contains a material entity other than the organism.
host role
An infection resulting from a transmission process that unfolds in a hospital.
nosocomial infection
hospital-acquired infection
An infection resulting from a transmission process that did not unfold in a health care facility.
community-acquired infection
An infection established as a result of spread from another infection in a non-adjacent location in the extended organism of the host.
metatstatic infection
An infection resulting from a transmission process that unfolds in a nursing home.
nursing-home acquired infection
An infection comprised of infectious organisms all of the same Species.
simple infection
An infection that has as part organisms of the Genus Candida.
candidiasis
An infection that has as part organisms of the Species Trichomonas vaginalis.
trichomoniasis
An infection that has as part organisms of the Genus Leptospira.
leptospirosis
An infection located in the bowel and that has as part organisms of the Genus Shigella.
Shigellosis
An infection located in the colon and that has as part organisms of the Species Entamoeba histolytica
amebiasis
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
an regulator role that is borne by a material entity that regulates an interaction.
regulator role
an interactor role that is borne by a material entity that acts as an input of an interaction.
an interactor role that is borne by a material entity that acts as an output of an interaction.
a positive regulator role that is borne by a material entity that activates an interaction.
activator role
a role that is borne by a material entity to act as a participant in an interaction process.
an interactor role that is played by a material entity that starts or speeds up a chemical reaction while undergoing no permanent change itself.
chemical reaction catalyst role
an interactor role that is borne by a material entity that positively regulates an interaction.
positive regulator role
an interactor role that is borne by a material entity that negatively regulates an interaction.
negative regulator role
a negative regulator role that is borne by a material entity that deactivates, inhibits, blocks, or disrupts the action of a biological agent (e.g., enzyme).
deactivator role
an input interactor role that is borne by a material entity that motivates a process.
motivator role
an input interactor role that is borne by a material entity (e.g. status, job security, salary and fringe benefits) that do not motivate if present, but, if absent, result in demotivation.
hygiene factor role
Cricetulus griseus
灰仓鼠
Mus musculus
小家鼠
Herpes simplex virus (type 1 / strain 17)
infectious bovine rhinotracheitis virus BHV-1
Avian infectious laryngotracheitis virus
Venezuelan equine encephalitis virus VEE
Venezuelan equine encephalomyelitis virus
negative-sense genome single-stranded RNA viruses
Cell-associated subacute sclerosing panencephalitis
Subacute sclerosing panencephalitis virus
subacute sclerosing panencephalitis virus, SSPEV
Human respiratory syncytial virus (strain A2)
Infectious haematopoietic necrosis virus
human immunodeficiency virus type 1 ,HIV-1
human immunodeficiency virus type 1 HIV 1
human immunodeficiency virus type 1 HIV-1
human immunodeficiency virus type 1 HIV1
human immunodeficiency virus type 1, HIV-1
human immunodeficiency virus type I HIV-1
human immunodeficiency virus type-1 HIV-1
Chimpanzee immunodeficiency virus (SIV(CPZ))
Francisella tularensis var. palaearctica
Francisella tularensis subsp. holarctica
purple photosynthetic bacteria and relatives
Neisseria meningitidis serogroup B strain MC58
Neisseria meningitidis serogroup A strain Z2491
Yersinia enterocolitica subsp. enterocolitica
Staphylococcus aureus (strain Mu50 / ATCC 700699)
Staphylococcus aureus subsp. aureus Mu50
Staphylococcus aureus subsp. aureus N315
Streptococcus pyogenes (serotype 1 / M1 GAS)
Streptococcus pyogenes (serotype 5 / Manfredo)
Streptococcus pneumoniae (strain ATCC BAA-255 / R6)
Mycobacterium tuberculosis typus gallinaceus
Mycobacterium tuberculosis typus humanus
Francisella tularensis subsp. tularensis str. SCHU S4
Francisella tularensis subsp. tularensis strain SCHU S4
Francisella tularensis Biovar A str. SCHU S4
Francisella tularensis Biovar A str. Schu 4
Francisella tularensis subsp. tularensis Schu 4
Francisella tularensis subsp. tularensis SCHU S4
Streptococcus pyogenes (serotype 18 / MGAS8232)
Leptospira interrogans serovar Lai str. 56601
Campylobacter jejuni subsp. jejuni ATCC 700819 = NCTC 11168
Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819
Campylobacter jejuni subsp. jejuni ATCC 700819
Campylobacter jejuni subsp. jejuni NCTC 11168
Clostridium perfringens strain ATCC 13124
Staphylococcus aureus subsp. aureus str. MW2
Shigella flexneri serotype 2a str. 2457T
Brucella melitensis biovar Suis str. 1330
Salmonella enterica subsp. enterica serovar Typhi strain Ty2
Salmonella enterica subsp. enterica serovar Typhi Ty2
Salmonella enterica subsp. enterica serovar Typhi str. Ty2
Influenza A virus ( A/Puerto Rico/8/1934(H1N1))
Influenza A virus (A/Puerto Rico/8/1934(H0N1))
Influenza A virus (A/Puerto Rico/8/34(H1N1))
Influenza A virus (STRAIN A/PUERTO RICO/8/34)
Influenza A virus (A/Puerto Rico/8/1934(H1N1))
Cryptococcus neoformans var. neoformans strain JEC21
Cryptococcus neoformans var. neoformans serotype D JEC21
Filobasidiella neoformans var. neoformans strain JEC21
Cryptococcus neoformans var. neoformans JEC21
Salmonella enterica subsp. enterica serovar Typhi CT18
Salmonella enterica subsp. enterica serovar Typhi strain CT18
Salmonella enterica subsp. enterica serovar Typhi str. CT18
Brucella melitensis biotype 1 (strain 16m / atcc 23456 / nctc 10094)
Yersinia pestis biovar Microtus strain 91001
Yersinia pestis biovar Mediaevails str. 91001
Yersinia pestis biovar Medievalis str. 91001
Yersinia pestis biovar Microtus str. 91001
Vibrio cholerae serotype O1 biotype El Tor strain N16961
Vibrio cholerae serotype O1 biotype ElTor strain N16961
Vibrio cholerae O1 biovar eltor str. N16961
Vibrio cholerae O1 biovar El Tor str. N16961
Bacillus anthracis strain 'Ames Ancestor'
Orgya pseudotsugata nucleopolyhedrovirus
Orgyia pseudotsugata multicapsid nuclear polyhedrosis virus
Orgyia pseudotsugata multicapsid nuclear polyhedrosis virus OpMNPV
Orgyia pseudotsugata multicapsid nucleopolyhedrovirus
Orgyia pseudotsugata multicapsid polyhedrosis virus
Orgyia pseudotsugata multinucleocapsid nuclear polyhedrosis virus
Orgyia pseudotsugata multiple nucleopolyhedrovirus
Mycobacterium avium subsp. paratuberculosis str. K-10
Mycobacterium avium subsp. paratuberculosis strain K-10
Mycobacterium avium subsp. paratuberculosis K10
Mycobacterium avium subsp. paratuberculosis K-10
Listeria monocytogenes serotype 4b strain F2365
Listeria monocytogenes serotype 4b str. F2365
Bombyx mori S nuclear polyhedrosis virus
Bombyx mori nuclear polyhedrosis virus BmNPV
Bombyx mori nuclear polyhedrosis virus, BmSNPV
Clostridium difficile 630 (epidemic type X)
Legionella pneumophila subsp. pneumophila 'Philadelphia 1'
Legionella pneumophila subsp. pneumophila strain Philadelphia 1
Legionella pneumophila subsp. pneumophila str. Philadelphia 1
Pasteurella multocida subsp. multocida Pm70
Pasteurella multocida subsp. multocida strain Pm70
Pasteurella multocida subsp. multocida str. Pm70
Yersinia pseudotuberculosis str. IP 32953
Yersinia pseudotuberculosis strain IP 32953
Staphylococcus aureus subsp. aureus str. MRSA252
Staphylococcus aureus subsp. aureus strain MRSA252
Staphylococcus aureus subsp. aureus MRSA252
Porcine reproductive and respiratory syndrome virus (PRRSV)
Porcine respiratory and reproductive syndrome virus
porcine reproductive and respiratory syndrome virus PRRSV
porcine reproductive and respiratory syndrome virus, PRRSV
Porcine reproductive and respiratory syndrome virus
Cryptococcus neoformans var. neoformans B-3501A
Influenza A virus (A/Vietnam/1203/04(H5N1))
Influenza A virus (A/Viet Nam/1203/2004(H5N1))
probable synonym or variety: "Pseudomonas polycolor" Clara 1930
Salmonella enterica subsp. enterica serovar Paratypi A str. ATCC 9150
Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150
Escherichia coli strain K12 substrain DH10B
Escherichia coli str. K-12 substr. DH10B
Salmonella enterica subsp. enterica serovar Choleraesuis SC-B67
Salmonella enterica subsp. enterica serovar Choleraesuis strain SC-B67
Salmonella enterica subsp. enterica serovar Choleraesuis str. SC-B67
Actinobacillus pleuropneumoniae serotype 2
Actinobacillus pleuropneumoniae serovar 2
Yersinia pseudotuberculosis str. IP 31758
Yersinia pseudotuberculosis strain IP 31758
ssRNA positive-strand viruses, no DNA stage
Cryptosporidium parvum strain Iowa type II
Campylobacter jejuni subsp. jejuni str. 81-176
Campylobacter jejuni subsp. jejuni strain 81-176
Campylobacter jejuni subsp. jejuni 81-176
Brucella melitensis biovar Abortus str. 2308
Brucella melitensis biovar Abortus strain 2308
Campylobacter jejuni subsp. doylei str. 269.97
Campylobacter jejuni subsp. doylei strain 269.97
Campylobacter jejuni subsp. doylei 362.97
Campylobacter jejuni subsp. doylei 269.97
Francisella tularensis subsp. holarctica str. LVS
Francisella tularensis subsp. holarctica strain LVS
Francisella tularensis subsp. holarctica LVS
Aeromonas salmonicida subsp. salmonicida str. A449
Aeromonas salmonicida subsp. salmonicida strain A449
Aeromonas salmonicida subsp. salmonicida A449
Yersinia enterocolitica subsp. enterocolitica str. 8081
Yersinia enterocolitica subsp. enterocolitica strain 8081
Yersinia enterocolitica subsp. enterocolitica 8081
Filobasidiella neoformans var. neoformans
Campylobacter jejuni subsp. jejuni str. 81116
Campylobacter jejuni subsp. jejuni strain 81116
Campylobacter jejuni subsp. jejuni NCTC 11828
Campylobacter jejuni subsp. jejuni 81116
Actinobacillus pleuropneumoniae serovar 5b strain L20
Actinobacillus pleuropneumoniae serovar 5b str. L20
Staphylococcus aureus subsp. aureus str. Mu3
Staphylococcus aureus subsp. aureus strain Mu3
Legionella pneumophila str. 2300/99 Alcoy
Legionella pneumophila strain 2300/99 Alcoy
Staphylococcus aureus subsp. aureus strain Newman
Staphylococcus aureus subsp. aureus Newman
Staphylococcus aureus subsp. aureus str. Newman
Actinobacillus pleuropneumoniae serovar 3 str. JL03
Clostridium botulinum A strain ATCC 19397
Francisella tularensis subsp. holarctica str. FTNF002-00
Francisella tularensis subsp. holarctica strain FTNF002-00
Francisella tularensis subsp. holarctica FTA
Francisella tularensis subsp. holarctica FTNF002-00
Autographa californica multicapsid nuclear polyhedrosis virus
Autographa californica multicapsid nuclear polyhedrosis virus AcMNPV
Autographa californica nuclear polyhedrosis virus
Autographa californica nuclear polyhedrosis virus AcMNPV
Autographa californica nuclear polyhedrosis virus AcNPV
Autographa californica nuclear polyhedrosis virus, AcMNPV
Autographa californica nucleopolyhedrovirus
Salmonella enterica subsp. enterica serovar Paratyphi C str. RKS4594
Salmonella enterica subsp. enterica serovar Paratyphi C strain RKS4594
Diplokokkus intracellularis meningitidis
Micrococcus meningitidis cerebrospinalis
Streptococcus pneumoniae str. Taiwan19F-14
Streptococcus pneumoniae strain Taiwan19F-14
Streptococcus pneumoniae str. Hungary19A-6
Streptococcus pneumoniae strain Hungary19A-6
Clostridium botulinum A3 strain Loch Maree
Clostridium botulinum A3 str. Loch Maree
Yersinia pseudotuberculosis strain YPIII
Yersinia pseudotuberculosis strain PB1/+
Clostridium botulinum E3 strain Alaska E43
Clostridium botulinum E3 str. Alaska E43
Escherichia coli str. K12 substr. MG1655
Escherichia coli str. K-12 substr. MG1655
Bordetella Moreno-Lopez 1952 (Approved Lists 1980) emend. Von Wintzingerode et al. 2001
Burkholderia pseudomallei strain MSHR346
Actinobacillus pleuropneumoniae serovar 7 strain AP76
Actinobacillus pleuropneumoniae serovar 7 str. AP76
Enterobacteraceae (ex Lapage 1979) Lapage 1982, fam. nov., nom. rev.
Enterobacteriaceae (ex Rahn 1937) Ewing et al. 1980, fam. nov., nom. rev.
Salmonella enterica subsp. enterica serovar Enteritidis strain P125109
Salmonella enterica subsp. enterica serovar Enteritidis str. P125109
Salmonella enterica subsp. enterica serovar Gallinarum strain 287/91
Salmonella enterica subsp. enterica serovar Gallinarum str. 287/91
Filobasidiella/Cryptococcus neoformans species complex
Cryptococcus neoformans var. shanghaiensis
Filobasidiella neoformans var. bacillispora
Streptococcus equi subsp. zooepidemicus str. MGCS10565
Streptococcus equi subsp. zooepidemicus strain MGCS10565
Streptococcus equi subsp. zooepidemicus MGCS10565
Streptococcus pneumoniae str. ATCC 700669
Streptococcus pneumoniae strain ATCC 700669
Bacillus anthracis CDC 684/NRRL 349S/NRS 234
Listeria monocytogenes serotype 4b strain CLIP 80459
Listeria monocytogenes strain CLIP 80459 serovar 4b
Listeria monocytogenes serotype 4b str. CLIP 80459
Escherichia coli O127:H6 strain E2348/69
Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S
Salmonella cholerae-suis subsp. cholerae-suis
Salmonella choleraesuis subsp. choleraesuis
Yersinia pseudotuberculosis subsp. pestis
Staphylococcus aureus subsp. aureus str. ED98
Staphylococcus aureus subsp. aureus strain ED98
Staphylococcus aureus subsp. aureus ED98
Severe acute respiratory syndrome-related coronavirus
Bartonella Strong et al. 1915 (Approved Lists 1980) emend. Birtles et al. 1995
Bartonella Strong et al. 1915 (Approved Lists 1980) emend. Brenner et al. 1993
Grahamella (ex Brumpt 1911) Ristic and Kreier 1984
Rochalimaea (Macchiavello 1947) Krieg 1961
Burkholderia/Oxalobacter/Ralstonia group
Legionella pneumophila serogroup 1 strain 130b
Salmonella enterica subsp. enterica serovar Typhi
Salmonella choleraesuis serotype typhimurium
Salmonella enterica serotype Typhimurium
Salmonella enterica subsp. enterica serovar 1,4,[5],12,:i:1,2
Salmonella enterica subsp. enterica serovar Typhimurium
Salmonella enterica subsp. enterica serovar Typhimurium strain ST4/74
Salmonella enterica subsp. enterica serovar Typhimurium str. 4/74
Salmonella enterica subsp. enterica serovar Typhimurium str. 474
Salmonella enterica subsp. enterica serovar Typhimurium str. ST4/74
Bacillus/Lactobacillus/Streptococcus group
Enterobacteriaceae and related endosymbionts
whales, hippos, ruminants, pigs, camels etc.
Staphylococcus aureus subsp. aureus str. NCTC 8325
Staphylococcus aureus subsp. aureus strain NCTC 8325
Staphylococcus aureus subsp. aureus NCTC 8325
influenza A virus (A/goose/Guangdong/1/96/(H5N1))
Influenza A virus (A/Goose/Guangdong/1/96(H5N1))
Influenza A virus (A/goose/Guangdong/1/1996(H5N1))
Chlorocebus aethiops
绿猴属
Homo sapiens
人类
Salmonella enterica subsp. enterica serovar Typhimurium LT2
Salmonella enterica subsp. enterica serovar Typhimurium strain LT2
Salmonella enterica subsp. enterica serovar Typhimurium strain LT2-LTL2
Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
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)
Fact sheet - Regulating the companies The role of the regulator. Ofwat is the economic regulator of the water and sewerage industry in England and Wales. http://www.ofwat.gov.uk/aptrix/ofwat/publish.nsf/Content/roleofregulator_factsheet170805
a regulatory role involved with making and/or enforcing relevant legislation and governmental orders
Person:Jennifer Fostel
OBI
regulatory role
Regulatory agency, Ethics committee, Approval letter; example: Browse these EPA Regulatory Role subtopics http://www.epa.gov/ebtpages/enviregulatoryrole.html Feb 29, 2008
a role which inheres in material entities and is realized in the processes of making, enforcing or being defined by legislation or orders issued by a governmental body.
GROUP: Role branch
OBI, CDISC
govt agents responsible for creating regulations; proxies for enforcing regulations. CDISC definition: regulatory authorities. Bodies having the power to regulate. NOTE: In the ICH GCP guideline the term includes the authorities that review submitted clinical data and those that conduct inspections. These bodies are sometimes referred to as competent
Jackson Labs is an organization which provide mice as experimental material
a role realized through the process of supplying materials such as animal subjects, reagents or other materials used in an investigation.
Supplier role is a special kind of service, e.g. biobank
PERSON:Jennifer Fostel
material supplier role
A data set that is produced as the output of a class prediction data transformation and consists of a data set with assigned class labels.
classified data set
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.
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
culture medium
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
Antigen is a role played by material which when introduced into an immune-competent organism causes an immune response
a role that inheres in a vaccine component and plays an antigen role, i.e., it is introducd into an immune-competent organism to cause an immune response
An antigen is a substance that prompts the generation of antibodies and can cause an immune response. Wikipedia http://en.wikipedia.org/wiki/Antigen. In the strict sense, immunogens are those substances that elicit a response from the immune system, whereas antigens are defined as substances that bind to specific antibodies. Not all antigens produce an immunogenic response, but all immunogens are antigens
Role Branch
9Mar09 waiting for discussion with immunology terms
antigen role
organization
PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods.
An entity that can bear roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members.
BP: The definition summarizes long email discussions on the OBI developer, roles, biomaterial and denrie branches. It leaves open if an organization is a material entity or a dependent continuant, as no consensus was reached on that. The current placement as material is therefore temporary, in order to move forward with development. Here is the entire email summary, on which the definition is based: 1) there are organization_member_roles (president, treasurer, branch editor), with individual persons as bearers 2) there are organization_roles (employer, owner, vendor, patent holder) 3) an organization has a charter / rules / bylaws, which specify what roles there are, how they should be realized, and how to modify the charter/rules/bylaws themselves. It is debatable what the organization itself is (some kind of dependent continuant or an aggregate of people). This also determines who/what the bearer of organization_roles' are. My personal favorite is still to define organization as a kind of 'legal entity', but thinking it through leads to all kinds of questions that are clearly outside the scope of OBI. Interestingly enough, it does not seem to matter much where we place organization itself, as long as we can subclass it (University, Corporation, Government Agency, Hospital), instantiate it (Affymetrix, NCBI, NIH, ISO, W3C, University of Oklahoma), and have it play roles. This leads to my proposal: We define organization through the statements 1 - 3 above, but without an 'is a' statement for now. We can leave it in its current place in the is_a hierarchy (material entity) or move it up to 'continuant'. We leave further clarifications to BFO, and close this issue for now.
组织
regulatory agency
A regulatory agency is a organization that has responsibility over or for the legislation (acts and regulations) for a given sector of the government.
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
Manufacturing is a process with the intent to produce a processed material which will have a function for future use. A person or organization (having manufacturer role) is a participant in this process
Manufacturing implies reproducibility and responsibility AR
This includes a single scientist making a processed material for personal use.
manufacturing
is the objective to manufacture a material of a certain function (device)
manufacturing objective
With respect to The Accuri C6 Flow Cytometer System, the organization Accuri bears the role manufacturer role. With respect to a transformed line of tissue culture cells derived by a specific lab, the lab whose personnel isolated the cll line bears the role manufacturer role. With respect to a specific antibody produced by an individual scientist, the scientist who purifies, characterizes and distributes the anitbody bears the role manufacturer role.
Manufacturer role is a role which inheres in a person or organization and which is realized by a manufacturing process.
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.
A clustered data set is the output of a K means clustering data transformation
A data set that is produced as the output of a class discovery data transformation and consists of a data set with assigned discovered class labels.
data set with assigned discovered class labels
clustered data set
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
class prediction data transformation
A class prediction data transformation (sometimes called supervised classification) is a data transformation that has objective class prediction.
supervised classification data transformation
PERSON: James Malone
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.
A support vector machine is a data transformation with a class prediction objective based on the construction of a separating hyperplane that maximizes the margin between two data sets of vectors in n-dimensional space.
A decision tree induction objective is a data transformation objective in which a tree-like graph of edges and nodes is created and from which the selection of each branch requires that some type of logical decision is made.
decision tree building data transformation
A decision tree building data transformation is a data transformation that has objective decision tree induction.
a software that provides access to more than 100 tools for gene expression analysis, proteomics, SNP analysis and common data processing tasks.
WEB: http://www.broadinstitute.org/cancer/software/genepattern/
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
Peak matching is a data transformation performed on a dataset of a graph of ordered data points (e.g. a spectrum) with the objective of pattern matching local maxima above a noise threshold
k-nearest neighbors
A k-nearest neighbors is a data transformation which achieves a class discovery or partitioning objective, in which an input data object with vector y is assigned to a class label based upon the k closest training data set points to y; where k is the largest value that class label is assigned.
James Malone
CART
A CART (classification and regression trees) is a data transformation method for producing a classification or regression model with a tree-based structure.
BOOK: David J. Hand, Heikki Mannila and Padhraic Smyth (2001) Principles of Data Mining.
Using the expression levels of 20 proteins to predict whether a cancer patient will respond to a drug. A practical goal would be to determine which subset of the 20 features should be used to produce the best predictive model. - wikipedia
A data transformation which assesses how the results of a statistical analysis will generalize to an independent data set.
An objective specification maintains some or all of the qualities of a material over time.
A person or organization that has a manufacturer role
a process with that achieves the objective to maintain some or all of the characteristics of an input material over time
Jackson Lab provides experimental animals, EBI provides training on databases, a core facility provides access to a DNA sequencer.
is a role which inheres in a person or organization and is realized in in a planned process which provides access to training, materials or execution of protocols for an organization or person
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.
The labels 'positive' vs. 'negative', or 'left handed', 'right handed', 'ambidexterous', or 'strongly binding', 'weakly binding' , 'not binding', or '+++', '++', '+', '-' etc. form scales of categorical labels.
A label that is part of a categorical datum and that indicates the value of the data item on the categorical scale.
A document with a set of printed or written questions with a choice of answers, devised for the purposes of a survey or statistical study.
JT: It plays a role in collecting data that could be fleshed out more; but I'm thinking it is, in itself, an edited document. JZ: based on textual definition of edited document, it can be defined as N&S. I prefer to leave questionnaire as a document now. We can add more restrictions in the future and use that to determine it is an edited document or not.
Need to clarify if this is a document or a directive information entity (or what their connection is))
PERSON: Jessica Turner
Merriam-Webster
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
A cultured cell that has been passaged or derives from a cell that has been passaged in culture.
The term 'secondary cell culture' is generally used in biological texts/protocols to refer to any culture following an initial passage. We include it here because there are often a number of passages between a primary culture and the establishment of a stable, homogenous cell line. Such cultures are considered to be 'secondary cultures' but not 'cell lines' during this intermediate passaging/selection period between their derivation from a 'primary cell culture' and derivation into a 'cell line', which is a more specific type of secondary culture.
A secondary cultured cell has been passaged in culture or is a descendant of such a cell that is derived through propagation in culture.
a process whereby a new type of cell line is created, either through passaging of a primary cell culture to relative genetic stability and compositional homogeneity, or through some experimental modification of an existing cell line to produce a new line with novel characteristics (e.g. immortalization or some other stable genetic modification, or selection of some defined subset).
2013-4-20 MHB: For cases of initial establilshment of a line from a primary culture, successive passaging and/or selection processes can confer increasing degrees of genetic stability and compositional homogeneity as compared to the input primary culture. Historically, many texts consider the first passage as the clearest point to define the beginning of a line. However, in practice it is more often that case that more than one passage, and possibly additional selective techniques, may be required before a culture is deemed to have sufficient stability and homogeneity to be considered cell line. This is the view taken in OBI. Regardless, what is important is that some intentional, experimental step has been taken to establish a more homogenous and stable culture that can be characterized and progatated over time.
establishing cell line
建立细胞系
A cultured cell population that is derived through one or more passages in culture.
The term 'secondary cell culture' is generally used in biological texts/protocols to refer to any culture of cells following an initial passage. We include it here because there are often a number of passages between a primary culture and the establishment of a stable, homogenous cell line. Such cultures are considered to be 'secondary cultures' but not 'cell lines' during this intermediate passaging/selection period between their derivation from a 'primary cell culture' and derivation into a 'cell line', which is a more specific type of secondary culture.
The concept of a 'secondary cultured cell population' covers cell lines as well as cultured cell populations more immediately derived from a primary culture which have yet to achieve adequate genetic stability and compositional homogeneity to be considered a cell line. The extent of the collection of cells in a 'secondary 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). Secondary cultured cell populations can be under active culture, stored in a quiescent state for future use, or applied experimentally.
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 is specifies one category out of a fixed number of nominal categories
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.
collection of specimens
Blood cells collected from multiple donors over the course of a study.
A material entity that has two or more specimens as its parts.
Details see tracker: https://sourceforge.net/p/obi/obi-terms/778/
Person: Chris Stoeckert, Jie Zheng
histologic grade according to AJCC 7th edition
A categorical value specification that is a histologic grade assigned to a tumor slide specimen according to the American Joint Committee on Cancer (AJCC) 7th Edition grading system.
histologic grade according to the Fuhrman Nuclear Grading System
A categorical value specification that is a histologic grade assigned to a tumor slide specimen according to the Fuhrman Nuclear Grading System.
Histologic Grade (Fuhrman Nuclear Grading System)
A categorical value specification that is a histologic grade assigned to a ovarian tumor.
histologic grade for ovarian tumor according to a two-tier grading system
A histologic grade for ovarian tumor that is from a two-tier histological classification of tumors.
histologic grade for ovarian tumor according to the World Health Organization
A histologic grade for ovarian tumor that is from a histological classification by the World Health Organization (WHO).
pathologic primary tumor stage for colon and rectum according to AJCC 7th edition
A categorical value specification that is a pathologic finding about one or more characteristics of colorectal cancer following the rules of the TNM American Joint Committee on Cancer (AJCC) version 7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
pT: Pathologic spread colorectal primary tumor (AJCC 7th Edition)
pathologic primary tumor stage for lung according to AJCC 7th edition
A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM American Joint Committee on Cancer (AJCC) version 7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
pT: Pathologic spread lung primary tumor (AJCC 7th Edition)
pathologic primary tumor stage for kidney according to AJCC 7th edition
A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
pT: Pathologic spread kidney primary tumor (AJCC 7th Edition)
pathologic primary tumor stage for ovary according to AJCC 7th edition
A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
pT: Pathologic spread ovarian primary tumor (AJCC 7th Edition)
pathologic lymph node stage for colon and rectum according to AJCC 7th edition
A categorical value specification that is a pathologic finding about one or more characteristics of colorectal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes.
pN: Pathologic spread colon lymph nodes (AJCC 7th Edition)
pathologic lymph node stage for lung according to AJCC 7th edition
A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes.
pathologic lymph node stage for kidney according to AJCC 7th edition
A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes.
pN: Pathologic spread kidney lymph nodes (AJCC 7th Edition)
pathologic lymph node stage for ovary according to AJCC 7th edition
A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes.
pN: Pathologic spread ovarian lymph nodes (AJCC 7th Edition)
pathologic distant metastases stage for colon according to AJCC 7th edition
A categorical value specification that is a pathologic finding about one or more characteristics of colon cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
M: colon distant metastases (AJCC 7th Edition)
pathologic distant metastases stage for lung according to AJCC 7th edition
A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
M: lung distant metastases (AJCC 7th Edition)
pathologic distant metastases stage for kidney according to AJCC 7th edition
A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
M: kidney distant Metastases (AJCC 7th Edition)
pathologic distant metastases stage for ovary according to AJCC 7th edition
A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
M: ovarian distant metastases (AJCC 7th Edition)
clinical tumor stage group according to AJCC 7th edition
A categorical value specification that is an assessment of the stage of a cancer according to the American Joint Committee on Cancer (AJCC) v7 staging systems.
Clinical tumor stage group (AJCC 7th Edition)
International Federation of Gynecology and Obstetrics cervical cancer stage value specification
A categorical value specification that is an assessment of the stage of a gynecologic cancer according to the International Federation of Gynecology and Obstetrics (FIGO) staging systems.
International Federation of Gynecology and Obstetrics ovarian cancer stage value specification
A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the FIGO classification system.
Pathologic Tumor Stage Grouping for ovarian cancer (FIGO)
A categorical value specification that is an assessment of a participant's performance status (general well-being and activities of daily life).
Eastern Cooperative Oncology Group score value specification
A performance status value specification designed by the Eastern Cooperative Oncology Group to assess disease progression and its affect on the daily living abilities of the patient.
A performance status value specification designed for classifying patients 16 years of age or older by their functional impairment.
Epstein Barr virus transformed B cell
PMID: 8777380. Expression of thyroid peroxidase in EBV-transformed B cell lines using adenovirus.Thyroid. 1996 Feb;6(1):23-8.
A material entity which results from viral transformation process using EBV as transformation agent when applied to B-cell entity
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.
data transformation
The application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value.
A planned process that produces output data from input data.
Elisabetta Manduchi
Helen Parkinson
Melanie Courtot
Richard Scheuermann
Ryan Brinkman
Tina Hernandez-Boussard
data analysis
data processing
Branch editors
leave one out cross validation method
The authors conducted leave-one-out cross validation to estimate the strength and accuracy of the differentially expressed filtered genes. http://bioinformatics.oxfordjournals.org/cgi/content/abstract/19/3/368
is a data transformation : leave-one-out cross-validation (LOOCV) involves using a single observation from the original sample as the validation data, and the remaining observations as the training data. This is repeated such that each observation in the sample is used once as the validation data
2009-11-10. Tracker: https://sourceforge.net/tracker/?func=detail&aid=2893049&group_id=177891&atid=886178
k-means clustering
A k-means clustering is a data transformation which achieves a class discovery or partitioning objective, which takes as input a collection of objects (represented as points in multidimensional space) and which partitions them into a specified number k of clusters. The algorithm attempts to find the centers of natural clusters in the data. The most common form of the algorithm starts by partitioning the input points into k initial sets, either at random or using some heuristic data. It then calculates the mean point, or centroid, of each set. It constructs a new partition by associating each point with the closest centroid. Then the centroids are recalculated for the new clusters, and the algorithm repeated by alternate applications of these two steps until convergence, which is obtained when the points no longer switch clusters (or alternatively centroids are no longer changed).
WEB: http://en.wikipedia.org/wiki/K-means
hierarchical clustering
A hierarchical clustering is a data transformation which achieves a class discovery objective, which takes as input data item and builds a hierarchy of clusters. The traditional representation of this hierarchy is a tree (visualized by a dendrogram), with the individual input objects at one end (leaves) and a single cluster containing every object at the other (root).
WEB: http://en.wikipedia.org/wiki/Data_clustering#Hierarchical_clustering
dimensionality reduction
A dimensionality reduction is data partitioning which transforms each input m-dimensional vector (x_1, x_2, ..., x_m) into an output n-dimensional vector (y_1, y_2, ..., y_n), where n is smaller than m.
PERSON: Elisabetta Manduchi
principal components analysis dimensionality reduction
A principal components analysis dimensionality reduction is a dimensionality reduction achieved by applying principal components analysis and by keeping low-order principal components and excluding higher-order ones.
pca data reduction
Generation of a heatmap from a microarray dataset
An planned process that creates images, diagrams or animations from the input data.
Tina Boussard
visualization
PERSON: Tina Boussard
Possible future hierarchy might include this: information_encoding >data_encoding >>image_encoding
data visualization
data transformation objective
normalize objective
An objective specification to transformation input data into output data
Modified definition in 2013 Philly OBI workshop
partitioning data transformation
A partitioning data transformation is a data transformation that has objective partitioning.
partitioning objective
A k-means clustering which has partitioning objective is a data transformation in which the input data is partitioned into k output sets.
A partitioning objective is a data transformation objective where the aim is to generate a collection of disjoint non-empty subsets whose union equals a non-empty input set.
class discovery data transformation
A class discovery data transformation (sometimes called unsupervised classification) is a data transformation that has objective class discovery.
unsupervised classification data transformation
class discovery objective
A class discovery objective (sometimes called unsupervised classification) is a data transformation objective where the aim is to organize input data (typically vectors of attributes) into classes, where the number of classes and their specifications are not known a priori. Depending on usage, the class assignment can be definite or probabilistic.
discriminant analysis objective
unsupervised classification objective
class prediction objective
A class prediction objective (sometimes called supervised classification) is a data transformation objective where the aim is to create a predictor from training data through a machine learning technique. The training data consist of pairs of objects (typically vectors of attributes) and class labels for these objects. The resulting predictor can be used to attach class labels to any valid novel input object. Depending on usage, the prediction can be definite or probabilistic. A classification is learned from the training data and can then be tested on test data.
supervised classification objective
cross validation objective
A cross validation objective is a data transformation objective in which the aim is to partition a sample of data into subsets such that the analysis is initially performed on a single subset, while the other subset(s) are retained for subsequent use in confirming and validating the initial analysis.
rotation estimation objective
WEB: http://en.wikipedia.org/wiki/Cross_validation
A data visualization which has input of a clustered data set and produces an output of a report graph which is capable of rendering data of this type.
material component separation
Using a cell sorter to separate a mixture of T cells into two fractions; one with surface receptor CD8 and the other lacking the receptor, or purification
a material processing in which components of an input material become segregated in space
Bjoern Peters
IEDB
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.
cell culture splitting
The act of taking a cell culture of high density, counting the cells, removing part of the cells, and re-seeding a select number of the cells into new flasks with fresh tissue culture media.
The act of taking part of a homogeneous cell culture and creating one or more additional separate cultures of similar qualities. input: cell_culture, output cell_culture min cardinality 2. part of cell culturing
An active cell culture is typically split when it has grown to confluence in its culture dish. Cell culture splitting of a cell culture sample results in an increase in its passage number, which measures how long a sample has been propagated in vitro, and therefore how many selective or genetic changes it is likely to have undergone.
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/
In addition to the coding regions (exons), a gene includes transcription-control regions and sometimes introns. Although the majority of genes encode proteins, some encode tRNAs, rRNAs, and other types of RNA.
gene
a disposition that a gene can be used as a blueprint for generating a new form of product such as protein.
WEB: http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/objects/entrezgene/entrezgene.asn
According to NCBI Gene project, there are two gene types: unknown (0) , tRNA (1) , rRNA (2) , snRNA (3) , scRNA (4) , snoRNA (5) , protein-coding (6) , pseudo (7) , transposon (8) , miscRNA (9) , ncRNA (10) , other (255).
gene type
a gene type that is protein-coding, i.e., the gene encodes for a protein. .
protein-coding gene type
a gene type that is tRNA, i.e., this gene encodes for a RNA.
RNA gene type
a RNA gene type that is tRNA, i.e., this gene encodes for a rRNA.
rRNA gene type
snRNA gene type
a RNA gene type that is tRNA, i.e., this gene encodes for a tRNA.
tRNA gene type
a RNA gene type that is scRNA, i.e., this gene encodes for a scRNA.
scRNA gene type
a RNA gene type that is snoRNA, i.e., this gene encodes for a snoRNA.
snoRNA gene type
a RNA gene type that is miscRNA, i.e., this gene encodes for a miscRNA.
miscRNA gene type
a RNA gene type that is ncRNA, i.e., this gene encodes for a ncRNA.
ncRNA gene type
a gene type that is pseudo, i.e., the gene is a pseudogene.
pseudo gene type
a gene type that is transposon, i.e., the gene encodes for a transposon.
transposon gene type
a gene type that is "other", i.e., the gene is for a gene product that is not listed for another other gene type.
other gene type
a gene type that is "unknown", i.e., the gene product is unknown.
unknown gene type
The genome of an organism of Spirochaetales
The genome of an organism of Borrelia burgdorferi
The genome of an organism of Campylobacter jejuni
The genome of an organism of Helicobacter pylori
The genome of an organism of Brucella abortus
The genome of an organism of Francisella tularensis
The genome of an organism of Pseudomonas aeruginosa
The genome of an organism of Rhizobiales
The genome of an organism of Legionella pneumophila
The genome of an organism of Neisseria meningitidis
The genome of an organism of Bordetella pertussis
The genome of an organism of Enterobacteriaceae
The genome of an organism of Escherichia coli
The genome of an organism of Shigella boydii
The genome of an organism of Shigella flexneri
The genome of an organism of Yersinia <bacteria>
The genome of an organism of Yersinia enterocolitica
The genome of an organism of Yersinia pestis
The genome of an organism of Yersinia pseudotuberculosis
The genome of an organism of Vibrio cholerae
The genome of an organism of Pasteurellaceae
The genome of an organism of Actinobacillus pleuropneumoniae
genome of Actinobacillus pleuropneumoniae
The genome of an organism of Haemophilus influenzae
The genome of an organism of Pasteurella multocida
The genome of an organism of Proteobacteria
The genome of an organism of Gammaproteobacteria
The genome of an organism of Staphylococcus aureus
The genome of an organism of Streptococcus
The genome of an organism of Streptococcus agalactiae
The genome of an organism of Streptococcus pneumoniae
The genome of an organism of Streptococcus pyogenes
The genome of an organism of Enterococcus
The genome of an organism of Enterococcus faecalis
The genome of an organism of Enterococcus faecium
The genome of an organism of Bacillus anthracis
The genome of an organism of Clostridium
The genome of an organism of Clostridium botulinum
The genome of an organism of [Clostridium] difficile
The genome of an organism of Clostridium perfringens
The genome of an organism of Listeria monocytogenes
The genome of an organism of Mycobacterium
The genome of an organism of Mycobacterium tuberculosis
The genome of an organism of Saccharomycetales
The genome of an organism of Saccharomycetaceae
The genome of an organism of Saccharomyces cerevisiae
The genome of an organism of Ajellomyces capsulatus
The genome of an organism of Cryptococcus neoformans
The genome of an organism of Candida albicans
The genome of an organism of Candida glabrata
The genome of an organism of Trypanosomatidae
The genome of an organism of Leishmania donovani
The genome of an organism of Leishmania major
The genome of an organism of Leishmania mexicana
The genome of an organism of Leishmania infantum
The genome of an organism of Trypanosoma
The genome of an organism of Trypanosoma cruzi
The genome of an organism of Entamoeba histolytica
The genome of an organism of Apicomplexa
The genome of an organism of Toxoplasma gondii
The genome of an organism of Plasmodium berghei ANKA
The genome of an organism of Plasmodium yoelii
The genome of an organism of Exophiala dermatitidis
The genome of an organism of Chordopoxvirinae
The genome of an organism of Orthopoxvirus
The genome of an organism of Cowpox virus
The genome of an organism of Vaccinia virus
The genome of an organism of Vaccinia virus Tian Tan
The genome of an organism of Vaccinia virus WR
The genome of an organism of Sheeppox virus
The genome of an organism of Leporipoxvirus
The genome of an organism of Rabbit fibroma virus
The genome of an organism of Myxoma virus
The genome of an organism of Herpesviridae
The genome of an organism of Alphaherpesvirinae
The genome of an organism of Simplexvirus
The genome of an organism of Human herpesvirus 1
The genome of an organism of Herpes simplex virus (type 1 / strain 17)
genome of Herpes simplex virus (type 1 / strain 17)
The genome of an organism of Human herpesvirus 2
The genome of an organism of Varicellovirus
The genome of an organism of Bovine herpesvirus 1
The genome of an organism of Equid herpesvirus 1
The genome of an organism of Felid herpesvirus 1
The genome of an organism of Human herpesvirus 3
The genome of an organism of Suid herpesvirus 1
The genome of an organism of Gallid herpesvirus 1
The genome of an organism of Gallid herpesvirus 2
The genome of an organism of African swine fever virus
The genome of an organism of Ross River virus
The genome of an organism of Sindbis virus
The genome of an organism of Venezuelan equine encephalitis virus
genome of Venezuelan equine encephalitis virus
The genome of an organism of Western equine encephalomyelitis virus
genome of Western equine encephalomyelitis virus
The genome of an organism of Flaviviridae
The genome of an organism of West Nile virus
The genome of an organism of Tick-borne encephalitis virus
The genome of an organism of Yellow fever virus
The genome of an organism of Classical swine fever virus
The genome of an organism of Classical swine fever virus - Brescia
genome of Classical swine fever virus - Brescia
The genome of an organism of Feline infectious peritonitis virus
genome of Feline infectious peritonitis virus
The genome of an organism of Porcine respiratory coronavirus
genome of Porcine respiratory coronavirus
The genome of an organism of Mononegavirales
The genome of an organism of Paramyxoviridae
The genome of an organism of Paramyxovirinae
The genome of an organism of Newcastle disease virus
The genome of an organism of Human parainfluenza virus 3
The genome of an organism of Measles virus
The genome of an organism of Pneumovirinae
The genome of an organism of Pneumovirus
The genome of an organism of Bovine respiratory syncytial virus
genome of Bovine respiratory syncytial virus
The genome of an organism of Human respiratory syncytial virus A2
genome of Human respiratory syncytial virus A2
The genome of an organism of Rhabdoviridae
The genome of an organism of Infectious hematopoietic necrosis virus
genome of Infectious hematopoietic necrosis virus
The genome of an organism of Rabies virus
The genome of an organism of Influenza A virus
The genome of an organism of Bunyaviridae
The genome of an organism of La Crosse virus
The genome of an organism of Rift Valley fever virus
The genome of an organism of Hantaan virus
The genome of an organism of Primate lentivirus group
The genome of an organism of Feline immunodeficiency virus
The genome of an organism of Human immunodeficiency virus 1
genome of Human immunodeficiency virus 1
The genome of an organism of Simian immunodeficiency virus
The genome of an organism of Encephalomyocarditis virus
The genome of an organism of Chicken anemia virus
The genome of an organism of Ectromelia virus
The genome of an organism of Burkholderia mallei
The genome of an organism of Alphaproteobacteria
The genome of an organism of Betaproteobacteria
The genome of an organism of Porcine reproductive and respiratory syndrome virus
genome of Porcine reproductive and respiratory syndrome virus
The genome of an organism of Burkholderia pseudomallei
The genome of an organism of Trichocomaceae
The genome of an organism of Rotavirus A
The genome of an organism of Brucella melitensis
The genome of an organism of Yersinia ruckeri
The genome of an organism of Campylobacter jejuni subsp. jejuni
genome of Campylobacter jejuni subsp. jejuni
The genome of an organism of Opisthokonta
The genome of an organism of Suid herpesvirus 1 strain Kaplan
genome of Suid herpesvirus 1 strain Kaplan
The genome of an organism of Actinobacillus pleuropneumoniae serovar 2
genome of Actinobacillus pleuropneumoniae serovar 2
The genome of an organism of dsDNA viruses, no RNA stage
The genome of an organism of Bovine herpesvirus 5
The genome of an organism of ssRNA positive-strand viruses, no DNA stage
genome of ssRNA positive-strand viruses, no DNA stage
The genome of an organism of ssRNA negative-strand viruses
The genome of an organism of Dictyochales
The genome of an organism of Plasmodium falciparum 3D7
The genome of an organism of Rotavirus C
The genome of an organism of Clostridium botulinum A
The genome of an organism of Bartonella henselae
The genome of an organism of Leishmania <subgenus>
The genome of an organism of Leishmania donovani species complex
genome of Leishmania donovani species complex
The genome of an organism of Circoviridae
The genome of an organism of Cryptococcus neoformans var. neoformans
genome of Cryptococcus neoformans var. neoformans
The genome of an organism of Candida dubliniensis
The genome of an organism of Shigella flexneri 2a
The genome of an organism of Vibrio cholerae O139
The genome of an organism of Autographa californica nucleopolyhedrovirus
genome of Autographa californica nucleopolyhedrovirus
The genome of an organism of Staphylococcus aureus subsp. aureus
genome of Staphylococcus aureus subsp. aureus
The genome of an organism of Salmonella enterica subsp. enterica
genome of Salmonella enterica subsp. enterica
The genome of an organism of Legionella pneumophila serogroup 1
genome of Legionella pneumophila serogroup 1
The genome of an organism of Murine cytomegalovirus (strain K181)
genome of Murine cytomegalovirus (strain K181)
The genome of an organism of Haemophilus influenzae Rd KW20
genome of Haemophilus influenzae Rd KW20
The genome of an organism of Plasmodium yoelii yoelii
The genome of an organism of Mannheimia haemolytica
The genome of an organism of Nidovirales
The genome of an organism of Bovine herpesvirus type 1.1
The genome of an organism of Burkholderiales
The genome of an organism of Mycobacterium tuberculosis CDC1551
genome of Mycobacterium tuberculosis CDC1551
The genome of an organism of Mycobacterium tuberculosis H37Rv
genome of Mycobacterium tuberculosis H37Rv
The genome of an organism of Escherichia coli K-12
The genome of an organism of Escherichia coli O157:H7
The genome of an organism of Chlamydia pneumoniae
The genome of an organism of Corynebacterineae
The genome of an organism of Porcine circovirus 2
The genome of an organism of Helicobacter pylori 26695
The genome of an organism of Helicobacter pylori J99
The genome of an organism of Salmonella enterica subsp. enterica serovar Typhi
genome of Salmonella enterica subsp. enterica serovar Typhi
The genome of an organism of Salmonella enterica subsp. enterica serovar Typhimurium
genome of Salmonella enterica subsp. enterica serovar Typhimurium
The genome of an organism of Staphylococcus aureus subsp. aureus NCTC 8325
genome of Staphylococcus aureus subsp. aureus NCTC 8325
The genome of an organism of Influenza A virus (A/Goose/Guangdong/1/96(H5N1))
genome of Influenza A virus (A/Goose/Guangdong/1/96(H5N1))
The genome of an organism of Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
genome of Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
The genome of an organism of H5N1 subtype
The genome of an organism of Bartonella birtlesii
The genome of an organism of pseudomallei group
The genome of an organism of Chlamydophila pneumoniae CWL029
genome of Chlamydophila pneumoniae CWL029
The genome of an organism of Legionellales
The genome of an organism of Francisella tularensis subsp. holarctica
genome of Francisella tularensis subsp. holarctica
The genome of an organism of Nipah virus
The genome of an organism of Neisseria meningitidis MC58
The genome of an organism of Neisseria meningitidis Z2491
The genome of an organism of Neisseria meningitidis serogroup C
genome of Neisseria meningitidis serogroup C
The genome of an organism of Chlamydophila pneumoniae J138
The genome of an organism of Eurotiomycetes
The genome of an organism of Escherichia coli O157:H7 str. EDL933
genome of Escherichia coli O157:H7 str. EDL933
The genome of an organism of Staphylococcus aureus subsp. aureus Mu50
genome of Staphylococcus aureus subsp. aureus Mu50
The genome of an organism of Staphylococcus aureus subsp. aureus N315
genome of Staphylococcus aureus subsp. aureus N315
The genome of an organism of Streptococcus pyogenes M1 GAS
The genome of an organism of Streptococcus pyogenes str. Manfredo
genome of Streptococcus pyogenes str. Manfredo
The genome of an organism of Emericella nidulans
The genome of an organism of Listeria monocytogenes EGD-e
The genome of an organism of Streptococcus pneumoniae TIGR4
genome of Streptococcus pneumoniae TIGR4
The genome of an organism of Streptococcus pneumoniae R6
The genome of an organism of Francisella tularensis subsp. tularensis SCHU S4
genome of Francisella tularensis subsp. tularensis SCHU S4
The genome of an organism of WEEV complex
The genome of an organism of Cryptococcus neoformans var. grubii
genome of Cryptococcus neoformans var. grubii
The genome of an organism of Chlamydophila pneumoniae TW-183
genome of Chlamydophila pneumoniae TW-183
The genome of an organism of Trypanosoma brucei TREU927
The genome of an organism of Streptococcus pyogenes MGAS8232
genome of Streptococcus pyogenes MGAS8232
The genome of an organism of Zaire ebolavirus
The genome of an organism of Clostridiales
The genome of an organism of Lactobacillales
The genome of an organism of Yersinia pestis KIM10+
The genome of an organism of Leptospira interrogans serovar Lai str. 56601
genome of Leptospira interrogans serovar Lai str. 56601
The genome of an organism of Bacillus anthracis str. A2012
The genome of an organism of Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819
genome of Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819
The genome of an organism of Streptococcus pyogenes SSI-1
The genome of an organism of Campylobacter jejuni RM1221
The genome of an organism of Clostridium perfringens str. 13
genome of Clostridium perfringens str. 13
The genome of an organism of Clostridium perfringens ATCC 13124
genome of Clostridium perfringens ATCC 13124
The genome of an organism of Staphylococcus aureus subsp. aureus MW2
genome of Staphylococcus aureus subsp. aureus MW2
The genome of an organism of Bacillus anthracis str. Ames
The genome of an organism of Shigella flexneri 2a str. 301
The genome of an organism of Shigella flexneri 2a str. 2457T
genome of Shigella flexneri 2a str. 2457T
The genome of an organism of Streptococcus pyogenes MGAS315
genome of Streptococcus pyogenes MGAS315
The genome of an organism of Coccidioides posadasii
The genome of an organism of Escherichia coli CFT073
The genome of an organism of Brucella suis 1330
The genome of an organism of Streptococcus agalactiae A909
The genome of an organism of Streptococcus agalactiae 2603V/R
genome of Streptococcus agalactiae 2603V/R
The genome of an organism of Pseudomonas aeruginosa UCBPP-PA14
genome of Pseudomonas aeruginosa UCBPP-PA14
The genome of an organism of Pseudomonas aeruginosa PAO1
The genome of an organism of Salmonella enterica subsp. enterica serovar Typhi str. Ty2
genome of Salmonella enterica subsp. enterica serovar Typhi str. Ty2
The genome of an organism of Influenza A virus (A/Puerto Rico/8/1934(H1N1))
genome of Influenza A virus (A/Puerto Rico/8/1934(H1N1))
The genome of an organism of Streptococcus agalactiae NEM316
genome of Streptococcus agalactiae NEM316
The genome of an organism of Clostridium tetani E88
The genome of an organism of Campylobacterales
The genome of an organism of Yersinia pestis CO92
The genome of an organism of Cryptococcus neoformans var. neoformans JEC21
genome of Cryptococcus neoformans var. neoformans JEC21
The genome of an organism of Salmonella enterica subsp. enterica serovar Typhi str. CT18
genome of Salmonella enterica subsp. enterica serovar Typhi str. CT18
The genome of an organism of Borrelia burgdorferi B31
The genome of an organism of Brucella melitensis bv. 1 str. 16M
genome of Brucella melitensis bv. 1 str. 16M
The genome of an organism of Enterococcus faecalis V583
The genome of an organism of Aspergillus nidulans FGSC A4
The genome of an organism of Coxiella burnetii RSA 493
The genome of an organism of Yersinia pestis biovar Microtus str. 91001
genome of Yersinia pestis biovar Microtus str. 91001
The genome of an organism of Candida albicans SC5314
The genome of an organism of Burkholderia mallei ATCC 23344
genome of Burkholderia mallei ATCC 23344
The genome of an organism of Vibrio cholerae O1 biovar El Tor str. N16961
genome of Vibrio cholerae O1 biovar El Tor str. N16961
The genome of an organism of Corynebacterium diphtheriae NCTC 13129
genome of Corynebacterium diphtheriae NCTC 13129
The genome of an organism of Bordetella bronchiseptica RB50
genome of Bordetella bronchiseptica RB50
The genome of an organism of Bordetella pertussis Tohama I
The genome of an organism of Bacillus anthracis str. Sterne
genome of Bacillus anthracis str. Sterne
The genome of an organism of Bacillus anthracis str. 'Ames Ancestor'
genome of Bacillus anthracis str. 'Ames Ancestor'
The genome of an organism of Orgyia pseudotsugata MNPV
The genome of an organism of Mycobacterium avium subsp. paratuberculosis K-10
genome of Mycobacterium avium subsp. paratuberculosis K-10
The genome of an organism of Listeria monocytogenes serotype 4b str. F2365
genome of Listeria monocytogenes serotype 4b str. F2365
The genome of an organism of Pneumonia virus of mice J3666
The genome of an organism of Bombyx mori NPV
The genome of an organism of Burkholderia pseudomallei K96243
genome of Burkholderia pseudomallei K96243
The genome of an organism of Chlamydia trachomatis D/UW-3/CX
genome of Chlamydia trachomatis D/UW-3/CX
The genome of an organism of Clostridium difficile 630
The genome of an organism of Legionella pneumophila subsp. pneumophila str. Philadelphia 1
genome of Legionella pneumophila subsp. pneumophila str. Philadelphia 1
The genome of an organism of Neisseria meningitidis FAM18
The genome of an organism of Pasteurella multocida subsp. multocida str. Pm70
genome of Pasteurella multocida subsp. multocida str. Pm70
The genome of an organism of Rickettsia prowazekii str. Madrid E
genome of Rickettsia prowazekii str. Madrid E
The genome of an organism of Staphylococcus aureus RF122
The genome of an organism of Yersinia pseudotuberculosis IP 32953
genome of Yersinia pseudotuberculosis IP 32953
The genome of an organism of Haemophilus influenzae 86-028NP
genome of Haemophilus influenzae 86-028NP
The genome of an organism of Staphylococcus aureus subsp. aureus MRSA252
genome of Staphylococcus aureus subsp. aureus MRSA252
The genome of an organism of Bartonella henselae str. Houston-1
genome of Bartonella henselae str. Houston-1
The genome of an organism of Cryptococcus neoformans var. neoformans B-3501A
genome of Cryptococcus neoformans var. neoformans B-3501A
The genome of an organism of Influenza A virus (A/Viet Nam/1203/2004(H5N1))
genome of Influenza A virus (A/Viet Nam/1203/2004(H5N1))
The genome of an organism of Candida glabrata CBS 138
The genome of an organism of Streptococcus pyogenes MGAS10394
genome of Streptococcus pyogenes MGAS10394
The genome of an organism of Clostridium perfringens SM101
The genome of an organism of Streptococcus pyogenes MGAS5005
genome of Streptococcus pyogenes MGAS5005
The genome of an organism of Entamoeba histolytica HM-1:IMSS
genome of Entamoeba histolytica HM-1:IMSS
The genome of an organism of Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150
genome of Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150
The genome of an organism of Legionella pneumophila str. Lens
genome of Legionella pneumophila str. Lens
The genome of an organism of Legionella pneumophila str. Paris
genome of Legionella pneumophila str. Paris
The genome of an organism of Shigella dysenteriae Sd197
The genome of an organism of Shigella boydii Sb227
The genome of an organism of Shigella sonnei Ss046
The genome of an organism of Streptococcus pyogenes serotype M1
genome of Streptococcus pyogenes serotype M1
The genome of an organism of Streptococcus pyogenes serotype M3
genome of Streptococcus pyogenes serotype M3
The genome of an organism of Escherichia coli str. K-12 substr. DH10B
genome of Escherichia coli str. K-12 substr. DH10B
The genome of an organism of Escherichia coli ETEC H10407
The genome of an organism of Streptococcus pyogenes MGAS6180
genome of Streptococcus pyogenes MGAS6180
The genome of an organism of Burkholderia pseudomallei 1710b
genome of Burkholderia pseudomallei 1710b
The genome of an organism of Burkholderia pseudomallei 668
The genome of an organism of Burkholderia mallei SAVP1
The genome of an organism of Burkholderia mallei NCTC 10247
genome of Burkholderia mallei NCTC 10247
The genome of an organism of Salmonella enterica subsp. enterica serovar Choleraesuis str. SC-B67
genome of Salmonella enterica subsp. enterica serovar Choleraesuis str. SC-B67
The genome of an organism of Aspergillus fumigatus Af293
The genome of an organism of Escherichia coli E24377A
The genome of an organism of Escherichia coli HS
The genome of an organism of Mycobacterium tuberculosis F11
genome of Mycobacterium tuberculosis F11
The genome of an organism of Streptococcus pyogenes serotype M12
genome of Streptococcus pyogenes serotype M12
The genome of an organism of Shigella boydii CDC 3083-94
The genome of an organism of SARS coronavirus ZJ0301
The genome of an organism of Vibrio cholerae O395
The genome of an organism of Leishmania major strain Friedlin
genome of Leishmania major strain Friedlin
The genome of an organism of Yersinia pestis Angola
The genome of an organism of Yersinia pseudotuberculosis IP 31758
genome of Yersinia pseudotuberculosis IP 31758
The genome of an organism of Plasmodium yoelii yoelii 17XNL
genome of Plasmodium yoelii yoelii 17XNL
The genome of an organism of Cryptosporidium parvum Iowa II
genome of Cryptosporidium parvum Iowa II
The genome of an organism of Trypanosoma cruzi strain CL Brener
genome of Trypanosoma cruzi strain CL Brener
The genome of an organism of Campylobacter jejuni subsp. jejuni 81-176
genome of Campylobacter jejuni subsp. jejuni 81-176
The genome of an organism of Burkholderia pseudomallei 1106a
genome of Burkholderia pseudomallei 1106a
The genome of an organism of Brucella melitensis biovar Abortus 2308
genome of Brucella melitensis biovar Abortus 2308
The genome of an organism of Bartonella bacilliformis KC583
genome of Bartonella bacilliformis KC583
The genome of an organism of Yersinia pestis Antiqua
The genome of an organism of Campylobacter jejuni subsp. doylei 269.97
genome of Campylobacter jejuni subsp. doylei 269.97
The genome of an organism of Bordetella avium 197N
The genome of an organism of Escherichia coli 536
The genome of an organism of Escherichia coli UTI89
The genome of an organism of Streptococcus pyogenes MGAS9429
genome of Streptococcus pyogenes MGAS9429
The genome of an organism of Streptococcus pyogenes MGAS10270
genome of Streptococcus pyogenes MGAS10270
The genome of an organism of Streptococcus pyogenes MGAS2096
genome of Streptococcus pyogenes MGAS2096
The genome of an organism of Streptococcus pyogenes MGAS10750
genome of Streptococcus pyogenes MGAS10750
The genome of an organism of Streptococcus pneumoniae D39
The genome of an organism of Shigella flexneri 5 str. 8401
The genome of an organism of Neisseria meningitidis 053442
The genome of an organism of Francisella tularensis subsp. holarctica LVS
genome of Francisella tularensis subsp. holarctica LVS
The genome of an organism of Escherichia coli O26:H-
The genome of an organism of Yersinia pestis Nepal516
The genome of an organism of Aeromonas salmonicida subsp. salmonicida A449
genome of Aeromonas salmonicida subsp. salmonicida A449
The genome of an organism of Bartonella tribocorum CIP 105476
genome of Bartonella tribocorum CIP 105476
The genome of an organism of Escherichia coli O157:H7 str. Sakai
genome of Escherichia coli O157:H7 str. Sakai
The genome of an organism of Yersinia pestis Pestoides F
The genome of an organism of Yersinia enterocolitica subsp. enterocolitica 8081
genome of Yersinia enterocolitica subsp. enterocolitica 8081
The genome of an organism of Legionella pneumophila str. Corby
genome of Legionella pneumophila str. Corby
The genome of an organism of Escherichia coli APEC O1
The genome of an organism of Campylobacter jejuni subsp. jejuni 81116
genome of Campylobacter jejuni subsp. jejuni 81116
The genome of an organism of Escherichia coli SE11
The genome of an organism of Burkholderia mallei NCTC 10229
genome of Burkholderia mallei NCTC 10229
The genome of an organism of Yersinia pestis CA88-4125
The genome of an organism of Escherichia coli B str. REL606
genome of Escherichia coli B str. REL606
The genome of an organism of Actinobacillus pleuropneumoniae serovar 5b str. L20
genome of Actinobacillus pleuropneumoniae serovar 5b str. L20
The genome of an organism of Plasmodium (Vinckeia)
The genome of an organism of Staphylococcus aureus subsp. aureus Mu3
genome of Staphylococcus aureus subsp. aureus Mu3
The genome of an organism of Mycobacterium tuberculosis H37Ra
genome of Mycobacterium tuberculosis H37Ra
The genome of an organism of Eimeriorina
The genome of an organism of Legionella pneumophila 2300/99 Alcoy
genome of Legionella pneumophila 2300/99 Alcoy
The genome of an organism of Staphylococcus aureus subsp. aureus str. Newman
genome of Staphylococcus aureus subsp. aureus str. Newman
The genome of an organism of Actinobacillus pleuropneumoniae serovar 3 str. JL03
genome of Actinobacillus pleuropneumoniae serovar 3 str. JL03
The genome of an organism of ssRNA viruses
The genome of an organism of Escherichia coli SMS-3-5
The genome of an organism of Clostridium botulinum A str. ATCC 19397
genome of Clostridium botulinum A str. ATCC 19397
The genome of an organism of Clostridium botulinum A str. Hall
genome of Clostridium botulinum A str. Hall
The genome of an organism of Escherichia coli O157:H7 str. EC4115
genome of Escherichia coli O157:H7 str. EC4115
The genome of an organism of Borrelia burgdorferi 156a
The genome of an organism of Borrelia burgdorferi ZS7
The genome of an organism of Eurotiomycetidae
The genome of an organism of Francisella tularensis subsp. holarctica FTNF002-00
genome of Francisella tularensis subsp. holarctica FTNF002-00
The genome of an organism of Streptococcus pyogenes NZ131
The genome of an organism of Enterococcus faecalis OG1RF
The genome of an organism of Salmonella enterica subsp. enterica serovar Paratyphi C strain RKS4594
genome of Salmonella enterica subsp. enterica serovar Paratyphi C strain RKS4594
The genome of an organism of Paenibacillus sp. Y412MC10
The genome of an organism of Streptococcus pneumoniae Taiwan19F-14
genome of Streptococcus pneumoniae Taiwan19F-14
The genome of an organism of Streptococcus pneumoniae Hungary19A-6
genome of Streptococcus pneumoniae Hungary19A-6
The genome of an organism of Streptococcus pneumoniae 70585
genome of Streptococcus pneumoniae 70585
The genome of an organism of Streptococcus pneumoniae JJA
The genome of an organism of Streptococcus pneumoniae P1031
genome of Streptococcus pneumoniae P1031
The genome of an organism of Clostridium botulinum B1 str. Okra
genome of Clostridium botulinum B1 str. Okra
The genome of an organism of Clostridium botulinum A3 str. Loch Maree
genome of Clostridium botulinum A3 str. Loch Maree
The genome of an organism of Edwardsiella tarda EIB202
The genome of an organism of Yersinia pseudotuberculosis YPIII
genome of Yersinia pseudotuberculosis YPIII
The genome of an organism of Yersinia pseudotuberculosis PB1/+
genome of Yersinia pseudotuberculosis PB1/+
The genome of an organism of Clostridium botulinum E3 str. Alaska E43
genome of Clostridium botulinum E3 str. Alaska E43
The genome of an organism of Toxoplasma gondii ME49
The genome of an organism of Escherichia coli str. K-12 substr. MG1655
genome of Escherichia coli str. K-12 substr. MG1655
The genome of an organism of Streptococcus pneumoniae G54
The genome of an organism of Streptococcus pneumoniae CGSP14
genome of Streptococcus pneumoniae CGSP14
The genome of an organism of Borrelia burgdorferi N40
The genome of an organism of Borrelia burgdorferi 297
The genome of an organism of Burkholderia pseudomallei MSHR346
genome of Burkholderia pseudomallei MSHR346
The genome of an organism of Actinobacillus pleuropneumoniae serovar 7 str. AP76
genome of Actinobacillus pleuropneumoniae serovar 7 str. AP76
The genome of an organism of Escherichia coli O157:H7 str. TW14359
genome of Escherichia coli O157:H7 str. TW14359
The genome of an organism of Salmonella enterica subsp. enterica serovar Enteritidis str. P125109
genome of Salmonella enterica subsp. enterica serovar Enteritidis str. P125109
The genome of an organism of Salmonella enterica subsp. enterica serovar Gallinarum str. 287/91
genome of Salmonella enterica subsp. enterica serovar Gallinarum str. 287/91
The genome of an organism of Filobasidiella/Cryptococcus neoformans species complex
genome of Filobasidiella/Cryptococcus neoformans species complex
The genome of an organism of Cryptococcus gattii
The genome of an organism of Streptococcus equi subsp. zooepidemicus MGCS10565
genome of Streptococcus equi subsp. zooepidemicus MGCS10565
The genome of an organism of Listeria monocytogenes HCC23
The genome of an organism of Pseudomonas aeruginosa LESB58
The genome of an organism of Alphabaculovirus
The genome of an organism of Saccharomyces cerevisiae S288c
genome of Saccharomyces cerevisiae S288c
The genome of an organism of Streptococcus pneumoniae ATCC 700669
genome of Streptococcus pneumoniae ATCC 700669
The genome of an organism of Helicobacter pylori G27
The genome of an organism of Listeria monocytogenes L99
The genome of an organism of Escherichia coli Vir68
The genome of an organism of Bacillus anthracis str. CDC 684
genome of Bacillus anthracis str. CDC 684
The genome of an organism of Listeria monocytogenes serotype 4b str. CLIP 80459
genome of Listeria monocytogenes serotype 4b str. CLIP 80459
The genome of an organism of Helicobacter pylori P12
The genome of an organism of Escherichia coli O26:H11 str. 11368
genome of Escherichia coli O26:H11 str. 11368
The genome of an organism of Escherichia coli O127:H6 str. E2348/69
genome of Escherichia coli O127:H6 str. E2348/69
The genome of an organism of Vibrio cholerae M66-2
The genome of an organism of Escherichia coli IAI1
The genome of an organism of Escherichia coli S88
The genome of an organism of Escherichia coli 55989
The genome of an organism of Escherichia coli UMN026
The genome of an organism of Escherichia coli IAI39
The genome of an organism of Escherichia coli O103:H2 str. 12009
genome of Escherichia coli O103:H2 str. 12009
The genome of an organism of Escherichia coli O111:H- str. 11128
genome of Escherichia coli O111:H- str. 11128
The genome of an organism of Escherichia coli ED1a
The genome of an organism of Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S
genome of Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S
The genome of an organism of Bacillus anthracis str. A0248
The genome of an organism of Helicobacter pylori B38
The genome of an organism of Escherichia coli BW2952
The genome of an organism of SARS coronavirus ExoN1
The genome of an organism of Listeria monocytogenes 08-5923
genome of Listeria monocytogenes 08-5923
The genome of an organism of Listeria monocytogenes 08-5578
genome of Listeria monocytogenes 08-5578
The genome of an organism of Neisseria meningitidis alpha14
genome of Neisseria meningitidis alpha14
The genome of an organism of Staphylococcus aureus subsp. aureus ED98
genome of Staphylococcus aureus subsp. aureus ED98
The genome of an organism of Coronavirinae
The genome of an organism of Alphacoronavirus 1
The genome of an organism of Severe acute respiratory syndrome-related coronavirus
genome of Severe acute respiratory syndrome-related coronavirus
The genome of an organism of Human metapneumovirus CAN97-83
genome of Human metapneumovirus CAN97-83
The genome of an organism of Mileewa branchiuma
The genome of an organism of Staphylococcus aureus 04-02981
genome of Staphylococcus aureus 04-02981
The genome of an organism of Mycoplasma gallisepticum str. R(low)
genome of Mycoplasma gallisepticum str. R(low)
The genome of an organism of saccharomyceta
The genome of an organism of Legionella pneumophila 130b
The genome of an organism of Salmonella enterica subsp. enterica serovar Typhimurium str. ST4/74
genome of Salmonella enterica subsp. enterica serovar Typhimurium str. ST4/74
A gene of an organism of Borrelia burgdorferi
A gene of an organism of Campylobacter jejuni
A gene of an organism of Helicobacter pylori
A gene of an organism of Brucella abortus
A gene of an organism of Francisella tularensis
A gene of an organism of Pseudomonas aeruginosa
A gene of an organism of Legionella pneumophila
A gene of an organism of Neisseria meningitidis
A gene of an organism of Bordetella pertussis
A gene of an organism of Enterobacteriaceae
A gene of an organism of Escherichia coli
A gene of an organism of Shigella boydii
A gene of an organism of Shigella flexneri
A gene of an organism of Yersinia <bacteria>
A gene of an organism of Yersinia enterocolitica
A gene of an organism of Yersinia pestis
A gene of an organism of Yersinia pseudotuberculosis
A gene of an organism of Vibrio cholerae
A gene of an organism of Pasteurellaceae
A gene of an organism of Actinobacillus pleuropneumoniae
A gene of an organism of Haemophilus influenzae
A gene of an organism of Pasteurella multocida
A gene of an organism of Gammaproteobacteria
A gene of an organism of Staphylococcus aureus
A gene of an organism of Streptococcus agalactiae
A gene of an organism of Streptococcus pneumoniae
A gene of an organism of Streptococcus pyogenes
A gene of an organism of Enterococcus faecalis
A gene of an organism of Enterococcus faecium
A gene of an organism of Bacillus anthracis
A gene of an organism of Clostridium botulinum
A gene of an organism of [Clostridium] difficile
A gene of an organism of Clostridium perfringens
A gene of an organism of Listeria monocytogenes
A gene of an organism of Mycobacterium tuberculosis
A gene of an organism of Saccharomycetales
A gene of an organism of Saccharomycetaceae
A gene of an organism of Saccharomyces cerevisiae
A gene of an organism of Ajellomyces capsulatus
A gene of an organism of Cryptococcus neoformans
A gene of an organism of Candida albicans
A gene of an organism of Candida glabrata
A gene of an organism of Trypanosomatidae
A gene of an organism of Leishmania donovani
A gene of an organism of Leishmania major
A gene of an organism of Leishmania mexicana
A gene of an organism of Leishmania infantum
A gene of an organism of Trypanosoma cruzi
A gene of an organism of Entamoeba histolytica
A gene of an organism of Toxoplasma gondii
A gene of an organism of Plasmodium berghei ANKA
A gene of an organism of Plasmodium yoelii
A gene of an organism of Exophiala dermatitidis
A gene of an organism of Chordopoxvirinae
A gene of an organism of Vaccinia virus Tian Tan
A gene of an organism of Vaccinia virus WR
A gene of an organism of Rabbit fibroma virus
A gene of an organism of Alphaherpesvirinae
A gene of an organism of Human herpesvirus 1
A gene of an organism of Herpes simplex virus (type 1 / strain 17)
gene of Herpes simplex virus (type 1 / strain 17)
A gene of an organism of Human herpesvirus 2
A gene of an organism of Bovine herpesvirus 1
A gene of an organism of Equid herpesvirus 1
A gene of an organism of Felid herpesvirus 1
A gene of an organism of Human herpesvirus 3
A gene of an organism of Suid herpesvirus 1
A gene of an organism of Gallid herpesvirus 1
A gene of an organism of Gallid herpesvirus 2
A gene of an organism of African swine fever virus
A gene of an organism of Ross River virus
A gene of an organism of Venezuelan equine encephalitis virus
gene of Venezuelan equine encephalitis virus
A gene of an organism of Western equine encephalomyelitis virus
gene of Western equine encephalomyelitis virus
A gene of an organism of West Nile virus
A gene of an organism of Tick-borne encephalitis virus
A gene of an organism of Yellow fever virus
A gene of an organism of Classical swine fever virus
A gene of an organism of Classical swine fever virus - Brescia
gene of Classical swine fever virus - Brescia
A gene of an organism of Feline infectious peritonitis virus
gene of Feline infectious peritonitis virus
A gene of an organism of Porcine respiratory coronavirus
A gene of an organism of Mononegavirales
A gene of an organism of Paramyxoviridae
A gene of an organism of Paramyxovirinae
A gene of an organism of Newcastle disease virus
A gene of an organism of Human parainfluenza virus 3
A gene of an organism of Bovine respiratory syncytial virus
gene of Bovine respiratory syncytial virus
A gene of an organism of Human respiratory syncytial virus A2
gene of Human respiratory syncytial virus A2
A gene of an organism of Infectious hematopoietic necrosis virus
gene of Infectious hematopoietic necrosis virus
A gene of an organism of Influenza A virus
A gene of an organism of La Crosse virus
A gene of an organism of Rift Valley fever virus
A gene of an organism of Primate lentivirus group
A gene of an organism of Feline immunodeficiency virus
A gene of an organism of Human immunodeficiency virus 1
A gene of an organism of Simian immunodeficiency virus
A gene of an organism of Encephalomyocarditis virus
A gene of an organism of Chicken anemia virus
A gene of an organism of Ectromelia virus
A gene of an organism of Burkholderia mallei
A gene of an organism of Alphaproteobacteria
A gene of an organism of Betaproteobacteria
A gene of an organism of Porcine reproductive and respiratory syndrome virus
gene of Porcine reproductive and respiratory syndrome virus
A gene of an organism of Burkholderia pseudomallei
A gene of an organism of Brucella melitensis
A gene of an organism of Yersinia ruckeri
A gene of an organism of Campylobacter jejuni subsp. jejuni
gene of Campylobacter jejuni subsp. jejuni
A gene of an organism of Suid herpesvirus 1 strain Kaplan
gene of Suid herpesvirus 1 strain Kaplan
A gene of an organism of Actinobacillus pleuropneumoniae serovar 2
gene of Actinobacillus pleuropneumoniae serovar 2
A gene of an organism of dsDNA viruses, no RNA stage
A gene of an organism of Bovine herpesvirus 5
A gene of an organism of ssRNA positive-strand viruses, no DNA stage
gene of ssRNA positive-strand viruses, no DNA stage
A gene of an organism of ssRNA negative-strand viruses
A gene of an organism of Plasmodium falciparum 3D7
A gene of an organism of Clostridium botulinum A
A gene of an organism of Bartonella henselae
A gene of an organism of Leishmania <subgenus>
A gene of an organism of Leishmania donovani species complex
gene of Leishmania donovani species complex
A gene of an organism of Cryptococcus neoformans var. neoformans
gene of Cryptococcus neoformans var. neoformans
A gene of an organism of Candida dubliniensis
A gene of an organism of Shigella flexneri 2a
A gene of an organism of Vibrio cholerae O139
A gene of an organism of Autographa californica nucleopolyhedrovirus
gene of Autographa californica nucleopolyhedrovirus
A gene of an organism of Staphylococcus aureus subsp. aureus
gene of Staphylococcus aureus subsp. aureus
A gene of an organism of Salmonella enterica subsp. enterica
gene of Salmonella enterica subsp. enterica
A gene of an organism of Legionella pneumophila serogroup 1
gene of Legionella pneumophila serogroup 1
A gene of an organism of Murine cytomegalovirus (strain K181)
gene of Murine cytomegalovirus (strain K181)
A gene of an organism of Haemophilus influenzae Rd KW20
A gene of an organism of Plasmodium yoelii yoelii
A gene of an organism of Mannheimia haemolytica
A gene of an organism of Bovine herpesvirus type 1.1
A gene of an organism of Burkholderiales
A gene of an organism of Mycobacterium tuberculosis CDC1551
gene of Mycobacterium tuberculosis CDC1551
A gene of an organism of Mycobacterium tuberculosis H37Rv
gene of Mycobacterium tuberculosis H37Rv
A gene of an organism of Escherichia coli K-12
A gene of an organism of Escherichia coli O157:H7
A gene of an organism of Chlamydia pneumoniae
A gene of an organism of Corynebacterineae
A gene of an organism of Porcine circovirus 2
A gene of an organism of Helicobacter pylori 26695
A gene of an organism of Helicobacter pylori J99
A gene of an organism of Salmonella enterica subsp. enterica serovar Typhi
gene of Salmonella enterica subsp. enterica serovar Typhi
A gene of an organism of Salmonella enterica subsp. enterica serovar Typhimurium
gene of Salmonella enterica subsp. enterica serovar Typhimurium
A gene of an organism of Staphylococcus aureus subsp. aureus NCTC 8325
gene of Staphylococcus aureus subsp. aureus NCTC 8325
A gene of an organism of Influenza A virus (A/Goose/Guangdong/1/96(H5N1))
gene of Influenza A virus (A/Goose/Guangdong/1/96(H5N1))
A gene of an organism of Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
gene of Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
A gene of an organism of Bartonella birtlesii
A gene of an organism of pseudomallei group
A gene of an organism of Chlamydophila pneumoniae CWL029
A gene of an organism of Francisella tularensis subsp. holarctica
gene of Francisella tularensis subsp. holarctica
A gene of an organism of Neisseria meningitidis MC58
A gene of an organism of Neisseria meningitidis Z2491
A gene of an organism of Neisseria meningitidis serogroup C
gene of Neisseria meningitidis serogroup C
A gene of an organism of Chlamydophila pneumoniae J138
A gene of an organism of Escherichia coli O157:H7 str. EDL933
gene of Escherichia coli O157:H7 str. EDL933
A gene of an organism of Staphylococcus aureus subsp. aureus Mu50
gene of Staphylococcus aureus subsp. aureus Mu50
A gene of an organism of Staphylococcus aureus subsp. aureus N315
gene of Staphylococcus aureus subsp. aureus N315
A gene of an organism of Streptococcus pyogenes M1 GAS
A gene of an organism of Streptococcus pyogenes str. Manfredo
gene of Streptococcus pyogenes str. Manfredo
A gene of an organism of Emericella nidulans
A gene of an organism of Listeria monocytogenes EGD-e
A gene of an organism of Streptococcus pneumoniae TIGR4
A gene of an organism of Streptococcus pneumoniae R6
A gene of an organism of Francisella tularensis subsp. tularensis SCHU S4
gene of Francisella tularensis subsp. tularensis SCHU S4
A gene of an organism of Cryptococcus neoformans var. grubii
gene of Cryptococcus neoformans var. grubii
A gene of an organism of Chlamydophila pneumoniae TW-183
A gene of an organism of Trypanosoma brucei TREU927
A gene of an organism of Streptococcus pyogenes MGAS8232
A gene of an organism of Zaire ebolavirus
A gene of an organism of Lactobacillales
A gene of an organism of Yersinia pestis KIM10+
A gene of an organism of Leptospira interrogans serovar Lai str. 56601
gene of Leptospira interrogans serovar Lai str. 56601
A gene of an organism of Bacillus anthracis str. A2012
A gene of an organism of Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819
gene of Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819
A gene of an organism of Streptococcus pyogenes SSI-1
A gene of an organism of Campylobacter jejuni RM1221
A gene of an organism of Clostridium perfringens str. 13
A gene of an organism of Clostridium perfringens ATCC 13124
gene of Clostridium perfringens ATCC 13124
A gene of an organism of Staphylococcus aureus subsp. aureus MW2
gene of Staphylococcus aureus subsp. aureus MW2
A gene of an organism of Bacillus anthracis str. Ames
A gene of an organism of Shigella flexneri 2a str. 301
A gene of an organism of Shigella flexneri 2a str. 2457T
A gene of an organism of Streptococcus pyogenes MGAS315
A gene of an organism of Coccidioides posadasii
A gene of an organism of Escherichia coli CFT073
A gene of an organism of Brucella suis 1330
A gene of an organism of Streptococcus agalactiae A909
A gene of an organism of Streptococcus agalactiae 2603V/R
gene of Streptococcus agalactiae 2603V/R
A gene of an organism of Pseudomonas aeruginosa UCBPP-PA14
gene of Pseudomonas aeruginosa UCBPP-PA14
A gene of an organism of Pseudomonas aeruginosa PAO1
A gene of an organism of Salmonella enterica subsp. enterica serovar Typhi str. Ty2
gene of Salmonella enterica subsp. enterica serovar Typhi str. Ty2
A gene of an organism of Influenza A virus (A/Puerto Rico/8/1934(H1N1))
gene of Influenza A virus (A/Puerto Rico/8/1934(H1N1))
A gene of an organism of Streptococcus agalactiae NEM316
A gene of an organism of Clostridium tetani E88
A gene of an organism of Campylobacterales
A gene of an organism of Yersinia pestis CO92
A gene of an organism of Cryptococcus neoformans var. neoformans JEC21
gene of Cryptococcus neoformans var. neoformans JEC21
A gene of an organism of Salmonella enterica subsp. enterica serovar Typhi str. CT18
gene of Salmonella enterica subsp. enterica serovar Typhi str. CT18
A gene of an organism of Borrelia burgdorferi B31
A gene of an organism of Brucella melitensis bv. 1 str. 16M
gene of Brucella melitensis bv. 1 str. 16M
A gene of an organism of Enterococcus faecalis V583
A gene of an organism of Aspergillus nidulans FGSC A4
A gene of an organism of Coxiella burnetii RSA 493
A gene of an organism of Yersinia pestis biovar Microtus str. 91001
gene of Yersinia pestis biovar Microtus str. 91001
A gene of an organism of Candida albicans SC5314
A gene of an organism of Burkholderia mallei ATCC 23344
A gene of an organism of Vibrio cholerae O1 biovar El Tor str. N16961
gene of Vibrio cholerae O1 biovar El Tor str. N16961
A gene of an organism of Corynebacterium diphtheriae NCTC 13129
gene of Corynebacterium diphtheriae NCTC 13129
A gene of an organism of Bordetella bronchiseptica RB50
A gene of an organism of Bordetella pertussis Tohama I
A gene of an organism of Bacillus anthracis str. Sterne
A gene of an organism of Bacillus anthracis str. 'Ames Ancestor'
gene of Bacillus anthracis str. 'Ames Ancestor'
A gene of an organism of Orgyia pseudotsugata MNPV
A gene of an organism of Mycobacterium avium subsp. paratuberculosis K-10
gene of Mycobacterium avium subsp. paratuberculosis K-10
A gene of an organism of Listeria monocytogenes serotype 4b str. F2365
gene of Listeria monocytogenes serotype 4b str. F2365
A gene of an organism of Pneumonia virus of mice J3666
A gene of an organism of Bombyx mori NPV
A gene of an organism of Burkholderia pseudomallei K96243
gene of Burkholderia pseudomallei K96243
A gene of an organism of Chlamydia trachomatis D/UW-3/CX
A gene of an organism of Clostridium difficile 630
A gene of an organism of Legionella pneumophila subsp. pneumophila str. Philadelphia 1
gene of Legionella pneumophila subsp. pneumophila str. Philadelphia 1
A gene of an organism of Neisseria meningitidis FAM18
A gene of an organism of Pasteurella multocida subsp. multocida str. Pm70
gene of Pasteurella multocida subsp. multocida str. Pm70
A gene of an organism of Rickettsia prowazekii str. Madrid E
gene of Rickettsia prowazekii str. Madrid E
A gene of an organism of Staphylococcus aureus RF122
A gene of an organism of Yersinia pseudotuberculosis IP 32953
gene of Yersinia pseudotuberculosis IP 32953
A gene of an organism of Haemophilus influenzae 86-028NP
A gene of an organism of Staphylococcus aureus subsp. aureus MRSA252
gene of Staphylococcus aureus subsp. aureus MRSA252
A gene of an organism of Bartonella henselae str. Houston-1
gene of Bartonella henselae str. Houston-1
A gene of an organism of Cryptococcus neoformans var. neoformans B-3501A
gene of Cryptococcus neoformans var. neoformans B-3501A
A gene of an organism of Influenza A virus (A/Viet Nam/1203/2004(H5N1))
gene of Influenza A virus (A/Viet Nam/1203/2004(H5N1))
A gene of an organism of Candida glabrata CBS 138
A gene of an organism of Streptococcus pyogenes MGAS10394
gene of Streptococcus pyogenes MGAS10394
A gene of an organism of Clostridium perfringens SM101
A gene of an organism of Streptococcus pyogenes MGAS5005
A gene of an organism of Entamoeba histolytica HM-1:IMSS
A gene of an organism of Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150
gene of Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150
A gene of an organism of Legionella pneumophila str. Lens
gene of Legionella pneumophila str. Lens
A gene of an organism of Legionella pneumophila str. Paris
gene of Legionella pneumophila str. Paris
A gene of an organism of Shigella dysenteriae Sd197
A gene of an organism of Shigella boydii Sb227
A gene of an organism of Shigella sonnei Ss046
A gene of an organism of Streptococcus pyogenes serotype M1
gene of Streptococcus pyogenes serotype M1
A gene of an organism of Streptococcus pyogenes serotype M3
gene of Streptococcus pyogenes serotype M3
A gene of an organism of Escherichia coli str. K-12 substr. DH10B
gene of Escherichia coli str. K-12 substr. DH10B
A gene of an organism of Escherichia coli ETEC H10407
A gene of an organism of Streptococcus pyogenes MGAS6180
A gene of an organism of Burkholderia pseudomallei 1710b
A gene of an organism of Burkholderia pseudomallei 668
A gene of an organism of Burkholderia mallei SAVP1
A gene of an organism of Burkholderia mallei NCTC 10247
A gene of an organism of Salmonella enterica subsp. enterica serovar Choleraesuis str. SC-B67
gene of Salmonella enterica subsp. enterica serovar Choleraesuis str. SC-B67
A gene of an organism of Aspergillus fumigatus Af293
A gene of an organism of Escherichia coli E24377A
A gene of an organism of Escherichia coli HS
A gene of an organism of Mycobacterium tuberculosis F11
A gene of an organism of Streptococcus pyogenes serotype M12
gene of Streptococcus pyogenes serotype M12
A gene of an organism of Shigella boydii CDC 3083-94
A gene of an organism of SARS coronavirus ZJ0301
A gene of an organism of Vibrio cholerae O395
A gene of an organism of Leishmania major strain Friedlin
gene of Leishmania major strain Friedlin
A gene of an organism of Yersinia pestis Angola
A gene of an organism of Yersinia pseudotuberculosis IP 31758
gene of Yersinia pseudotuberculosis IP 31758
A gene of an organism of Plasmodium yoelii yoelii 17XNL
A gene of an organism of Cryptosporidium parvum Iowa II
A gene of an organism of Trypanosoma cruzi strain CL Brener
gene of Trypanosoma cruzi strain CL Brener
A gene of an organism of Campylobacter jejuni subsp. jejuni 81-176
gene of Campylobacter jejuni subsp. jejuni 81-176
A gene of an organism of Burkholderia pseudomallei 1106a
A gene of an organism of Brucella melitensis biovar Abortus 2308
gene of Brucella melitensis biovar Abortus 2308
A gene of an organism of Bartonella bacilliformis KC583
A gene of an organism of Yersinia pestis Antiqua
A gene of an organism of Campylobacter jejuni subsp. doylei 269.97
gene of Campylobacter jejuni subsp. doylei 269.97
A gene of an organism of Bordetella avium 197N
A gene of an organism of Escherichia coli 536
A gene of an organism of Escherichia coli UTI89
A gene of an organism of Streptococcus pyogenes MGAS9429
A gene of an organism of Streptococcus pyogenes MGAS10270
gene of Streptococcus pyogenes MGAS10270
A gene of an organism of Streptococcus pyogenes MGAS2096
A gene of an organism of Streptococcus pyogenes MGAS10750
gene of Streptococcus pyogenes MGAS10750
A gene of an organism of Streptococcus pneumoniae D39
A gene of an organism of Shigella flexneri 5 str. 8401
A gene of an organism of Neisseria meningitidis 053442
A gene of an organism of Francisella tularensis subsp. holarctica LVS
gene of Francisella tularensis subsp. holarctica LVS
A gene of an organism of Escherichia coli O26:H-
A gene of an organism of Yersinia pestis Nepal516
A gene of an organism of Aeromonas salmonicida subsp. salmonicida A449
gene of Aeromonas salmonicida subsp. salmonicida A449
A gene of an organism of Bartonella tribocorum CIP 105476
gene of Bartonella tribocorum CIP 105476
A gene of an organism of Escherichia coli O157:H7 str. Sakai
gene of Escherichia coli O157:H7 str. Sakai
A gene of an organism of Yersinia pestis Pestoides F
A gene of an organism of Yersinia enterocolitica subsp. enterocolitica 8081
gene of Yersinia enterocolitica subsp. enterocolitica 8081
A gene of an organism of Legionella pneumophila str. Corby
gene of Legionella pneumophila str. Corby
A gene of an organism of Escherichia coli APEC O1
A gene of an organism of Campylobacter jejuni subsp. jejuni 81116
gene of Campylobacter jejuni subsp. jejuni 81116
A gene of an organism of Escherichia coli SE11
A gene of an organism of Burkholderia mallei NCTC 10229
A gene of an organism of Yersinia pestis CA88-4125
A gene of an organism of Escherichia coli B str. REL606
A gene of an organism of Actinobacillus pleuropneumoniae serovar 5b str. L20
gene of Actinobacillus pleuropneumoniae serovar 5b str. L20
A gene of an organism of Plasmodium (Vinckeia)
A gene of an organism of Staphylococcus aureus subsp. aureus Mu3
gene of Staphylococcus aureus subsp. aureus Mu3
A gene of an organism of Mycobacterium tuberculosis H37Ra
gene of Mycobacterium tuberculosis H37Ra
A gene of an organism of Legionella pneumophila 2300/99 Alcoy
gene of Legionella pneumophila 2300/99 Alcoy
A gene of an organism of Staphylococcus aureus subsp. aureus str. Newman
gene of Staphylococcus aureus subsp. aureus str. Newman
A gene of an organism of Actinobacillus pleuropneumoniae serovar 3 str. JL03
gene of Actinobacillus pleuropneumoniae serovar 3 str. JL03
A gene of an organism of Escherichia coli SMS-3-5
A gene of an organism of Clostridium botulinum A str. ATCC 19397
gene of Clostridium botulinum A str. ATCC 19397
A gene of an organism of Clostridium botulinum A str. Hall
gene of Clostridium botulinum A str. Hall
A gene of an organism of Escherichia coli O157:H7 str. EC4115
gene of Escherichia coli O157:H7 str. EC4115
A gene of an organism of Borrelia burgdorferi 156a
A gene of an organism of Borrelia burgdorferi ZS7
A gene of an organism of Eurotiomycetidae
A gene of an organism of Francisella tularensis subsp. holarctica FTNF002-00
gene of Francisella tularensis subsp. holarctica FTNF002-00
A gene of an organism of Streptococcus pyogenes NZ131
A gene of an organism of Enterococcus faecalis OG1RF
A gene of an organism of Salmonella enterica subsp. enterica serovar Paratyphi C strain RKS4594
gene of Salmonella enterica subsp. enterica serovar Paratyphi C strain RKS4594
A gene of an organism of Paenibacillus sp. Y412MC10
A gene of an organism of Streptococcus pneumoniae Taiwan19F-14
gene of Streptococcus pneumoniae Taiwan19F-14
A gene of an organism of Streptococcus pneumoniae Hungary19A-6
gene of Streptococcus pneumoniae Hungary19A-6
A gene of an organism of Streptococcus pneumoniae 70585
A gene of an organism of Streptococcus pneumoniae JJA
A gene of an organism of Streptococcus pneumoniae P1031
A gene of an organism of Clostridium botulinum B1 str. Okra
gene of Clostridium botulinum B1 str. Okra
A gene of an organism of Clostridium botulinum A3 str. Loch Maree
gene of Clostridium botulinum A3 str. Loch Maree
A gene of an organism of Edwardsiella tarda EIB202
A gene of an organism of Yersinia pseudotuberculosis YPIII
gene of Yersinia pseudotuberculosis YPIII
A gene of an organism of Yersinia pseudotuberculosis PB1/+
gene of Yersinia pseudotuberculosis PB1/+
A gene of an organism of Clostridium botulinum E3 str. Alaska E43
gene of Clostridium botulinum E3 str. Alaska E43
A gene of an organism of Toxoplasma gondii ME49
A gene of an organism of Escherichia coli str. K-12 substr. MG1655
gene of Escherichia coli str. K-12 substr. MG1655
A gene of an organism of Streptococcus pneumoniae G54
A gene of an organism of Streptococcus pneumoniae CGSP14
A gene of an organism of Borrelia burgdorferi N40
A gene of an organism of Borrelia burgdorferi 297
A gene of an organism of Burkholderia pseudomallei MSHR346
gene of Burkholderia pseudomallei MSHR346
A gene of an organism of Actinobacillus pleuropneumoniae serovar 7 str. AP76
gene of Actinobacillus pleuropneumoniae serovar 7 str. AP76
A gene of an organism of Escherichia coli O157:H7 str. TW14359
gene of Escherichia coli O157:H7 str. TW14359
A gene of an organism of Salmonella enterica subsp. enterica serovar Enteritidis str. P125109
gene of Salmonella enterica subsp. enterica serovar Enteritidis str. P125109
A gene of an organism of Salmonella enterica subsp. enterica serovar Gallinarum str. 287/91
gene of Salmonella enterica subsp. enterica serovar Gallinarum str. 287/91
A gene of an organism of Filobasidiella/Cryptococcus neoformans species complex
gene of Filobasidiella/Cryptococcus neoformans species complex
A gene of an organism of Cryptococcus gattii
A gene of an organism of Streptococcus equi subsp. zooepidemicus MGCS10565
gene of Streptococcus equi subsp. zooepidemicus MGCS10565
A gene of an organism of Listeria monocytogenes HCC23
A gene of an organism of Pseudomonas aeruginosa LESB58
A gene of an organism of Alphabaculovirus
A gene of an organism of Saccharomyces cerevisiae S288c
A gene of an organism of Streptococcus pneumoniae ATCC 700669
gene of Streptococcus pneumoniae ATCC 700669
A gene of an organism of Helicobacter pylori G27
A gene of an organism of Listeria monocytogenes L99
A gene of an organism of Escherichia coli Vir68
A gene of an organism of Bacillus anthracis str. CDC 684
A gene of an organism of Listeria monocytogenes serotype 4b str. CLIP 80459
gene of Listeria monocytogenes serotype 4b str. CLIP 80459
A gene of an organism of Helicobacter pylori P12
A gene of an organism of Escherichia coli O26:H11 str. 11368
gene of Escherichia coli O26:H11 str. 11368
A gene of an organism of Escherichia coli O127:H6 str. E2348/69
gene of Escherichia coli O127:H6 str. E2348/69
A gene of an organism of Vibrio cholerae M66-2
A gene of an organism of Escherichia coli IAI1
A gene of an organism of Escherichia coli S88
A gene of an organism of Escherichia coli 55989
A gene of an organism of Escherichia coli UMN026
A gene of an organism of Escherichia coli IAI39
A gene of an organism of Escherichia coli O103:H2 str. 12009
gene of Escherichia coli O103:H2 str. 12009
A gene of an organism of Escherichia coli O111:H- str. 11128
gene of Escherichia coli O111:H- str. 11128
A gene of an organism of Escherichia coli ED1a
A gene of an organism of Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S
gene of Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S
A gene of an organism of Bacillus anthracis str. A0248
A gene of an organism of Helicobacter pylori B38
A gene of an organism of Escherichia coli BW2952
A gene of an organism of SARS coronavirus ExoN1
A gene of an organism of Listeria monocytogenes 08-5923
A gene of an organism of Listeria monocytogenes 08-5578
A gene of an organism of Neisseria meningitidis alpha14
A gene of an organism of Staphylococcus aureus subsp. aureus ED98
gene of Staphylococcus aureus subsp. aureus ED98
A gene of an organism of Alphacoronavirus 1
A gene of an organism of Severe acute respiratory syndrome-related coronavirus
gene of Severe acute respiratory syndrome-related coronavirus
A gene of an organism of Human metapneumovirus CAN97-83
A gene of an organism of Mileewa branchiuma
A gene of an organism of Staphylococcus aureus 04-02981
A gene of an organism of Mycoplasma gallisepticum str. R(low)
gene of Mycoplasma gallisepticum str. R(low)
A gene of an organism of Legionella pneumophila 130b
A gene of an organism of Salmonella enterica subsp. enterica serovar Typhimurium str. ST4/74
gene of Salmonella enterica subsp. enterica serovar Typhimurium str. ST4/74
A gene of Francisella tularensis subsp. holarctica LVS that has a tRNA gene type
tRNA gene of Francisella tularensis subsp. holarctica LVS
A gene of Francisella tularensis subsp. tularensis SCHU S4 that has a rRNA gene type
rRNA gene of Francisella tularensis subsp. tularensis SCHU S4
A gene of Francisella tularensis subsp. holarctica LVS that has a rRNA gene type
rRNA gene of Francisella tularensis subsp. holarctica LVS
A gene of Campylobacter jejuni that has a protein-coding gene type
protein-coding gene of Campylobacter jejuni
A gene of Escherichia coli that has a protein-coding gene type
A gene of Yersinia enterocolitica that has a protein-coding gene type
protein-coding gene of Yersinia enterocolitica
A gene of Yersinia pestis that has a protein-coding gene type
A gene of Enterococcus faecalis that has a protein-coding gene type
protein-coding gene of Enterococcus faecalis
A gene of Clostridium botulinum that has a protein-coding gene type
protein-coding gene of Clostridium botulinum
A gene of Clostridium perfringens that has a protein-coding gene type
protein-coding gene of Clostridium perfringens
A gene of Listeria monocytogenes that has a protein-coding gene type
protein-coding gene of Listeria monocytogenes
A gene of Plasmodium berghei ANKA that has a protein-coding gene type
protein-coding gene of Plasmodium berghei ANKA
A gene of Cowpox virus that has a protein-coding gene type
A gene of Vaccinia virus that has a protein-coding gene type
A gene of Sheeppox virus that has a protein-coding gene type
A gene of Rabbit fibroma virus that has a protein-coding gene type
protein-coding gene of Rabbit fibroma virus
A gene of Myxoma virus that has a protein-coding gene type
A gene of Human herpesvirus 1 that has a protein-coding gene type
protein-coding gene of Human herpesvirus 1
A gene of Human herpesvirus 2 that has a protein-coding gene type
protein-coding gene of Human herpesvirus 2
A gene of Bovine herpesvirus 1 that has a protein-coding gene type
protein-coding gene of Bovine herpesvirus 1
A gene of Felid herpesvirus 1 that has a protein-coding gene type
protein-coding gene of Felid herpesvirus 1
A gene of Human herpesvirus 3 that has a protein-coding gene type
protein-coding gene of Human herpesvirus 3
A gene of Suid herpesvirus 1 that has a protein-coding gene type
protein-coding gene of Suid herpesvirus 1
A gene of Gallid herpesvirus 1 that has a protein-coding gene type
protein-coding gene of Gallid herpesvirus 1
A gene of Gallid herpesvirus 2 that has a protein-coding gene type
protein-coding gene of Gallid herpesvirus 2
A gene of African swine fever virus that has a protein-coding gene type
protein-coding gene of African swine fever virus
A gene of Ross River virus that has a protein-coding gene type
A gene of Classical swine fever virus that has a protein-coding gene type
protein-coding gene of Classical swine fever virus
A gene of Feline infectious peritonitis virus that has a protein-coding gene type
protein-coding gene of Feline infectious peritonitis virus
A gene of Measles virus that has a protein-coding gene type
A gene of Bovine respiratory syncytial virus that has a protein-coding gene type
protein-coding gene of Bovine respiratory syncytial virus
A gene of Infectious hematopoietic necrosis virus that has a protein-coding gene type
protein-coding gene of Infectious hematopoietic necrosis virus
A gene of Rabies virus that has a protein-coding gene type
A gene of La Crosse virus that has a protein-coding gene type
A gene of Hantaan virus that has a protein-coding gene type
A gene of Feline immunodeficiency virus that has a protein-coding gene type
protein-coding gene of Feline immunodeficiency virus
A gene of Human immunodeficiency virus 1 that has a protein-coding gene type
protein-coding gene of Human immunodeficiency virus 1
A gene of Simian immunodeficiency virus that has a protein-coding gene type
protein-coding gene of Simian immunodeficiency virus
A gene of Ectromelia virus that has a protein-coding gene type
A gene of Rotavirus A that has a protein-coding gene type
A gene of Bovine herpesvirus 5 that has a protein-coding gene type
protein-coding gene of Bovine herpesvirus 5
A gene of Plasmodium falciparum 3D7 that has a protein-coding gene type
protein-coding gene of Plasmodium falciparum 3D7
A gene of Rotavirus C that has a protein-coding gene type
A gene of Autographa californica nucleopolyhedrovirus that has a protein-coding gene type
protein-coding gene of Autographa californica nucleopolyhedrovirus
A gene of Haemophilus influenzae Rd KW20 that has a protein-coding gene type
protein-coding gene of Haemophilus influenzae Rd KW20
A gene of Mycobacterium tuberculosis CDC1551 that has a protein-coding gene type
protein-coding gene of Mycobacterium tuberculosis CDC1551
A gene of Mycobacterium tuberculosis H37Rv that has a protein-coding gene type
protein-coding gene of Mycobacterium tuberculosis H37Rv
A gene of Porcine circovirus 2 that has a protein-coding gene type
protein-coding gene of Porcine circovirus 2
A gene of Helicobacter pylori 26695 that has a protein-coding gene type
protein-coding gene of Helicobacter pylori 26695
A gene of Helicobacter pylori J99 that has a protein-coding gene type
protein-coding gene of Helicobacter pylori J99
A gene of Staphylococcus aureus subsp. aureus NCTC 8325 that has a protein-coding gene type
protein-coding gene of Staphylococcus aureus subsp. aureus NCTC 8325
A gene of Influenza A virus (A/Goose/Guangdong/1/96(H5N1)) that has a protein-coding gene type
protein-coding gene of Influenza A virus (A/Goose/Guangdong/1/96(H5N1))
A gene of Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 that has a protein-coding gene type
protein-coding gene of Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
A gene of Chlamydophila pneumoniae CWL029 that has a protein-coding gene type
protein-coding gene of Chlamydophila pneumoniae CWL029
A gene of Neisseria meningitidis MC58 that has a protein-coding gene type
protein-coding gene of Neisseria meningitidis MC58
A gene of Neisseria meningitidis Z2491 that has a protein-coding gene type
protein-coding gene of Neisseria meningitidis Z2491
A gene of Chlamydophila pneumoniae J138 that has a protein-coding gene type
protein-coding gene of Chlamydophila pneumoniae J138
A gene of Escherichia coli O157:H7 str. EDL933 that has a protein-coding gene type
protein-coding gene of Escherichia coli O157:H7 str. EDL933
A gene of Staphylococcus aureus subsp. aureus Mu50 that has a protein-coding gene type
protein-coding gene of Staphylococcus aureus subsp. aureus Mu50
A gene of Staphylococcus aureus subsp. aureus N315 that has a protein-coding gene type
protein-coding gene of Staphylococcus aureus subsp. aureus N315
A gene of Streptococcus pyogenes M1 GAS that has a protein-coding gene type
protein-coding gene of Streptococcus pyogenes M1 GAS
A gene of Streptococcus pyogenes str. Manfredo that has a protein-coding gene type
protein-coding gene of Streptococcus pyogenes str. Manfredo
A gene of Listeria monocytogenes EGD-e that has a protein-coding gene type
protein-coding gene of Listeria monocytogenes EGD-e
A gene of Streptococcus pneumoniae TIGR4 that has a protein-coding gene type
protein-coding gene of Streptococcus pneumoniae TIGR4
A gene of Streptococcus pneumoniae R6 that has a protein-coding gene type
protein-coding gene of Streptococcus pneumoniae R6
A gene of Francisella tularensis subsp. tularensis SCHU S4 that has a protein-coding gene type
protein-coding gene of Francisella tularensis subsp. tularensis SCHU S4
A gene of Chlamydophila pneumoniae TW-183 that has a protein-coding gene type
protein-coding gene of Chlamydophila pneumoniae TW-183
A gene of Streptococcus pyogenes MGAS8232 that has a protein-coding gene type
protein-coding gene of Streptococcus pyogenes MGAS8232
A gene of Yersinia pestis KIM10+ that has a protein-coding gene type
protein-coding gene of Yersinia pestis KIM10+
A gene of Leptospira interrogans serovar Lai str. 56601 that has a protein-coding gene type
protein-coding gene of Leptospira interrogans serovar Lai str. 56601
A gene of Bacillus anthracis str. A2012 that has a protein-coding gene type
protein-coding gene of Bacillus anthracis str. A2012
A gene of Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 that has a protein-coding gene type
protein-coding gene of Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819
A gene of Streptococcus pyogenes SSI-1 that has a protein-coding gene type
protein-coding gene of Streptococcus pyogenes SSI-1
A gene of Campylobacter jejuni RM1221 that has a protein-coding gene type
protein-coding gene of Campylobacter jejuni RM1221
A gene of Clostridium perfringens str. 13 that has a protein-coding gene type
protein-coding gene of Clostridium perfringens str. 13
A gene of Clostridium perfringens ATCC 13124 that has a protein-coding gene type
protein-coding gene of Clostridium perfringens ATCC 13124
A gene of Staphylococcus aureus subsp. aureus MW2 that has a protein-coding gene type
protein-coding gene of Staphylococcus aureus subsp. aureus MW2
A gene of Bacillus anthracis str. Ames that has a protein-coding gene type
protein-coding gene of Bacillus anthracis str. Ames
A gene of Shigella flexneri 2a str. 301 that has a protein-coding gene type
protein-coding gene of Shigella flexneri 2a str. 301
A gene of Shigella flexneri 2a str. 2457T that has a protein-coding gene type
protein-coding gene of Shigella flexneri 2a str. 2457T
A gene of Streptococcus pyogenes MGAS315 that has a protein-coding gene type
protein-coding gene of Streptococcus pyogenes MGAS315
A gene of Escherichia coli CFT073 that has a protein-coding gene type
protein-coding gene of Escherichia coli CFT073
A gene of Brucella suis 1330 that has a protein-coding gene type
protein-coding gene of Brucella suis 1330
A gene of Streptococcus agalactiae A909 that has a protein-coding gene type
protein-coding gene of Streptococcus agalactiae A909
A gene of Streptococcus agalactiae 2603V/R that has a protein-coding gene type
protein-coding gene of Streptococcus agalactiae 2603V/R
A gene of Pseudomonas aeruginosa UCBPP-PA14 that has a protein-coding gene type
protein-coding gene of Pseudomonas aeruginosa UCBPP-PA14
A gene of Pseudomonas aeruginosa PAO1 that has a protein-coding gene type
protein-coding gene of Pseudomonas aeruginosa PAO1
A gene of Influenza A virus (A/Puerto Rico/8/1934(H1N1)) that has a protein-coding gene type
protein-coding gene of Influenza A virus (A/Puerto Rico/8/1934(H1N1))
A gene of Streptococcus agalactiae NEM316 that has a protein-coding gene type
protein-coding gene of Streptococcus agalactiae NEM316
A gene of Clostridium tetani E88 that has a protein-coding gene type
protein-coding gene of Clostridium tetani E88
A gene of Yersinia pestis CO92 that has a protein-coding gene type
protein-coding gene of Yersinia pestis CO92
A gene of Cryptococcus neoformans var. neoformans JEC21 that has a protein-coding gene type
protein-coding gene of Cryptococcus neoformans var. neoformans JEC21
A gene of Salmonella enterica subsp. enterica serovar Typhi str. CT18 that has a protein-coding gene type
protein-coding gene of Salmonella enterica subsp. enterica serovar Typhi str. CT18
A gene of Borrelia burgdorferi B31 that has a protein-coding gene type
protein-coding gene of Borrelia burgdorferi B31
A gene of Brucella melitensis bv. 1 str. 16M that has a protein-coding gene type
protein-coding gene of Brucella melitensis bv. 1 str. 16M
A gene of Enterococcus faecalis V583 that has a protein-coding gene type
protein-coding gene of Enterococcus faecalis V583
A gene of Aspergillus nidulans FGSC A4 that has a protein-coding gene type
protein-coding gene of Aspergillus nidulans FGSC A4
A gene of Coxiella burnetii RSA 493 that has a protein-coding gene type
protein-coding gene of Coxiella burnetii RSA 493
A gene of Yersinia pestis biovar Microtus str. 91001 that has a protein-coding gene type
protein-coding gene of Yersinia pestis biovar Microtus str. 91001
A gene of Candida albicans SC5314 that has a protein-coding gene type
protein-coding gene of Candida albicans SC5314
A gene of Burkholderia mallei ATCC 23344 that has a protein-coding gene type
protein-coding gene of Burkholderia mallei ATCC 23344
A gene of Vibrio cholerae O1 biovar El Tor str. N16961 that has a protein-coding gene type
protein-coding gene of Vibrio cholerae O1 biovar El Tor str. N16961
A gene of Corynebacterium diphtheriae NCTC 13129 that has a protein-coding gene type
protein-coding gene of Corynebacterium diphtheriae NCTC 13129
A gene of Bordetella bronchiseptica RB50 that has a protein-coding gene type
protein-coding gene of Bordetella bronchiseptica RB50
A gene of Bordetella pertussis Tohama I that has a protein-coding gene type
protein-coding gene of Bordetella pertussis Tohama I
A gene of Bacillus anthracis str. Sterne that has a protein-coding gene type
protein-coding gene of Bacillus anthracis str. Sterne
A gene of Bacillus anthracis str. 'Ames Ancestor' that has a protein-coding gene type
protein-coding gene of Bacillus anthracis str. 'Ames Ancestor'
A gene of Orgyia pseudotsugata MNPV that has a protein-coding gene type
protein-coding gene of Orgyia pseudotsugata MNPV
A gene of Mycobacterium avium subsp. paratuberculosis K-10 that has a protein-coding gene type
protein-coding gene of Mycobacterium avium subsp. paratuberculosis K-10
A gene of Listeria monocytogenes serotype 4b str. F2365 that has a protein-coding gene type
protein-coding gene of Listeria monocytogenes serotype 4b str. F2365
A gene of Bombyx mori NPV that has a protein-coding gene type
A gene of Burkholderia pseudomallei K96243 that has a protein-coding gene type
protein-coding gene of Burkholderia pseudomallei K96243
A gene of Chlamydia trachomatis D/UW-3/CX that has a protein-coding gene type
protein-coding gene of Chlamydia trachomatis D/UW-3/CX
A gene of Clostridium difficile 630 that has a protein-coding gene type
protein-coding gene of Clostridium difficile 630
A gene of Legionella pneumophila subsp. pneumophila str. Philadelphia 1 that has a protein-coding gene type
protein-coding gene of Legionella pneumophila subsp. pneumophila str. Philadelphia 1
A gene of Neisseria meningitidis FAM18 that has a protein-coding gene type
protein-coding gene of Neisseria meningitidis FAM18
A gene of Pasteurella multocida subsp. multocida str. Pm70 that has a protein-coding gene type
protein-coding gene of Pasteurella multocida subsp. multocida str. Pm70
A gene of Rickettsia prowazekii str. Madrid E that has a protein-coding gene type
protein-coding gene of Rickettsia prowazekii str. Madrid E
A gene of Staphylococcus aureus RF122 that has a protein-coding gene type
protein-coding gene of Staphylococcus aureus RF122
A gene of Yersinia pseudotuberculosis IP 32953 that has a protein-coding gene type
protein-coding gene of Yersinia pseudotuberculosis IP 32953
A gene of Haemophilus influenzae 86-028NP that has a protein-coding gene type
protein-coding gene of Haemophilus influenzae 86-028NP
A gene of Staphylococcus aureus subsp. aureus MRSA252 that has a protein-coding gene type
protein-coding gene of Staphylococcus aureus subsp. aureus MRSA252
A gene of Bartonella henselae str. Houston-1 that has a protein-coding gene type
protein-coding gene of Bartonella henselae str. Houston-1
A gene of Cryptococcus neoformans var. neoformans B-3501A that has a protein-coding gene type
protein-coding gene of Cryptococcus neoformans var. neoformans B-3501A
A gene of Candida glabrata CBS 138 that has a protein-coding gene type
protein-coding gene of Candida glabrata CBS 138
A gene of Streptococcus pyogenes MGAS10394 that has a protein-coding gene type
protein-coding gene of Streptococcus pyogenes MGAS10394
A gene of Clostridium perfringens SM101 that has a protein-coding gene type
protein-coding gene of Clostridium perfringens SM101
A gene of Streptococcus pyogenes MGAS5005 that has a protein-coding gene type
protein-coding gene of Streptococcus pyogenes MGAS5005
A gene of Entamoeba histolytica HM-1:IMSS that has a protein-coding gene type
protein-coding gene of Entamoeba histolytica HM-1:IMSS
A gene of Legionella pneumophila str. Lens that has a protein-coding gene type
protein-coding gene of Legionella pneumophila str. Lens
A gene of Legionella pneumophila str. Paris that has a protein-coding gene type
protein-coding gene of Legionella pneumophila str. Paris
A gene of Shigella dysenteriae Sd197 that has a protein-coding gene type
protein-coding gene of Shigella dysenteriae Sd197
A gene of Shigella boydii Sb227 that has a protein-coding gene type
protein-coding gene of Shigella boydii Sb227
A gene of Shigella sonnei Ss046 that has a protein-coding gene type
protein-coding gene of Shigella sonnei Ss046
A gene of Escherichia coli str. K-12 substr. DH10B that has a protein-coding gene type
protein-coding gene of Escherichia coli str. K-12 substr. DH10B
A gene of Escherichia coli ETEC H10407 that has a protein-coding gene type
protein-coding gene of Escherichia coli ETEC H10407
A gene of Streptococcus pyogenes MGAS6180 that has a protein-coding gene type
protein-coding gene of Streptococcus pyogenes MGAS6180
A gene of Burkholderia pseudomallei 1710b that has a protein-coding gene type
protein-coding gene of Burkholderia pseudomallei 1710b
A gene of Burkholderia pseudomallei 668 that has a protein-coding gene type
protein-coding gene of Burkholderia pseudomallei 668
A gene of Burkholderia mallei SAVP1 that has a protein-coding gene type
protein-coding gene of Burkholderia mallei SAVP1
A gene of Burkholderia mallei NCTC 10247 that has a protein-coding gene type
protein-coding gene of Burkholderia mallei NCTC 10247
A gene of Aspergillus fumigatus Af293 that has a protein-coding gene type
protein-coding gene of Aspergillus fumigatus Af293
A gene of Escherichia coli E24377A that has a protein-coding gene type
protein-coding gene of Escherichia coli E24377A
A gene of Escherichia coli HS that has a protein-coding gene type
protein-coding gene of Escherichia coli HS
A gene of Mycobacterium tuberculosis F11 that has a protein-coding gene type
protein-coding gene of Mycobacterium tuberculosis F11
A gene of Shigella boydii CDC 3083-94 that has a protein-coding gene type
protein-coding gene of Shigella boydii CDC 3083-94
A gene of Vibrio cholerae O395 that has a protein-coding gene type
protein-coding gene of Vibrio cholerae O395
A gene of Leishmania major strain Friedlin that has a protein-coding gene type
protein-coding gene of Leishmania major strain Friedlin
A gene of Yersinia pestis Angola that has a protein-coding gene type
protein-coding gene of Yersinia pestis Angola
A gene of Yersinia pseudotuberculosis IP 31758 that has a protein-coding gene type
protein-coding gene of Yersinia pseudotuberculosis IP 31758
A gene of Plasmodium yoelii yoelii 17XNL that has a protein-coding gene type
protein-coding gene of Plasmodium yoelii yoelii 17XNL
A gene of Cryptosporidium parvum Iowa II that has a protein-coding gene type
protein-coding gene of Cryptosporidium parvum Iowa II
A gene of Trypanosoma cruzi strain CL Brener that has a protein-coding gene type
protein-coding gene of Trypanosoma cruzi strain CL Brener
A gene of Campylobacter jejuni subsp. jejuni 81-176 that has a protein-coding gene type
protein-coding gene of Campylobacter jejuni subsp. jejuni 81-176
A gene of Burkholderia pseudomallei 1106a that has a protein-coding gene type
protein-coding gene of Burkholderia pseudomallei 1106a
A gene of Brucella melitensis biovar Abortus 2308 that has a protein-coding gene type
protein-coding gene of Brucella melitensis biovar Abortus 2308
A gene of Bartonella bacilliformis KC583 that has a protein-coding gene type
protein-coding gene of Bartonella bacilliformis KC583
A gene of Yersinia pestis Antiqua that has a protein-coding gene type
protein-coding gene of Yersinia pestis Antiqua
A gene of Campylobacter jejuni subsp. doylei 269.97 that has a protein-coding gene type
protein-coding gene of Campylobacter jejuni subsp. doylei 269.97
A gene of Bordetella avium 197N that has a protein-coding gene type
protein-coding gene of Bordetella avium 197N
A gene of Escherichia coli 536 that has a protein-coding gene type
protein-coding gene of Escherichia coli 536
A gene of Escherichia coli UTI89 that has a protein-coding gene type
protein-coding gene of Escherichia coli UTI89
A gene of Streptococcus pyogenes MGAS9429 that has a protein-coding gene type
protein-coding gene of Streptococcus pyogenes MGAS9429
A gene of Streptococcus pyogenes MGAS10270 that has a protein-coding gene type
protein-coding gene of Streptococcus pyogenes MGAS10270
A gene of Streptococcus pyogenes MGAS2096 that has a protein-coding gene type
protein-coding gene of Streptococcus pyogenes MGAS2096
A gene of Streptococcus pyogenes MGAS10750 that has a protein-coding gene type
protein-coding gene of Streptococcus pyogenes MGAS10750
A gene of Streptococcus pneumoniae D39 that has a protein-coding gene type
protein-coding gene of Streptococcus pneumoniae D39
A gene of Shigella flexneri 5 str. 8401 that has a protein-coding gene type
protein-coding gene of Shigella flexneri 5 str. 8401
A gene of Neisseria meningitidis 053442 that has a protein-coding gene type
protein-coding gene of Neisseria meningitidis 053442
A gene of Francisella tularensis subsp. holarctica LVS that has a protein-coding gene type
protein-coding gene of Francisella tularensis subsp. holarctica LVS
A gene of Escherichia coli O26:H- that has a protein-coding gene type
protein-coding gene of Escherichia coli O26:H-
A gene of Yersinia pestis Nepal516 that has a protein-coding gene type
protein-coding gene of Yersinia pestis Nepal516
A gene of Aeromonas salmonicida subsp. salmonicida A449 that has a protein-coding gene type
protein-coding gene of Aeromonas salmonicida subsp. salmonicida A449
A gene of Bartonella tribocorum CIP 105476 that has a protein-coding gene type
protein-coding gene of Bartonella tribocorum CIP 105476
A gene of Escherichia coli O157:H7 str. Sakai that has a protein-coding gene type
protein-coding gene of Escherichia coli O157:H7 str. Sakai
A gene of Yersinia pestis Pestoides F that has a protein-coding gene type
protein-coding gene of Yersinia pestis Pestoides F
A gene of Yersinia enterocolitica subsp. enterocolitica 8081 that has a protein-coding gene type
protein-coding gene of Yersinia enterocolitica subsp. enterocolitica 8081
A gene of Legionella pneumophila str. Corby that has a protein-coding gene type
protein-coding gene of Legionella pneumophila str. Corby
A gene of Escherichia coli APEC O1 that has a protein-coding gene type
protein-coding gene of Escherichia coli APEC O1
A gene of Campylobacter jejuni subsp. jejuni 81116 that has a protein-coding gene type
protein-coding gene of Campylobacter jejuni subsp. jejuni 81116
A gene of Escherichia coli SE11 that has a protein-coding gene type
protein-coding gene of Escherichia coli SE11
A gene of Burkholderia mallei NCTC 10229 that has a protein-coding gene type
protein-coding gene of Burkholderia mallei NCTC 10229
A gene of Yersinia pestis CA88-4125 that has a protein-coding gene type
protein-coding gene of Yersinia pestis CA88-4125
A gene of Escherichia coli B str. REL606 that has a protein-coding gene type
protein-coding gene of Escherichia coli B str. REL606
A gene of Actinobacillus pleuropneumoniae serovar 5b str. L20 that has a protein-coding gene type
protein-coding gene of Actinobacillus pleuropneumoniae serovar 5b str. L20
A gene of Staphylococcus aureus subsp. aureus Mu3 that has a protein-coding gene type
protein-coding gene of Staphylococcus aureus subsp. aureus Mu3
A gene of Mycobacterium tuberculosis H37Ra that has a protein-coding gene type
protein-coding gene of Mycobacterium tuberculosis H37Ra
A gene of Legionella pneumophila 2300/99 Alcoy that has a protein-coding gene type
protein-coding gene of Legionella pneumophila 2300/99 Alcoy
A gene of Staphylococcus aureus subsp. aureus str. Newman that has a protein-coding gene type
protein-coding gene of Staphylococcus aureus subsp. aureus str. Newman
A gene of Actinobacillus pleuropneumoniae serovar 3 str. JL03 that has a protein-coding gene type
protein-coding gene of Actinobacillus pleuropneumoniae serovar 3 str. JL03
A gene of Escherichia coli SMS-3-5 that has a protein-coding gene type
protein-coding gene of Escherichia coli SMS-3-5
A gene of Clostridium botulinum A str. ATCC 19397 that has a protein-coding gene type
protein-coding gene of Clostridium botulinum A str. ATCC 19397
A gene of Clostridium botulinum A str. Hall that has a protein-coding gene type
protein-coding gene of Clostridium botulinum A str. Hall
A gene of Escherichia coli O157:H7 str. EC4115 that has a protein-coding gene type
protein-coding gene of Escherichia coli O157:H7 str. EC4115
A gene of Borrelia burgdorferi 156a that has a protein-coding gene type
protein-coding gene of Borrelia burgdorferi 156a
A gene of Borrelia burgdorferi ZS7 that has a protein-coding gene type
protein-coding gene of Borrelia burgdorferi ZS7
A gene of Francisella tularensis subsp. holarctica FTNF002-00 that has a protein-coding gene type
protein-coding gene of Francisella tularensis subsp. holarctica FTNF002-00
A gene of Streptococcus pyogenes NZ131 that has a protein-coding gene type
protein-coding gene of Streptococcus pyogenes NZ131
A gene of Paenibacillus sp. Y412MC10 that has a protein-coding gene type
protein-coding gene of Paenibacillus sp. Y412MC10
A gene of Streptococcus pneumoniae Taiwan19F-14 that has a protein-coding gene type
protein-coding gene of Streptococcus pneumoniae Taiwan19F-14
A gene of Streptococcus pneumoniae Hungary19A-6 that has a protein-coding gene type
protein-coding gene of Streptococcus pneumoniae Hungary19A-6
A gene of Streptococcus pneumoniae 70585 that has a protein-coding gene type
protein-coding gene of Streptococcus pneumoniae 70585
A gene of Streptococcus pneumoniae JJA that has a protein-coding gene type
protein-coding gene of Streptococcus pneumoniae JJA
A gene of Streptococcus pneumoniae P1031 that has a protein-coding gene type
protein-coding gene of Streptococcus pneumoniae P1031
A gene of Clostridium botulinum B1 str. Okra that has a protein-coding gene type
protein-coding gene of Clostridium botulinum B1 str. Okra
A gene of Clostridium botulinum A3 str. Loch Maree that has a protein-coding gene type
protein-coding gene of Clostridium botulinum A3 str. Loch Maree
A gene of Edwardsiella tarda EIB202 that has a protein-coding gene type
protein-coding gene of Edwardsiella tarda EIB202
A gene of Yersinia pseudotuberculosis YPIII that has a protein-coding gene type
protein-coding gene of Yersinia pseudotuberculosis YPIII
A gene of Yersinia pseudotuberculosis PB1/+ that has a protein-coding gene type
protein-coding gene of Yersinia pseudotuberculosis PB1/+
A gene of Clostridium botulinum E3 str. Alaska E43 that has a protein-coding gene type
protein-coding gene of Clostridium botulinum E3 str. Alaska E43
A gene of Toxoplasma gondii ME49 that has a protein-coding gene type
protein-coding gene of Toxoplasma gondii ME49
A gene of Escherichia coli str. K-12 substr. MG1655 that has a protein-coding gene type
protein-coding gene of Escherichia coli str. K-12 substr. MG1655
A gene of Streptococcus pneumoniae G54 that has a protein-coding gene type
protein-coding gene of Streptococcus pneumoniae G54
A gene of Streptococcus pneumoniae CGSP14 that has a protein-coding gene type
protein-coding gene of Streptococcus pneumoniae CGSP14
A gene of Borrelia burgdorferi N40 that has a protein-coding gene type
protein-coding gene of Borrelia burgdorferi N40
A gene of Borrelia burgdorferi 297 that has a protein-coding gene type
protein-coding gene of Borrelia burgdorferi 297
A gene of Burkholderia pseudomallei MSHR346 that has a protein-coding gene type
protein-coding gene of Burkholderia pseudomallei MSHR346
A gene of Actinobacillus pleuropneumoniae serovar 7 str. AP76 that has a protein-coding gene type
protein-coding gene of Actinobacillus pleuropneumoniae serovar 7 str. AP76
A gene of Escherichia coli O157:H7 str. TW14359 that has a protein-coding gene type
protein-coding gene of Escherichia coli O157:H7 str. TW14359
A gene of Streptococcus equi subsp. zooepidemicus MGCS10565 that has a protein-coding gene type
protein-coding gene of Streptococcus equi subsp. zooepidemicus MGCS10565
A gene of Listeria monocytogenes HCC23 that has a protein-coding gene type
protein-coding gene of Listeria monocytogenes HCC23
A gene of Pseudomonas aeruginosa LESB58 that has a protein-coding gene type
protein-coding gene of Pseudomonas aeruginosa LESB58
A gene of Saccharomyces cerevisiae S288c that has a protein-coding gene type
protein-coding gene of Saccharomyces cerevisiae S288c
A gene of Streptococcus pneumoniae ATCC 700669 that has a protein-coding gene type
protein-coding gene of Streptococcus pneumoniae ATCC 700669
A gene of Helicobacter pylori G27 that has a protein-coding gene type
protein-coding gene of Helicobacter pylori G27
A gene of Escherichia coli Vir68 that has a protein-coding gene type
protein-coding gene of Escherichia coli Vir68
A gene of Bacillus anthracis str. CDC 684 that has a protein-coding gene type
protein-coding gene of Bacillus anthracis str. CDC 684
A gene of Listeria monocytogenes serotype 4b str. CLIP 80459 that has a protein-coding gene type
protein-coding gene of Listeria monocytogenes serotype 4b str. CLIP 80459
A gene of Helicobacter pylori P12 that has a protein-coding gene type
protein-coding gene of Helicobacter pylori P12
A gene of Escherichia coli O26:H11 str. 11368 that has a protein-coding gene type
protein-coding gene of Escherichia coli O26:H11 str. 11368
A gene of Escherichia coli O127:H6 str. E2348/69 that has a protein-coding gene type
protein-coding gene of Escherichia coli O127:H6 str. E2348/69
A gene of Vibrio cholerae M66-2 that has a protein-coding gene type
protein-coding gene of Vibrio cholerae M66-2
A gene of Escherichia coli IAI1 that has a protein-coding gene type
protein-coding gene of Escherichia coli IAI1
A gene of Escherichia coli S88 that has a protein-coding gene type
protein-coding gene of Escherichia coli S88
A gene of Escherichia coli 55989 that has a protein-coding gene type
protein-coding gene of Escherichia coli 55989
A gene of Escherichia coli UMN026 that has a protein-coding gene type
protein-coding gene of Escherichia coli UMN026
A gene of Escherichia coli IAI39 that has a protein-coding gene type
protein-coding gene of Escherichia coli IAI39
A gene of Escherichia coli O103:H2 str. 12009 that has a protein-coding gene type
protein-coding gene of Escherichia coli O103:H2 str. 12009
A gene of Escherichia coli O111:H- str. 11128 that has a protein-coding gene type
protein-coding gene of Escherichia coli O111:H- str. 11128
A gene of Escherichia coli ED1a that has a protein-coding gene type
protein-coding gene of Escherichia coli ED1a
A gene of Bacillus anthracis str. A0248 that has a protein-coding gene type
protein-coding gene of Bacillus anthracis str. A0248
A gene of Helicobacter pylori B38 that has a protein-coding gene type
protein-coding gene of Helicobacter pylori B38
A gene of Escherichia coli BW2952 that has a protein-coding gene type
protein-coding gene of Escherichia coli BW2952
A gene of Listeria monocytogenes 08-5923 that has a protein-coding gene type
protein-coding gene of Listeria monocytogenes 08-5923
A gene of Listeria monocytogenes 08-5578 that has a protein-coding gene type
protein-coding gene of Listeria monocytogenes 08-5578
A gene of Neisseria meningitidis alpha14 that has a protein-coding gene type
protein-coding gene of Neisseria meningitidis alpha14
A gene of Staphylococcus aureus subsp. aureus ED98 that has a protein-coding gene type
protein-coding gene of Staphylococcus aureus subsp. aureus ED98
A gene of Mycoplasma gallisepticum str. R(low) that has a protein-coding gene type
protein-coding gene of Mycoplasma gallisepticum str. R(low)
A gene of Feline infectious peritonitis virus that has a pseudo gene type
pseudo gene of Feline infectious peritonitis virus
A gene of Haemophilus influenzae Rd KW20 that has a pseudo gene type
pseudo gene of Haemophilus influenzae Rd KW20
A gene of Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 that has a pseudo gene type
pseudo gene of Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
A gene of Streptococcus pneumoniae TIGR4 that has a pseudo gene type
pseudo gene of Streptococcus pneumoniae TIGR4
A gene of Francisella tularensis subsp. tularensis SCHU S4 that has a pseudo gene type
pseudo gene of Francisella tularensis subsp. tularensis SCHU S4
A gene of Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 that has a pseudo gene type
pseudo gene of Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819
A gene of Brucella suis 1330 that has a pseudo gene type
A gene of Vibrio cholerae O1 biovar El Tor str. N16961 that has a pseudo gene type
pseudo gene of Vibrio cholerae O1 biovar El Tor str. N16961
A gene of Listeria monocytogenes serotype 4b str. F2365 that has a pseudo gene type
pseudo gene of Listeria monocytogenes serotype 4b str. F2365
A gene of Clostridium difficile 630 that has a pseudo gene type
pseudo gene of Clostridium difficile 630
A gene of Brucella melitensis biovar Abortus 2308 that has a pseudo gene type
pseudo gene of Brucella melitensis biovar Abortus 2308
A gene of Neisseria meningitidis 053442 that has a pseudo gene type
pseudo gene of Neisseria meningitidis 053442
A gene of Francisella tularensis subsp. holarctica LVS that has a pseudo gene type
pseudo gene of Francisella tularensis subsp. holarctica LVS
A gene of Aeromonas salmonicida subsp. salmonicida A449 that has a pseudo gene type
pseudo gene of Aeromonas salmonicida subsp. salmonicida A449
A gene of Escherichia coli IAI39 that has a pseudo gene type
A gene of Yersinia pestis CO92 that has a miscRNA gene type
A gene of Yersinia pestis biovar Microtus str. 91001 that has a miscRNA gene type
miscRNA gene of Yersinia pestis biovar Microtus str. 91001
A gene of Yersinia pestis Angola that has a miscRNA gene type
A gene of Yersinia pestis Antiqua that has a miscRNA gene type
A gene of Yersinia pestis Nepal516 that has a miscRNA gene type
miscRNA gene of Yersinia pestis Nepal516
A gene of Yersinia pestis Pestoides F that has a miscRNA gene type
miscRNA gene of Yersinia pestis Pestoides F
A gene of Francisella tularensis subsp. tularensis SCHU S4 that has a RNA gene type
RNA gene of Francisella tularensis subsp. tularensis SCHU S4
A gene of Yersinia pestis CO92 that has a RNA gene type
A gene of Yersinia pestis biovar Microtus str. 91001 that has a RNA gene type
RNA gene of Yersinia pestis biovar Microtus str. 91001
A gene of Yersinia pestis Angola that has a RNA gene type
A gene of Yersinia pestis Antiqua that has a RNA gene type
A gene of Francisella tularensis subsp. holarctica LVS that has a RNA gene type
RNA gene of Francisella tularensis subsp. holarctica LVS
A gene of Yersinia pestis Nepal516 that has a RNA gene type
A gene of Yersinia pestis Pestoides F that has a RNA gene type
A gene of Haemophilus influenzae Rd KW20 that has a other gene type
gene of Haemophilus influenzae Rd KW20 with other gene type
A gene of Brucella suis 1330 that has a other gene type
gene of Brucella suis 1330 with other gene type
A gene of Plasmodium yoelii yoelii 17XNL that has a other gene type
gene of Plasmodium yoelii yoelii 17XNL with other gene type
MUTATION: A mutation in the vif gene reduces viral replication and infectivity in nonpermissive cells [PMID:15989462].
MUTATION: T cell infections using vesicular stomatitis virus G (VSV-G) pseudotyped HIV-1 Vpr R77Q result in less (P = 0.01) T cell death than infections using wild-type Vpr, despite similar levels of viral replication. Wild-type Vpr-associated events, including procaspase-8 and -3 cleavage, loss of mitochondrial transmembrane potential (deltapsi(m)), and DNA fragmentation factor activation are attenuated by R77Q Vpr. There is also a higher frequency of R77Q Vpr mutations in patients with LTNP than in patients with progressive disease [PMID:12750404].
MUTATION: HIV-1 replication in vivo can be separated from its pathogenic activity, in that the HXB/LW virus replicated to high levels in SCID-hu Thy/Liv mice, with no significant thymocyte depletion. Restoration of the nef gene in the recombinant HXB/LW genome restored its pathogenic activity, with no significant effect on HIV-1 replication in the thymus. Implicating nef as a determinant of pathogenicity [PMID:11264380].
MUTATION: CelTOS mutant has reduced infectivity in rat liver and almost abolished its cell-passage ability [PMID:16468982].
MUTATION: pbs36 had arrested intracellular growth in liver HC-04 cells [PMID:19625622].
MUTATION: KAHRP mutant has reduced adherence to CD36 when tested under flow conditions that mimic those of postcapillary venules [PMID:9108483].
MUTATION: msp7 mutant is attenuated for invasion of erythrocytes compared to the wild type [PMID:18820076].
Merozoite Surface Protein 7 precursor, MSP7
MUTATION: TRAP mutant is attenuated for sporozoite infection of rat liver [PMID:9267031].
Thrombospondin-related anonymous protein, TRAP
MUTATION: leu2 mutant is attenuated in mice [PMID:11606528].
MUTATION: ade2 mutant is attenuated in mice [PMID:11606528].
phosphoribosylaminoimidazole carboxylase ADE2
MUTATION: mip1 mutant is attenuated in mice [PMID:11606528].
MUTATION: ura3 mutant is attenuated in mice [PMID:11606528].
MUTATION: mxiC mutant has a 10-fold decrease in efficiency in invading epithelial cells [PMID:19017268].
MUTATION: virF knockouts are non-invasive to host cells [PMID:20237205].
MUTATION: spa47 mutants form needle-less type III structure which is defective, and thus incapable of invasion of host cells [PMID:10921870].
MUTATION: spa15 mutant was attenuated in entry into epithelial cells compared to the wild-type [PMID:11952903].
MUTATION: transposon mutants of ipgA cannot invade epithelial cells and cannot induce keratoconjunctivitis in mice [PMID:8376337].
MUTATION: ipaD mutants are completely unable to invade cultured cells or lyse RBCs [PMID:15731041] .
MUTATION: ipgC mutant attenuated in infecting Caco-2 cells monolayer [PMID:11207551].
MUTATION: ipaC mutants cannot invade cultured cells or lyse red blood cells [PMID:18656530].
MUTATION: ipaB mutant is unable to infect HeLa cells [PMID:20086081].
MUTATION: spa33 mutants are unable to secrete effectors necessary to cell invasion [PMID:16246841].
MUTATION: virA mutants did not move within the host cytoplasm and failed to move into adjacent cells [PMID:17095701].
MUTATION: virG mutants are able to replicate in cells, but cell to cell spread is attenuated in monkey kidney epithelial cells [PMID:2644195].
MUTATION: transposon mutants of ipgB cannot invade epithelial cells and cannot induce keratoconjunctivitis in mice [PMID:8376337].
MUTATION: ipgD mutant is unable to dephosphorylate phosphatidylinositol 4,5-bisphosphate [PtdIns(4,5)P2] and induces shorter filapodia in host cells [PMID:12356723].
MUTATION: mxiG mutant was unable to enter HeLa cells and to provoke keratoconjunctivitis in guinea-pigs [PMID:8559065].
MUTATION: spa32 mutants are unable to invade HeLa cells and do not secrete type III effectors [PMID:11844752].
MUTATION: mxiI mutant is unable to invade HeLa cells [PMID:11169106].
MUTATION: mxiM mutants are phenotypically avirulent, and also unable to invade semiconfluent L2 cell monolayers [PMID:10085046].
MUTATION: mxiJ mutant was unable to invade HeLa cells, to induce the formation of plaques on confluent monolayers of HeLa cells, and to provoke keratoconjunctivitis in guinea pigs [PMID:1332940].
MUTATION: mxiD mutant is unable to invade HeLa cells or to provoke keratoconjunctivitis in guinea-pigs [PMID:8437520].
MUTATION: mxiE deletion mutants are unable to block apoptosis of host epithelial cells [PMID:17339354].
MUTATION: mxiK mutants are unable to invade HeLa cells [PMID:12864857].
MUTATION: virB mutants have an avirulent phenotype and do not invade host cells [PMID:8385666].
MUTATION: mxiA mutants were attenuated in invasion of HeLa cells [PMID:2037361].
MUTATION: icsB mutants are attenuated in guinea pig eyes [PMID:12753186].
MUTATION: virK mutants have attenuated ability for intracellular spreading in host cells [PMID:15664968].
MUTATION: mxiH mutants are unable to invade HeLa cells [PMID:11169106].
MUTATION: ipaA mutants are attenuated in invasion of HeLa cells [PMID:9184218].
MUTATION: ipaH9.8 deletion mutant caused more severe inflammatory responses with increased pro-inflammatory cytokine production levels than did wild-type Shigella, which resulted in a 30-fold decrease in bacterial colonization in murine lungs [PMID:15950937].
MUTATION: sopA mutant was able to infect HeLa cells, but was attenuated in its ability to spread to other cells compared to the wild type [PMID:9076742].
MUTATION: sepA mutant has attenuated virulence in ligated rabbit ileal loop model [PMID:7476198].
MUTATION: ipaH7.8 mutants had a lower rate of exit from the endocytic vacuoles into the cytoplasm in mouse macrophages than the wild-type strain [PMID:10816519].
MUTATION: cca mutant is attenuated in rats [PMID:14641575].
multifunctional tRNA nucleotidyl transferase/2'3'-cyclic phosphodiesterase/2'nucleotidase/phosphatase
MUTATION: modA mutant is attenuated in rats [PMID:14641575].
molybdate-binding periplasmic protein ModA
MUTATION: metE mutant is attenuated in rats [PMID:14641575].
5-methyltetrahydropteroyltriglutamate/homocysteine S-methyltransferase
MUTATION: algR mutant is attenuated in mice [PMID:12379685].
alginate biosynthesis regulatory protein AlgR
MUTATION: PA5441 mutant is attenuated in rats [PMID:14641575].
MUTATION: pilY1 mutant is attenuated in rats [PMID:14641575].
type 4 fimbrial biogenesis protein PilY1
MUTATION: pilD mutant is attenuated in rats [PMID:14641575].
MUTATION: PA5437 mutant is attenuated in rats [PMID:14641575].
MUTATION: PA0151 mutant is attenuated in rats [PMID:14641575].
MUTATION: mucC mutant is attenuated in rats [PMID:14641575].
positive regulator for alginate biosynthesis MucC
MUTATION: PA5312 mutant is attenuated in rats [PMID:14641575].
MUTATION: wbpX mutant is attenuated in rats [PMID:14641575].
MUTATION: When compared to PAO1 wild-type and the rpoS- mutant, the hfq- mutant decreased virulence in Galleria mellonella by a factor of 1 x 10(4) and 5 x 10(3), respectively. Likewise, when compared to wild-type, the PAO1hfq- mutant was significantly attenuated in virulence when administered intraperitoneally in mice [PMID:14521880].
MUTATION: pgm mutant is attenuated in rats [PMID:14641575].
MUTATION: pilI mutant is attenuated in rats [PMID:14641575].
MUTATION: purD mutant is attenuated in rats [PMID:14641575].
MUTATION: PA5327 mutant is attenuated in rats [PMID:14641575].
MUTATION: PA0073 mutant is attenuated in rats [PMID:14641575].
MUTATION: PA0041 mutant is attenuated in rats [PMID:14641575].
MUTATION: estA mutant is attenuated in rats [PMID:14641575].
MUTATION: rhlB mutant is attenuated in rats [PMID:14641575].
MUTATION: PA1157 mutant is attenuated in rats [PMID:14641575].
MUTATION: pgk mutant is attenuated in rats [PMID:14641575].
MUTATION: PA1009 mutant is attenuated in rats [PMID:14641575].
MUTATION: mucA mutant is attenuated in wounded alfalfa seedling infection model [PMID:12426404].
MUTATION: PA0082 mutant is attenuated in rats [PMID:12023080].
MUTATION: algC mutant is attenuated in neonatal mouse model of infection [PMID:8557368].
MUTATION: clpV1 mutant is attenuated in rats [PMID:14641575].
MUTATION: mdoG mutant is attenuated in rats [PMID:14641575].
MUTATION: purL mutant is attenuated in rats [PMID:14641575].
phosphoribosylformylglycinamidine synthase
MUTATION: PA4115 mutant is attenuated in rats [PMID:14641575].
MUTATION: narK2 mutant is attenuated in rats [PMID:14641575].
MUTATION: PA2972 mutant is attenuated in rats [PMID:14641575].
MUTATION: exoS mutant is attenuated in a silk worm oral infection model [PMID:20805335].
MUTATION: pepA mutant is attenuated in rats [PMID:14641575].
MUTATION: PA3826 mutant is attenuated in rats [PMID:14641575].
MUTATION: wzz (wzz1) mutant is attenuated in mouse pneumonia model of infection [PMID:18065548].
MUTATION: galU mutant is attenuated in corneal mouse model of infection [PMID:15213167].
UTP-glucose-1-phosphate uridylyltransferase
MUTATION: PA3498 mutant is attenuated in rats [PMID:14641575].
MUTATION: purH mutant is attenuated in rats [PMID:14641575].
bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase
MUTATION: ngrB mutant is attenuated in rats [PMID:14641575].
Na(+)-translocating NADH-quinone reductase subunit B
MUTATION: PA3756 mutant is attenuated in rats [PMID:14641575].
MUTATION: thrC mutant is attenuated in rats [PMID:14641575].
MUTATION: PA3001 mutant is attenuated in rats [PMID:14641575].
glyceraldehyde-3-phosphate dehydrogenase
MUTATION: phzM mutant is attenuated in mice [PMID:15213173].
MUTATION: PA4564 mutant is attenuated in rats [PMID:14641575].
MUTATION: algW mutant is attenuated in rats [PMID:14641575].
MUTATION: PA4491 mutant is attenuated in rats [PMID:14641575].
MUTATION: PA4489 mutant is attenuated in rats [PMID:14641575].
MUTATION: PA4488 mutant is attenuated in rats [PMID:14641575].
MUTATION: aprF mutant is attenuated in rats [PMID:14641575].
alkaline protease secretion outer membrane protein AprF
MUTATION: relA mutant is attenuated in D. melanogaster [PMID:15385461].
MUTATION: PA4692 mutant is attenuated in rats [PMID:14641575].
MUTATION: fur mutant is attenuated in mouse corneal scratch model [PMID:7642283].
MUTATION: lasR mutant is attenuated in neonatal mouse model of infection [PMID:8557368].
MUTATION: phzS mutant is attenuated in mice [PMID:15213173].
MUTATION: htpG mutant is attenuated in rats [PMID:12023080].
MUTATION: fliC mutant is attenuated in mice [PMID:9423837].
MUTATION: algU mutant is attenuated in rats [PMID:14641575].
MUTATION: PA0158 mutant is attenuated in rats [PMID:12023080].
resistance-nodulation-cell division (RND) efflux transporter
MUTATION: PA4887 mutant is attenuated in rats [PMID:14641575].
major facilitator superfamily (MFS) transporter
MUTATION: nuoD mutant is attenuated in rats [PMID:14641575].
bifunctional NADH:ubiquinone oxidoreductase subunit C/D
MUTATION: PA3286 mutant is attenuated in rats [PMID:14641575].
MUTATION: pyrF mutant is attenuated in rats [PMID:14641575].
MUTATION: PA2895 mutant is attenuated in rats [PMID:14641575].
MUTATION: PA3173 mutant is attenuated in rats [PMID:14641575].
MUTATION: pvdS mutant is attenuated in rabbit aortic endocarditis model [PMID:10720526].
extracytoplasmic-function sigma-70 factor
MUTATION: pld mutant is attenuated in guinea pigs [PMID:19506016].
MUTATION: mutations in CT135 were found responsible for different phenotypes of early clearance (less virulent) and late clearance (more virulent) in mouse urogenital tract [PMID:20547745].
MUTATION: IncA mutant showed decreased growth rate and infection in mice [PMID:18852248].
MUTATION: mprA mutant is attenuated in mice [PMID:11675502].
Mycobacterial persistence regulator MRPA (two component response transcriptional regulatory protein)
MUTATION: attenuated in mice [PMID:14569030].
Probable dipeptide-transport ATP-binding protein ABC transporter DppD
MUTATION: pks7 mutant is attenuated in mice [PMID:12855735].
MUTATION: pks10 mutant is attenuated in mice [PMID:12730158].
Possible segregation and condensation protein ScpB
Probable pantothenate kinase CoaA (pantothenic acid kinase)
Probable glutamate N-acetyltransferase ArgJ
MUTATION: prrA mutant is attenuated in murine macrophages [PMID:11953357].
Two component response transcriptional regulatory protein PrrA
MUTATION: cysH mutants are attenuated in mice [PMID:16553880].
Probable 3'-phosphoadenosine 5'-phosphosulfate reductase CysH (PAPS reductase, thioredoxin DEP.) (padops reductase) (3'-phosphoadenylylsulfate reductase) (PAPS sulfotransferase)
MUTATION: ompA mutant is impaired in its ability to grow in macrophages and in normal mice, although it was as virulent as the wild type in mice that lack T cells [PMID:12366842].
Probable oxygen-independent coproporphyrinogen III oxidase HemN (coproporphyrinogenase) (coprogen oxidase)
MUTATION: Rv1747 mutant is attenuated in mice [PMID:16040957].
Probable conserved transmembrane ATP-binding protein ABC transporter
Possible transferase (possibly glycosyltransferase)
MUTATION: Rv0986 mutant is attenuated in survival within macrophages [PMID:15340136].
Probable adhesion component transport ATP-binding protein ABC transporter
MUTATION: Rv3616c mutant is attenuated in mice [PMID:16030141].
ESX-1 secretion-associated protein A, EspA
MUTATION: pepD mutant has altered virulence in mouse model of infection [PMID:20061478].
Probable serine protease PepD (serine proteinase) (MTB32B)
Probable transcriptional regulatory protein
MUTATION: mgtC mutant is attenuated in human macrophages and mice [PMID:10760138].
Possible Mg2+ transport P-type ATPase C MgtC
MUTATION: panCD mutant is attenuated in mice [PMID:12219086].
Pantoate--beta-alanine ligase PanC (pantothenate synthetase) (pantoate activating enzyme)
Ferredoxin-dependent sulfite reductase SirA
MUTATION: Rv3676 mutant is attenuated in human macrophages and mice [PMID:15882420].
Transcriptional regulatory protein Crp (Crp/Fnr-family)
MUTATION: secA2 mutant is attenuated in mice [PMID:12675804].
Possible preprotein translocase ATPase SecA2
Probable aspartate 1-decarboxylase precursor PanD (aspartate alpha-decarboxylase)
MUTATION: katG mutant is attenuated in mice and guinea pigs [PMID:9534978].
Catalase-peroxidase-peroxynitritase T KatG
MUTATION: ahpC mutant has decreased survival in unstimulated macrophages compared to the wild type [PMID:12368447].
Alkyl hydroperoxide reductase C protein AhpC (alkyl hydroperoxidase C)
MUTATION: Rv3615c mutant is attenuated in mice and has growth defects in macrophages [PMID:16135231].
MUTATION: Rv3614c mutant is attenuated in mice and has growth defects in macrophages [PMID:16135231].
Probable conserved transmembrane protein
Probable DNA repair protein RecN (recombination protein N)
MUTATION: mbtB mutant is attenuated in macrophage like THP-1 cells [PMID:10655517].
Phenyloxazoline synthase MbtB (phenyloxazoline synthetase)
Probable heat shock protein transcriptional repressor HrcA
MUTATION: hspR is attenuated in mice [PMID:11385512].
Probable heat shock protein transcriptional repressor HspR (MerR family)
Probable short-chain type dehydrogenase/reductase
MUTATION: mce3A mutant is attenuated in mice [PMID:15804490].
MUTATION: plcABC triple mutants are attenuated in mice [PMID:12100560].
Membrane-associated phospholipase C 1 PlcA (MTP40 antigen)
Membrane-associated phospholipase C 2 PlcB
Probable zinc uptake regulation protein Zur
Probable serine acetyltransferase CysE (sat)
MUTATION: Rv0386 mutant is attenuated in mice [PMID:20039878].
Probable transcriptional regulatory protein (probably LuxR/UhpA-family)
Probable fatty-acid-AMP ligase FadD21 (fatty-acid-AMP synthetase) (fatty-acid-AMP synthase)
Probable conserved transmembrane transport protein MmpL10
Probable O-antigen/lipopolysaccharide transport ATP-binding protein ABC transporter RfbE
Integral membrane indolylacetylinositol arabinosyltransferase EmbA (arabinosylindolylacetylinositol synthase)
MUTATION: fbpA mutant is attenuated in mice [PMID:15557632].
Secreted antigen 85-a FbpA (mycolyl transferase 85A) (fibronectin-binding protein A) (antigen 85 complex A)
Possible arabinofuranosyltransferase AftB
Exported repetitive protein precursor PirG (cell surface protein) (EXP53)
MUTATION: mmpL8 mutant is attenuated in mice [PMID:12724526].
Conserved integral membrane transport protein MmpL8
ESX conserved component EccB1 ESX-1 type VII secretion system protein Possible membrane protein
MUTATION: Rv3865 mutant is attenuated in mice [PMID:16368961].
MUTATION: sodA mutant is attenuated in mice [PMID:11751190].
Transcriptional regulatory repressor protein (TetR-family) EthR
MUTATION: esxB (CFP-10) mutant is attenuated in mice [PMID:16030141].
10 kDa culture filtrate antigen EsxB (LHP) (CFP10)
ESX conserved component EccA1 ESX-1 type VII secretion system protein
MUTATION: Rv3866 mutant is attenuated in mice [PMID:16368961].
ESX-1 secretion-associated protein EspG1
MUTATION: Rv3871 mutant is attenuated in mice [PMID:14557536].
ESX conserved component EccCb1 ESX-1 type VII secretion system protein
MUTATION: Rv3870 mutant is attenuated in mice [PMID:14557536].
ESX conserved component EccCa1 ESX-1 type VII secretion system protein Possible transmembrane protein
ESX-1 secretion-associated protein EspI Conserved proline and alanine rich protein
MUTATION: Rv3877 (snm4) mutant is attenuated in mice [PMID:14557536].
ESX conserved component EccD1 ESX-1 type VII secretion system protein Probable transmembrane protein
ESX conserved component EccE1 ESX-1 type VII secretion system protein Possible membrane protein
MUTATION: esxA (ESAT-6) mutant is attenuated in mice [PMID:16030141].
6 kDa early secretory antigenic target EsxA (ESAT-6)
MUTATION: Rv3887c mutant is attenuated in mice [PMID:17353284].
ESX conserved component EccD2 ESX-2 type VII secretion system protein Probable transmembrane protein
MUTATION: Rv3881c (espB) mutant is attenuated in macrophages [PMID:17676952].
Secreted ESX-1 substrate protein B, EspB. Conserved alanine and glycine rich protein
MUTATION: mycP1 mutant is attenuated in chronic infection of mice [PMID:20227664].
Membrane-anchored mycosin MycP1 (serine protease) (subtilisin-like protease) (subtilase-like) (mycosin-1)
MUTATION: hbhA mutant is attenuated in attachment and invasion of pneumocytes [PMID:11449276].
Iron-regulated heparin binding hemagglutinin HbhA (adhesin)
MUTATION: pcaA mutant is attenuated in mice [PMID:10882107].
Mycolic acid synthase PcaA (cyclopropane synthase)
MUTATION: icl mutant is attenuated in activated macrophages [PMID:10963599].
Isocitrate lyase Icl (isocitrase) (isocitratase)
Possible osmoprotectant (glycine betaine/carnitine/choline/L-proline) transport ATP-binding protein ABC transporter ProV
Adenosylmethionine-8-amino-7-oxononanoate aminotransferase BioA
Probable 8-amino-7-oxononanoate synthase BioF1 (AONS) (8-amino-7-ketopelargonate synthase) (7-keto-8-amino-pelargonic acid synthetase) (7-KAP synthetase) (L-alanine--pimelyl CoA ligase)
MUTATION: sodC mutant is more susceptible to killing by activated murine macrophages than the wild type [PMID:11447176].
Periplasmic superoxide dismutase [Cu-Zn] SodC
Probable exodeoxyribonuclease III protein XthA (exonuclease III) (EXO III) (AP endonuclease VI)
Thiamine-phosphate pyrophosphorylase ThiE (TMP pyrophosphorylase) (TMP-PPASE) (thiamine-phosphate synthase)
MUTATION: pknG mutant is attenuated in mice [PMID:15186418].
Serine/threonine-protein kinase PknG (protein kinase G) (STPK G)
MUTATION: lspA mutant is attenuated in mice [PMID:18832305].
Probable lipoprotein signal peptidase LspA
MUTATION: pks5 mutant is attenuated in mice [PMID:12855735].
Possible nitrogen fixation related protein
Probable cation transporter P-type ATPase D CtpD
Probable succinate dehydrogenase [membrane anchor subunit] (succinic dehydrogenase)
Aminoglycosides/tetracycline-transport integral membrane protein
MUTATION: mmpL11 mutant is attenuated in mice [PMID:15908378].
Probable conserved transmembrane transport protein MmpL11
Probable conserved Mce associated transmembrane protein
Probable conserved Mce associated membrane protein
Possible Mce-family lipoprotein LprK (Mce-family lipoprotein Mce1E)
MUTATION: yrbE1B mutant is attenuated in mice [PMID:15804490].
Conserved integral membrane protein YrbE1B
MUTATION: fadD5 mutant is attenuated in mice [PMID:20214478].
Probable fatty-acid-CoA ligase FadD5 (fatty-acid-CoA synthetase) (fatty-acid-CoA synthase)
MUTATION: fadD33 mutant is attenuated in mice [PMID:12480891].
Probable acetyl-CoA acetyltransferase FadA4 (acetoacetyl-CoA thiolase)
Possible fatty-acid-CoA ligase FadD10 (fatty-acid-CoA synthetase) (fatty-acid-CoA synthase)
Probable fatty acyl CoA thioesterase type III FcoT
Probable ATP synthase a chain AtpB (protein 6)
MUTATION attenuated in mice [PMID:14569030].
Probable peptide synthetase Nrp (peptide synthase)
MUTATION: lysA mutant is markedly attenuated in SCID mice, and is strongly attenuated in mice when in combination with a secA2 mutation [PMID:21264335].
Diaminopimelate decarboxylase LysA (DAP decarboxylase)
Probable drugs-transport transmembrane ATP-binding protein ABC transporter
MUTATION: ino1 mutant is attenuated in resting macrophages and guinea pigs [PMID:14763976].
myo-inositol-1-phosphate synthase Ino1 (inositol 1-phosphate synthetase) (D-glucose 6-phosphate cycloaldolase) (glucose 6-phosphate cyclase) (glucocycloaldolase)
Probable sugar-transport ATP-binding protein ABC transporter SugC
Probable sugar-transport integral membrane protein ABC transporter SugB
Probable sugar-transport integral membrane protein ABC transporter SugA
Probable acetyl-/propionyl-CoA carboxylase (beta subunit) AccD1
MUTATION: Rv0485 mutant is attenuated in mice [PMID:19651861].
Possible transcriptional regulatory protein
MUTATION: senX3-regX3 deletion mutant is attenuated in mice [PMID:12777483].
Putative two component sensor histidine kinase SenX3
Two component sensory transduction protein RegX3 (transcriptional regulatory protein) (probably LuxR-family)
Transcriptional regulatory protein KstR (probably TetR-family)
Probable cell division protein FtsY (SRP receptor) (signal recognition particle receptor)
Probable aminomethyltransferase GcvT (glycine cleavage system T protein)
Possible CoA-transferase (alpha subunit)
Pyruvate dehydrogenase E1 component AceE (pyruvate decarboxylase) (pyruvate dehydrogenase) (pyruvic dehydrogenase)
MUTATION: proC mutant is attenuated in mice [PMID:11160012].
Probable pyrroline-5-carboxylate reductase ProC (P5CR) (P5C reductase)
Probable acetyl-CoA acetyltransferase FadA6 (acetoacetyl-CoA thiolase)
MUTATION: ilvB1 mutant is attenuated in mice [PMID:19542000].
Acetolactate synthase (large subunit) IlvB1 (acetohydroxy-acid synthase)
MUTATION: pks15 mutant is attenuated in mice [PMID:12730158].
Polyphosphate glucokinase PpgK (polyphosphate-glucose phosphotransferase)
Probable uracil-DNA glycosylase Ung (UDG)
MUTATION: fadD28 mutant is attenuated in mice [PMID:10573420].
Fatty-acid-AMP ligase FadD28 (fatty-acid-AMP synthetase) (fatty-acid-AMP synthase)
TRK system potassium uptake protein CeoC
MUTATION: mmpL7 mutant is attenuated in mice [PMID:10573420].
Conserved transmembrane transport protein MmpL7
MUTATION: hspX mutant is attenuated in murine macrophages and THP-1 cells [PMID:9689123].
Heat shock protein HspX (alpha-crystallin homolog) (14 kDa antigen) (HSP16.3)
MUTATION: sigD mutant is attenuated in human macrophages and mice [PMID:15659067].
Probable alternative RNA polymerase sigma-D factor SigD
Probable O-sialoglycoprotein endopeptidase Gcp (glycoprotease)
MUTATION: whiB3 mutant is attenuated in mice [PMID:11880648].
Transcriptional regulatory protein WhiB-like WhiB3 Contains [4FE-4S] cluster
MUTATION: fadD26 mutant is attenuated in mice [PMID:15958066].
Fatty-acid-AMP ligase FadD26 (fatty-acid-AMP synthetase) (fatty-acid-AMP synthase)
MUTATION: trpD mutant is attenuated in mice [PMID:11160012].
Probable anthranilate phosphoribosyltransferase TrpD
Probable short-chain type dehydrogenase/reductase Possible 17-beta-hydroxysteroid dehydrogenase
Possible transmembrane phospholipid biosynthesis bifunctional enzyme PlsC: putative L-3-phosphoserine phosphatase (O-phosphoserine phosphohydrolase) (PSP) (pspase) + 1-acyl-SN-glycerol-3-phosphate acyltransferase (1-AGP acyltransferase) (1-AGPAT) (lysophosphatidic acid acyltransferase) (LPAAT)
MUTATION: mce2A mutant is attenuated in mice [PMID:15804490].
Probable conserved transmembrane alanine and leucine rich protein
Probable phosphoserine phosphatase SerB2 (PSP) (O-phosphoserine phosphohydrolase) (pspase)
MUTATION: Long-term survival of the relA mutant during in vitro starvation or nutrient run out in normal media was significantly impaired compared to that in the wild type. In addition, the mutant was significantly less able to survive extended anaerobic incubation than the wild-type virulent organism [PMID:10940033].
Probable GTP pyrophosphokinase RelA (ATP:GTP 3'-pyrophosphotransferase) (PPGPP synthetase I) ((P)PPGPP synthetase) (GTP diphosphokinase)
Probable sugar-transport integral membrane protein ABC transporter
MUTATION: Rv2693c mutant is attenuated in mice [PMID:17353284].
Probable conserved integral membrane alanine and leucine rich protein
Daunorubicin-dim-transport integral membrane protein ABC transporter DrrB
Probable sugar-transport ATP-binding protein ABC transporter
Probable transcriptional regulatory protein (probably TetR-family)
Probable conserved integral membrane protein
(3R)-hydroxyacyl-ACP dehydratase subunit HadB
Possible triacylglycerol synthase (diacylglycerol acyltransferase)
Methoxy mycolic acid synthase 3 MmaA3 (methyl mycolic acid synthase 3) (MMA3) (hydroxy mycolic acid synthase)
Probable amidase AmiD (acylamidase) (acylase)
MUTATION: Rv3377c mutant is attenuated in survival inside of macrophages [PMID:15340136].
MUTATION: Rv3378c mutant is attenuated in survival within macrophages [PMID:15340136].
Possible ribonucleotide-transport ATP-binding protein ABC transporter Mkl
MUTATION: sigH mutant has diminished immunopathology and is nonlethal in mice [PMID:12060776].
Alternative RNA polymerase sigma-E factor (sigma-24) SigH (RPOE)
MUTATION: Rv2206 mutant is attenuated in mice [PMID:17353284].
MUTATION: pks1 mutant is attenuated in mice [PMID:12730158].
Daunorubicin-dim-transport ATP-binding protein ABC transporter DrrA
Probable endonuclease IV End (endodeoxyribonuclease IV) (apurinase)
MUTATION: leuD mutant is attenuated in mice [PMID:10768986].
Probable 3-isopropylmalate dehydratase (small subunit) LeuD (isopropylmalate isomerase) (alpha-IPM isomerase) (IPMI)
Probable lipid carrier protein or keto acyl-CoA thiolase Ltp3
MUTATION: Rv3527 mutant is attenuated for intramacrophage survival [PMID:15340136].
Conserved integral membrane protein YrbE4A Possible ABC transporter
Precorrin-6Y C(5,15)-methyltransferase (decarboxylating) CobL
MUTATION: pks12 mutant is attenuated in mice [PMID:12819062].
Possible Mce-family lipoprotein LprN (Mce-family lipoprotein Mce4E)
Probable 4-hydroxy-2-oxovalerate aldolase (HOA)
Probable D-alanine--D-alanine ligase DdlA (D-alanylalanine synthetase) (D-ala-D-ala ligase)
MUTATION: lipF mutant is attenuated in mice lungs [PMID:10564470].
Probable lipid transfer protein or keto acyl-CoA thiolase Ltp2
Conserved alanine and glycine and valine rich protein
MUTATION: drrC mutant is attenuated in mice [PMID:10564470].
Probable daunorubicin-dim-transport integral membrane protein ABC transporter DrrC
Probable prolyl-tRNA synthetase ProS (proline--tRNA ligase) (PRORS) (global RNA synthesis factor) (proline translase)
MUTATION: sigL mutant is attenuated in mice [PMID:16199577].
Probable alternative RNA polymerase sigma factor SigL
Probable metal cation-transporting P-type ATPase C CtpC
MUTATION: sigC mutant is attenuated in mice [PMID:15049808].
RNA polymerase sigma factor, ECF subfamily, SigC
MUTATION: sigF mutant is attenuated in mice [PMID:14977982].
Alternative RNA polymerase sigma factor SigF
Two component sensory transduction transcriptional regulatory protein MtrA
MUTATION: sigE mutant is unable to grow in unactivated human and murine macrophages and is more susceptible to killing by activated macrophages than the wild type [PMID:11489128].
Alternative RNA polymerase sigma factor SigE
MUTATION: phoP mutant is attenuated in mice [PMID:11454210].
Possible two component system response transcriptional positive regulator PhoP
Putative aminoglycoside phosphotransferase
Possible linoleoyl-CoA desaturase (delta(6)-desaturase)
MUTATION: devR mutant is attenuated in guinea pigs [PMID:14987770].
Two component transcriptional regulatory protein DevR (probably LuxR/UhpA-family)
Probable conserved integral membrane transport protein
Probable transcriptional regulatory protein (probably AsnC-family)
MUTATION: moeB1 mutant is attenuated in mice [PMID:17353284].
Probable molybdenum cofactor biosynthesis protein MoeB1 (MPT-synthase sulfurylase) (molybdopterin synthase sulphurylase)
MUTATION: mutant strains showed reduced colonization in piglets [PMID:8698465].
MUTATION: attenuated in monkeys [PMID:18395086].
cag island protein, cytotoxicity associated immunodominant antigen
MUTATION: mutant strain adhered less to AGS cells than wild-type strain [PMID:12018657].
MUTATION: deletion impaired adherence to host cells [PMID:16758245].
MUTATION: mutant strains showed reduced motility and colonization in piglets [PMID:8698465].
MUTATION: modified strain eliminated binding to LEB and gastric tissue [PMID:20123715].
MUTATION: knockout did not result in gastric ulcers in mice compared to wild type [PMID:20046046].
MUTATION: urease-negative strain showed reduced colonization in gnotobiotic piglets [PMID:8063376].
MUTATION: mutant showed attenuated virulence in lungs of mice [PMID:10736106].
MUTATION: a HP1206 mutant was attenuated for gastric colonization in a gerbil model [PMID:12668646]
MUTATION: a flgL mutant was attenuated for gastric colonization in a gerbil model [PMID:12668646]
MUTATION: a HP0350 mutant was attenuated for gastric colonization in a gerbil model [PMID:12668646]
MUTATION: a HP0758 mutant was attenuated for gastric colonization in a gerbil model [PMID:12668646]
MUTATION: a HP03292 mutant was attenuated for gastric colonization in a gerbil model [PMID:12668646]
MUTATION: a HP0797 mutant was attenuated for gastric colonization in a gerbil model [PMID:12668646]
MUTATION: a HP0169 mutant was attenuated for gastric colonization in a gerbil model [PMID:12668646]
MUTATION: a HP0254 mutant was attenuated for gastric colonization in a gerbil model [PMID:12668646]
MUTATION: a HP0017 mutant was attenuated for gastric colonization in a gerbil model [PMID:12668646]
MUTATION: a ureC mutant was attenuated for gastric colonization in a gerbil model [PMID:12668646]
MUTATION: a hemC mutant was attenuated for gastric colonization in a gerbil model [PMID:12668646]
MUTATION: a HP0055 mutant was attenuated for gastric colonization in a gerbil model [PMID:12668646]
MUTATION: a HP0289 mutant was attenuated for gastric colonization in a gerbil model [PMID:12668646]
MUTATION: a HP0360 mutant was attenuated for gastric colonization in a gerbil model [PMID:12668646]
MUTATION: a HP0366 mutant was attenuated for gastric colonization in a gerbil model [PMID:12668646]
spore coat polysaccharide biosynthesis protein C
MUTATION: mutated strain showed a reduction in adherence ability [PMID:12018657].
MUTATION: a HP0788 mutant was attenuated for gastric colonization in a gerbil model [PMID:12668646]
MUTATION: HP0859 knockout mutant exhibited a severe truncation of LPS, a decreased growth rate, and a higher susceptibility to novobiocin. Disruption of HP0859 also reduced the adhesive capacity of H. pylori to AGS cells [PMID:21256827].
MUTATION: a flgE mutant was attenuated for gastric colonization in a gerbil model [PMID:12668646]
MUTATION: a flgD mutant was attenuated for gastric colonization in a gerbil model [PMID:12668646]
flagellar basal body rod modification protein
MUTATION: a surE mutant was attenuated for gastric colonization in a gerbil model [PMID:12668646]
MUTATION: a HP0973 mutant was attenuated for gastric colonization in a gerbil model [PMID:12668646]
MUTATION: a HP1082 mutant was attenuated for gastric colonization in a gerbil model [PMID:12668646]
MUTATION: a HP1091 mutant was attenuated for gastric colonization in a gerbil model [PMID:12668646]
MUTATION: a HP1092 mutant was attenuated for gastric colonization in a gerbil model [PMID:12668646]
MUTATION: a flgC mutant was attenuated for gastric colonization in a gerbil model [PMID:12668646]
MUTATION: a HP1525 mutant was attenuated for gastric colonization in a gerbil model [PMID:12668646]
MUTATION: a HP1506 mutant was attenuated for gastric colonization in a gerbil model [PMID:12668646]
MUTATION: a HP1486 mutant was attenuated for gastric colonization in a gerbil model [PMID:12668646]
MUTATION: a HP1421 mutant was attenuated for gastric colonization in a gerbil model [PMID:12668646]
conjugative transfer regulon protein TrbB
MUTATION: a fliI mutant was attenuated for gastric colonization in a gerbil model [PMID:12668646]
MUTATION: a HP0601 mutant was attenuated for gastric colonization in a gerbil model [PMID:12668646]
MUTATION: a fliP mutant was attenuated for gastric colonization in a gerbil model [PMID:12668646]
MUTATION: a HP0067 mutant was attenuated for gastric colonization in a gerbil model [PMID:12668646]
MUTATION: a HP0071 mutant was attenuated for gastric colonization in a gerbil model [PMID:12668646]
MUTATION: a HP0393 mutant was attenuated for gastric colonization in a gerbil model [PMID:12668646]
MUTATION: a fliD mutant was attenuated for gastric colonization in a gerbil model [PMID:12668646]
MUTATION: a HP0486 mutant was attenuated for gastric colonization in a gerbil model [PMID:12668646]
MUTATION: a HP0288 mutant was attenuated for gastric colonization in a gerbil model [PMID:12668646]
MUTATION: a HP0245 mutant was attenuated for gastric colonization in a gerbil model [PMID:12668646]
MUTATION: a HP0073 mutant was attenuated for gastric colonization in a gerbil model [PMID:12668646]
MUTATION: a HP0232 mutant was attenuated for gastric colonization in a gerbil model [PMID:12668646]
MUTATION: a HP0302 mutant was attenuated for gastric colonization in a gerbil model [PMID:12668646]
dipeptide ABC transporter ATP-binding protein DppF
MUTATION: a flgH mutant was attenuated for gastric colonization in a gerbil model [PMID:12668646]
MUTATION: a HP0397 mutant was attenuated for gastric colonization in a gerbil model [PMID:12668646]
MUTATION: a HP0714 mutant was attenuated for gastric colonization in a gerbil model [PMID:12668646]
MUTATION: a fliF mutant was attenuated for gastric colonization in a gerbil model [PMID:12668646]
MUTATION: SPy_0019 (cdhA) mutant has severe cell division, growth defects and is attenuated in mice [PMID:20643653].
MUTATION: nga mutant is attenuated in mice [PMID:20470439].
MUTATION: sagA mutant is attenuated in mice [PMID:9529097].
MUTATION: lsp mutant is attenuated in a murine model of soft tissue infection [PMID:19398546].
MUTATION: dltA mutant was diminished in its ability to adhere to and invade cultured human pharyngeal epithelial cells [PMID:16166534].
D-alanine--poly(phosphoribitol) ligase subunit 1
MUTATION: scpA mutant is attenuated in mouse pneumonia model [PMID:9119483].
MUTATION: sic mutant was phagocytosed and killed by human polymorphonuclear leukocytes significantly better than the wild-type strain [PMID:12032337].
MUTATION: emm1 mutant had greatly reduced invasion of HeLa cells [PMID:10048029].
MUTATION: mga mutant is attenuated in a humanized mouse model for superficial skin infection [PMID:18588968].
M protein trans-acting positive regulator
MUTATION: Mice infected by M1, M3 and M49 speB mutants, through air pouch or intraperitoneal challenge, showed less mortality compared with that of the wild-type strains [PMID:18796357].
MUTATION: gidA mutant is highly attenuated in the murine ulcer model of soft tissue infection [PMID:18426891].
tRNA uridine 5-carboxymethylaminomethyl modification protein GidA
MUTATION: SPy_1633 (cvfA) mutant is attenuated in mice [PMID:20385762].
MUTATION: SPy_1718 (sse) mutant is attenuated in mice [PMID:19805529].
MUTATION: fba mutant showed diminished invasive capabilities to HEp-2 cells and low mortality in mice following skin infection [PMID:11679068].
MUTATION: metG mutant is attenuated in rats [PMID:11062540].
MUTATION: lipB mutant is attenuated in rats [PMID:11062540].
capsule polysaccharide modification protein
MUTATION: NMB0103 mutant was unable to colonize human nasopharyngeal tissue in an organ culture model [PMID:18936183].
MUTATION: rsmB mutant is attenuated in rats [PMID:11062540].
MUTATION: dprA mutant is attenuated in rats [PMID:11062540].
MUTATION: tufA mutant is attenuated in rats [PMID:11062540].
MUTATION: lpxA mutant is attenuated in mice [PMID:16988225].
MUTATION: aroG mutant is attenuated in rats [PMID:11062540].
phospho-2-dehydro-3-deoxyheptonate aldolase
MUTATION: NMB0313 mutant was unable to colonize human nasopharyngeal tissue in an organ culture model [PMID:18936183].
MUTATION: pilF mutant were unable to colonize human nasopharyngeal tissue in an organ culture model [PMID:18936183].
MUTATION: aroE mutant is attenuated in rats [PMID:11062540].
MUTATION: NadA mutation decreases epithelial adhesion of capsulate N. meningitidis and invasion by acapsulate N. meningitidis [PMID:19481311].
MUTATION: NMB0541 mutant was unable to colonize human nasopharyngeal tissue in an organ culture model [PMID:18936183].
MUTATION: galU mutant is attenuated in rats [PMID:11062540].
MUTATION: ampD mutant is attenuated in rats [PMID:11062540].
N-acetyl-anhydromuranmyl-L-alanine amidase
MUTATION: rnc mutant is attenuated in rats [PMID:11062540].
MUTATION: hfq mutant is attenuated in rats [PMID:19223479].
MUTATION: pgm mutant is attenuated in mice [PMID:16428785].
MUTATION: rfaD mutant is attenuated in mice [PMID:16988225].
MUTATION: metF mutant is attenuated in rats [PMID:11062540].
5,10-methylenetetrahydrofolate reductase
MUTATION: pilQ mutant were unable to colonize human nasopharyngeal tissue in an organ culture model [PMID:18936183].
MUTATION: NMB1012 mutant was unable to colonize human nasopharyngeal tissue in an organ culture model [PMID:18936183].
MUTATION: dedA mutant is attenuated in rats [PMID:11062540].
MUTATION: fhs mutant is attenuated in rats [PMID:11062540].
MUTATION: NMB1829 mutant was unable to colonize human nasopharyngeal tissue in an organ culture model [PMID:18936183].
MUTATION: aroB mutant is attenuated in rats [PMID:11062540].
MUTATION: grxC mutant is attenuated in rats [PMID:11062540].
MUTATION: tonB mutant is unable to replicate within human epithelial cells [PMID:11854233].
MUTATION: exbB mutant is attenuated in rats [PMID:11062540].
MUTATION: exbD mutant is attenuated in rats [PMID:11062540].
MUTATION: NMB1726 mutant was unable to colonize human nasopharyngeal tissue in an organ culture model [PMID:18936183].
MUTATION: gdhA mutant is attenuated in rats [PMID:11062540].
MUTATION: rfaK mutant is attenuated in rats [PMID:11062540].
alpha 1,2 N-acetylglucosamine transferase
MUTATION: aroC mutant is attenuated in rats [PMID:11062540].
MUTATION: hmbR mutant was attenuated in an infant rat model [PMID:7783623].
MUTATION: mpl-1 mutant is attenuated in rats [PMID:11062540].
UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl-meso-diaminopimelate ligase
MUTATION: aroD mutant is attenuated in rats [PMID:11062540].
MUTATION: MNB1638 (lptA) mutant had an approximately 10-fold decrease in N. meningitidis adhesion to four kinds of human endothelial and epithelial cell lines at an multiplicity of infection of 5,000 [PMID:18824535].
MUTATION: rfaF mutant is attenuated in rats [PMID:11062540].
MUTATION: ptsH mutant is attenuated in rats [PMID:11062540].
sugar transport PTS system phosphocarrier protein HPr
MUTATION: ptsI mutant is attenuated in rats [PMID:11062540].
phosphoenolpyruvate-protein phosphotransferase
MUTATION: dgkA mutant is attenuated in rats [PMID:11062540].
MUTATION: purL mutant is attenuated in rats [PMID:11062540].
MUTATION: NMB1966 mutant was less adhesive and invasive for human bronchial epithelial cells, had reduced survival in human blood and was attenuated in a systemic mouse model of infection [PMID:19050914].
MUTATION: ilvI mutant is attenuated in rats [PMID:11062540].
acetolactate synthase isozyme III large subunit
MUTATION: lgtA mutant is attenuated in rats [PMID:11062540].
lacto-N-neotetraose biosynthesis glycosyl transferase
MUTATION: a Cj0019c C. jejuni mutant was attenuated for colonization of the chick caeca [PMID:15066034]
MUTATION: a Cj0020c C. jejuni mutant was attenuated for colonization of the chick caeca [PMID:15066034]
MUTATION: fliA mutants showed reduced motility (25% that of the wild type) and did not colonize a chicken cecum [PMID:17761334]
MUTATION: a Cj0248 C. jejuni mutant was attenuated for colonization of the chick caeca [PMID:15066034]
MUTATION: a Cj0336c mutant C. jejuni was attenuated for colonization of the chicken caeca [PMID:15066034]
MUTATION: a Cj0337c C. jejuni mutant was attenuated for colonization of the chicken caeca [PMID:15066034]
MUTATION: a cj0415 mutant was impaired in establishing chicken colonization [PMID:18284594]
MUTATION: a Cj0454c C. jejuni mutant was attenuated for colonziation of the chick caeca [PMID:15066034]
MUTATION: a Cj0456c C. jejuni mutant was attenuated for colonization of the chick caeca [PMID:15066034]
MUTATION: a Cj0618 C. jejuni mutant was attenuated for the colonization of the chick caeca [PMID:15066034]
MUTATION: Cj0629 (capA) mutant had a significantly reduced capacity for association with and invasion of Caco-2 cells and failed to colonize and persist in chickens [PMID:17172331].
MUTATION: rpoN mutant cells lacked the spiral shape of C. jejuni and motility was reduced to 10% of the wild-type, mutants also showed significant colonization defects of a chicken cecum [PMID:17761334]
MUTATION: a Cj0688 C. jejuni mutant was attenuated for colonization of the chick caeca [PMID:15066034]
MUTATION: Invasion of HEp-2 cells by flaC null mutants was reduced to a level of 14% compared with wild type [PMID:15228533]
MUTATION: a Cj0903c C. jejuni mutant was attenuated for colonization of the chick caeca [PMID:15066034]
MUTATION: C. jejuni ciaB null mutants had a significant reduction in internalization [PMID:10361274]
MUTATION: a Cj0938c (aas) C. jejuni mutant was attenuated for colonization of the chick caeca [PMID:15066034]
2-acylglycerophosphoethanolamine acyltransferase
MUTATION: A Cj0977 mutant strain is fully motile but significantly reduced in the invasion of intestinal epithelial cells in vitro [PMID:18835274]
MUTATION: a Cj1019c (livJ) C. jejuni mutant was attenuated for colonization of the chick caeca [PMID:15066034]
branched-chain amino acid ABC transporter substrate-binding protein
MUTATION: a Cj1118c (cheY) C. jejuni mutant was attenuated for the colonization of chick caeca [PMID:15066034]
MUTATION: a Cj1120c C. jejuni mutant was attenuated for colonization of the chick caeca [PMID:15066034]
UDP-4-keto-6-deoxy-GlcNAc C4 aminotransferase
MUTATION: a Cj1129c C. jejuni mutant was attenuated for colonization of the chick caeca [PMID:15066034]
MUTATION: a Cj1179c C. jejuni mutant was attenuated for colonization of the chick caeca [PMID:15066034]
MUTATION: A DeltadccR (Delta Cj1223c) response regulator mutant exhibited significantly reduced colonization of immunocompetent limited flora (I-LF) mice [PMID:15554967]
MUTATION: hspR mutant was unable to form colonies at 44 degrees C [PMID:15758235]
MUTATION: a C. jejuni DnaJ mutant was unable to colonize newly hatched Leghorn chickens [PMID:9673247]
MUTATION: Cj1279c mutants had a significantly reduced adherence to chicken epithelial cells [PMID:19349427]
fibronectin domain-containing lipoprotein
MUTATION: Mutation of Cj1316c or pseA had been shown to result in loss of PseAm. C jejuni that produced flagella lacking PseAm failed to autoagglutinate. Mutants (81-176) defective in autoagglutination showed a modest reduction in adherence and invasion of INT407 cells [PMID:16573682]
pseudaminic acid biosynthesis PseA protein
MUTATION: colonization of chick ceca by a Δ(Cj1321-Cj1325/6) mutant was reduced [PMID:19307210]
MUTATION: A motile ΔCj1324 mutant with intact flagella was considerably less hydrophobic, less able to autoagglutinate and form biofilms, and less able to colonize chickens than the parent strain [PMID:19307210]
MUTATION: nonflagellated, nonmotile (flaA flaB Mot-) mutants of C. jejuni had a 30%-40% decrease in INT 407 cell internalization [PMID:8478066]
MUTATION: Cj1349c mutants had a significantly reduced ability to colonize chicken epithelial cells [PMID:19349427]
MUTATION: a mutation in the pldA gene impairs the ability of C. jejuni to colonize the cecum [PMID:11569726]
MUTATION: A Deltacj1461 mutant was sevenfold more adherent to but 50-fold less invasive of INT-407 human epithelial cells than the wild type [PMID:18689478]
MUTATION: a flgK mutant of C. jejuni expressing only the hook filament junction protein showed diminished motility and was completely attenuated for cecal colonization in chickens [PMID:17761334]
MUTATION: sdaA mutants completely failed to colonize 3-week-old chickens as assayed both by cloacal swabs taken over a 6-week period and by cecal colony counts postmortem [PMID:14688104]
MUTATION: reduced adherence to epithelial cells, attenuated in mice [PMID:9488379].
bifunctional adhesin/ABC transporter aspartate/glutamate-binding protein
MUTATION: fba mutant is attenuated in rats [PMID:11062540].
MUTATION: NMA0798 (phoP) mutant is avirulent in mice [PMID:14688113].
UTP--glucose-1-phosphate uridylyltransferase
MUTATION: rfaE mutant is attenuated in rats [PMID:11062540].
MUTATION: ilvD mutant is attenuated in rats [PMID:11062540].
MUTATION: mltB mutant is attenuated in rats [PMID:11062540].
MUTATION: VP35 mutant is avirulent in guinea pigs [PMID:20071589].
MUTATION: attenuated in mice [PMID:12117951].
MUTATION: A E2 mutant in Classical swine fever virus is attenuated in pigs [PMID:15837238].
MUTATION: mce-3 mutant is strongly attenuated in BALB/c mice [PMID:16388878].
MUTATION: hspR mutant is attenuated in mice [PMID:11385512].
ECF subfamily RNA polymerase sigma factor
MUTATION: a mce-2 mutant is a strongly attenuated in BALB/c mice [PMID:16388878].
MUTATION: ahpC mutant has decreased survival in unactivated macrophages compared to the wild type [PMID:12368447].
MUTATION: cysH mutant is attenuated in mice [PMID:16553880].
phosphoadenosine phosphosulfate reductase
MUTATION: mma4 mutant is attenuated in mice [PMID:10844652].
MUTATION: erp mutant is attenuated in mice [PMID:9784137].
MUTATION: MT3491.1 mutant is attenuated in survival within macrophages [PMID:15340136].
MUTATION: radA mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_1976 mutant is attenuated in mice [PMID:12207705].
pyruvate formate-lyase-activating enzyme
MUTATION: SP_2239 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_0049 mutant is attenuated in mice [PMID:12207705].
MUTATION: purH mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_0057 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_0063 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_2231 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_0071 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_0078 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_2210 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_0092 mutant is attenuated in mice [PMID:12207705].
ABC transporter substrate-binding protein
MUTATION: SP_0095 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_0100 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_0102 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_0110 mutant is attenuated in mice [PMID:12207705].
MUTATION: pspA mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_0121 mutant is attenuated in mice [PMID:12207705].
metallo-beta-lactamase superfamily protein
MUTATION: SP_0128 mutant is attenuated in mice [PMID:12207705].
ribosomal-protein-alanine acetyltransferase
MUTATION: SP_0136 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_0141 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_0145 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_0146 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_0150 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_0156 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_0157 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_0160 mutation is attenuated in mice [PMID:12207705].
MUTATION: SP_1964 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_0177 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_0198 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_0199 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_0240 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_0242 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_0246 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_0247 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_0251 mutant is attenuated in mice [PMID:12207705].
MUTATION: gldA mutant is attenuated in mice [PMID:12207705].
MUTATION: leuS mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_0625 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_0267 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_0268 mutant is attenuated in mice [PMID:12207705].
MUTATION: polC mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_0298 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_0306 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_0312 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_0314 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_0320 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_0332 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_0338 mutant is attenuated in mice [PMID:12207705].
ATP-dependent Clp protease ATP-binding subunit
MUTATION: dltB mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_2170 mutant is attenuated [PMID:12207705].
MUTATION: SP_2164 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_2162 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_2145 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_2143 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_2128 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_2108 mutant is attenuated in mice [PMID:12207705].
maltose/maltodextrin ABC transporter maltose/maltodextrin-binding protein
MUTATION: SP_2101 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_2098 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_2095 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_2076 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_1952 mutant is attenuated in mice [PMID:12207705]
MUTATION: cbpC mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_0385 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_0396 mutant is attenuated in mice [PMID:12207705].
PTS system mannitol-specific transporter subunit IIA
MUTATION: SP_0445 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_0454 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_0461 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_0468 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_0474 mutant is attenuated in mice [PMID:12207705].
PTS system cellobiose-specific transporter subunit IIC
MUTATION: SP_0478 mutant is attenuated in mice [PMID:12207705].
PTS system lactose-specific transporter subunit IIBC
MUTATION: SP_0479 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_0492 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_0494 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_0498 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_0510 mutant is attenuated in mice [PMID:12207705].
type I restriction-modification system, R subunit
MUTATION: blpA mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_0571 mutant is attenuated in mice [PMID:12207705].
cell filamentation protein Fic-like protein
MUTATION: SP_0586 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_0595 mutant is attenuated in mice [PMID:12207705].
MUTATION: vexp2 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_0614 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_0622 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_0633 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_0641 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_0645 mutation is attenuated in mice [PMID:12207705].
MUTATION: SP_0648 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_0655 mutant is attenuated in mice [PMID:12207705].
sodium/hydrogen exchanger family protein
MUTATION: SP_0661 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_0663 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_0664 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_0665 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_0686 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_0690 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_0719 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_0720 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_0736 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_0728 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_0729 mutant is attenuated in mice [PMID:12207705].
MUTATION: clpP mutant is attenuated in mice [PMID:15664911].
ATP-dependent Clp protease proteolytic subunit
MUTATION: SP_0766 mutant is attenuated in mice [PMID:12207705].
superoxide dismutase, manganese-dependent
MUTATION: SP_0767 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_0774 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_0785 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_0789 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_0797 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_0807 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_0829 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_0842 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_0856 mutant is attenuated in mice [PMID:12207705].
branched-chain amino acid aminotransferase
MUTATION: SP_0877 mutant is attenuated [PMID:12207705].
PTS system fructose specific transporter subunit IIABC
MUTATION: SP_0886 mutant is attenuated in mice [PMID:12207705].
type I restriction-modification system, M subunit
MUTATION: SP_0887 mutant is attenuated in mice [PMID:12207705].
type I restriction-modification system subunit S
MUTATION: SP_0892 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_0916 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_0927 is attenuated in mice [PMID:12207705].
MUTATION: SP_0939 mutant is attenuated in mice [PMID:12207705].
MUTATION: gid mutant is attenuated in mice [PMID:12207705].
MUTATION: AmiD mutant is attenuated in mice [PMID:12207705].
oligopeptide ABC transporter permease AmiD
MUTATION: SP_1898 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_1896 mutant is attenuated in mice [PMID:12207705].
MUTATION: AmiC mutant is attenuated in mice [PMID:12207705].
oligopeptide ABC transporter permease AmiC
MUTATION: AmiA mutant is attenuated in mice [PMID:12207705].
oligopeptide ABC transporter oligopeptide-binding protein AmiA
MUTATION: SP_1879 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_1869 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_1861 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_1859 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_1856 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_1855 mutation is attenuated in mice [PMID:12207705].
MUTATION: SP_1854 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_1847 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_1830 mutant is attenuated in mice [PMID:12207705].
phosphate transport system regulatory protein PhoU
MUTATION: SP_1817 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_1800 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_1816 mutant is attenuated in mice [PMID:12207705].
MUTATION: trpD mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_1793 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_1770 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_1780 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_1771 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_1779 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_1772 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_1760 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_1717 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_1715 mutant is attenuated in mice [PMID:12207705].
MUTATION: Sp_1706 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_1652 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_1654 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_1646 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_1645 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_1636 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_1633 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_1591 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_1580 mutant is attenuated in mice [PMID:12207705].
sugar ABC transporter ATP-binding protein
MUTATION: lytC mutant have reduced colonization of rat nasopharynx compared to wild type [PMID:10992472].
MUTATION: SP_0966 mutant is attenuated [PMID:12207705].
MUTATION: SP_1544 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_1538 mutant is attenuated in mice [PMID:12207705].
Cof family protein/peptidyl-prolyl cis-trans isomerase, cyclophilin type
MUTATION: SP_1529 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_1518 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_1483 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_1433 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_1434 mutant is attenuated in mice [PMID:12207705].
ABC transporter ATP-binding protein/permease
MUTATION: SP_1431 mutant is attenuated in mice [PMID:12207705].
type II DNA modification methyltransferase
MUTATION: SP_1400 mutant is attenuated in mice [PMID:12207705].
phosphate ABC transporter substrate-binding protein
MUTATION: SP_1339 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_1398 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_1396 mutant is attenuated in mice [PMID:12207705].
phosphate transporter ATP-binding protein
MUTATION: SP_1378 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_1382 mutant is attenuated in mice [PMID:12207705].
MUTATION: aroD mutant is attenuated in mice [PMID:12207705].
MUTATION: CoiA mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_0979 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_1001 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_1003 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_1018 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_1023 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_1029 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_1032 mutant is attenuated in mice [PMID:12207705].
iron-compound ABC transporter iron compound-binding protein
MUTATION: SP_1040 mutant is attenuated in mice [PMID:12207705].
resolvase family site-specific recombinase
MUTATION: Sp_1043 (phgA) mutant is attenuated in mice [PMID:15271918].
MUTATION: SP_1045 (phgC) mutant is attenuated in mice [PMID:15271918].
MUTATION: SP_1089 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_1111 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_1112 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_1115 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_1118 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_1121 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_1127 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_1143 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_1153 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_1154 mutant is attenuated in mice [PMID:12207705].
MUTATION: rnhB mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_1174 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_1175 mutant is attenuated in mice [PMID:12207705].
MUTATION: LacA mutant is attenuated in mice [PMID:12207705].
galactose-6-phosphate isomerase subunit LacA
MUTATION: RecN mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_1278 mutant is attenuated in mice [PMID:12207705].
bifunctional pyrimidine regulatory protein PyrR/uracil phosphoribosyltransferase
MUTATION: SP_1281 mutant is attenuated in mice [PMID:12207705].
MUTATION: gidB mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_1286 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_1292 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_1321 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_1328 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_1343 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_1344 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_1941 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_1970 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_1988 mutant is attenuated in mice [PMID:12207705].
MUTATION: cbpD mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_2236 mutant is attenuated in mice [PMID:12207705].
MUTATION: pneumolysin mutant is attenuated in mice [PMID:12207705].
MUTATION:SP_1956 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_2190 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_2176 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_2182 mutant is attenuated in mice [PMID:12207705].
MUTATION: fucK mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_2159 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_2146 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_2142 mutant is attenuated in mice [PMID:12207705].
MUTATION: PcpA mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_2131 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_2105 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_2086 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_2060 mutant is attenuated in mice [PMID:12207705].
MUTATION: CglB mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_1939 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_2002 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_2017 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_2022 mutant is attenuated in mice [PMID:12207705].
MUTATION: SP_2039 mutant is attenuated in mice [PMID:12207705].
MUTATION: glnP mutant is attenuated in mice [PMID:18174343].
MUTATION: pspA mutant is attenuated in mice [PMID:10603379].
MUTATION: psaA mutant is attenuated in mice [PMID:8945574].
manganese ABC transporter substrate-binding protein
MUTATION: mutX mutant is attenuated in mice [PMID:9826334].
MUTATION: zmpB mutant is attenuated in mice [PMID:12841855].
MUTATION: ccpA mutant is attenuated in mice [PMID:16321938].
MUTATION: pspC mutant had reduced ability to colonize the nasopharynx of mice [PMID:17261599].
MUTATION: lytA mutant is attenuated in mice [PMID:10603379].
MUTATION: ply mutant is attenuated in mice [PMID:10603379].
MUTATION: psaC mutant is attenuated in mice [PMID:11988523].
MUTATION: psaB mutant is attenuated in mice [PMID:11988523].
manganese ABC transporter ATP-binding protein
MUTATION: nanA mutant is attenuated in mice [PMID:9826334].
MUTATION: iga mutant is attenuated in mice [PMID:12841855].
MUTATION: codY mutant has lower bacterial loads during infection in mice compared to the wild type and have a diminished ability to adhere to nasopharangeal cells in vitro [PMID:18024519].
MUTATION: The srtA mutant colonized the nasopharynx of chinchillas at a significantly lower level than the wild type [PMID:16246506].
amino acid ABC transporter substrate-binding protein
MUTATION: spxB mutant has a loss in the ability to attach eukayrotic cells and is attenuated in rabbits [PMID:8820650].
MUTATION: clpP is attenuated in mice [PMID:15664911].
MUTATION: sodA mutant is attenuated in mice [PMID:10768978].
MUTATION: ciaR mutant is attenuated in mice [PMID:15292127].
MUTATION: lytB has reduced colonization of nasopharynx of rats compared to wild type [PMID:10992472].
MUTATION: potD mutant is attenuated in pulmonary and systemic models of infection in mice [PMID:16368990].
spermidine/putrescine ABC transporter substrate-binding protein
MUTATION: nox mutant is attenuated in mice [PMID:11158360].
MUTATION: pgdA mutant is attenuated in mice [PMID:12438406].
MUTATION: regR mutant is attenuated in mice [PMID:12704136].
MUTATION: luxS mutant has defective ability to persist in the nasopharyngeal tissues of mice [PMID:15102809].
MUTATION: glnA mutant had significantly reduced adhesion to Detroit 562 human pharyngeal epithelial cells [PMID:16787930].
MUTATION: cbpG has reduced colonization of nasopharynx of rats and reduced adherence to human epithelial cells [PMID:10992472].
MUTATION: cbpD has reduced colonization of nasopharynx of rats compared to the wild type [PMID:10992472].
MUTATION: A carAB mutant is attenuated in turkeys [PMID:8063392].
carbamoyl-phosphate synthase large subunit
MUTATION: OmpA− strains are unable to cause actin condensation needed for invasion of brain epithelial cells [PMID:10531228].
MUTATION: attenuated in mice [PMID:11553558].
membrane spanning protein in TonB-ExbB-ExbD transport complex
MUTATION: ibeB mutant is unable to invade BMEC and was attenuated in a newborn rat model [PMID:10225861].
copper/silver efflux system, outer membrane component
MUTATION: dppA mutant was attenuated 10- to 50-fold compared to the wild type for colonization of the bladders and kidneys of mice [PMID:17074858].
MUTATION: rfaL mutant is attenuated in rats [PMID:11430402].
DNA-binding transcriptional antiterminator
MUTATION: mutation of dsbA led to degradation of bundilin and an absence of localized adherence to host cells in EPEC [PMID:9224871].
periplasmic protein disulfide isomerase I
MUTATION: yijP mutant had reduced invasion of BMEC [PMID:10456927].
predicted LPS core phosphoethanolamine transferase
MUTATION: attenuated in humans and mice [PMID:18482721].
MUTATION: disruption mutant was less invasive in an in vitro HBMEC invasion assay than the wild-type E. coli K1 [PMID:10948126].
carbamoyl phosphate synthetase small subunit, glutamine amidotransferase
MUTATION: fliC deletion mutants had reduced adherence in bovine tissue compared to the wild type EHEC and EPEC strains [PMID:17693516].
flagellar filament structural protein (flagellin)
MUTATION: HI0364 mutant is attenuated in rats [PMID:12473436].
MUTATION: oapA mutant has significantly reduced binding to Chang epithelial cells than the wild type [PMID:10417187].
MUTATION: HI1018 mutant is attenuated in rats [PMID:12473436].
MUTATION: accA mutant is attenuated in rats [PMID:12473436].
acetyl-CoA carboxylase carboxyltransferase subunit alpha
MUTATION: nudC mutant is attenuated in rats [PMID:12473436].
MUTATION: HI1245 mutant is attenuated in rats [PMID:12473436]
MUTATION: fdx-2 mutant is attenuated in rats [PMID:12473436].
MUTATION: HI0700 mutant is attenuated in rats [PMID:12473436].
MUTATION: arcA mutant is attenuated in mice [PMID:12496162].
MUTATION: obgE mutant is attenuated in rats [PMID:12473436].
MUTATION: emrA mutant is attenuated in rats [PMID:12473436].
MUTATION: htkE mutant has attenuated virulence in interperitioneal infection of infant rats [PMID:7927766].
MUTATION: tehB mutant is attenuated in rats [PMID:20075041].
MUTATION: pmbA mutant is attenuated in rats [PMID:12473436].
MUTATION: ompA mutant had reduced adherence to human oropharyngeal cells in vitro, augmented clearance from the tympanum post-transbullar inoculation, and significantly reduced induction of OM post-intranasal inoculation in a chinchilla model compared to the wild type [PMID:7909539].
MUTATION: dsbA mutant is attenuated in mice [PMID:18212083].
MUTATION: HI0561 mutant is attenuated in rats [PMID:12473436].
MUTATION: HI1459 mutant is attenuated in rats [PMID:12473436].
MUTATION: parE mutant is attenuated in rats [PMID:12473436].
MUTATION: licA mutant is attenuated in rats [PMID:12473436].
MUTATION: HI1598 mutant is attenuated in rats [PMID:12473436].
MUTATION: HI1368 mutant is attenuated in rats [PMID:12473436].
MUTATION: HI0936 mutant is attenuated in rats [PMID:12473436].
MUTATION: lctP mutant is attenuated in rats [PMID:12473436].
MUTATION: alaS mutant is attenuated in rats [PMID:12473436].
MUTATION: ropE mutants are unable to survive intracellularly in macrophages [PMID:11796603].
MUTATION: dsbB mutant is attenuated in rats [PMID:12473436].
MUTATION: Compared to the wild-type strain, the ytfE (HI1677) mutant exhibited decreased survival when exposed to macrophages, a defect that was more pronounced after prior stimulation of macrophages with IFN-gamma or lipopolysaccharide. Complementation restored survival of the mutant to the level in the parental strain [PMID:19289513].
iron-sulfur cluster repair di-iron protein
MUTATION: ptsl mutant is attenuated in mice [PMID:12949188].
MUTATION: HI1732 mutant is attenuated in rats [PMID:12473436].
MUTATION: metB mutant is attenuated in rats [PMID:12473436].
MUTATION: afuB mutant is attenuated in rats [PMID:12473436].
ferric transport system permease-like protein
MUTATION: the introduction of functional NTHI ompP2 gene into the avirulent Hib ompP2 mutant restored the virulence of this strain to wild-type levels [PMID:7689543]. P2 mutants are unable to produce detectable bacteremia in infant rats [PMID:7689543].
MUTATION: dam mutants is attenuated in invasion of of human brain microvascular endothelial cells (HBMECs) and human respiratory epithelial cells (NCI-H292) [PMID:15228541].
MUTATION: deletions of one to four genes of kelch family both individually (single mutants) and in different combinations (double, triple and quadruple mutants). It was shown that deletion of any of the three genes EVMO18, EVM027 or EVM167 resulted in reduction of 50% lethal dose (LD50) by five and more orders in outbred white mice infected intraperitoneally. Deletion of mousepox kelch-gene EVM150 did not influence the virus virulence. Two or more kelch-genes deletion also resulted in high level of attenuation, which could evidently be due to the lack of three genes EVM167, EVM018 and/or EVM027 identified as virulence factors. [PMID:19807023]
MUTATION: Mutant influenza virus that lacks the transmembrane and cytoplasmic tail domains of M2 (M2 knockout [M2KO]) from Influenza A virus (A/Puerto Rico/8/34(H1N1)) is attenuated in both cell culture and mice [PMID:19321619].
MUTATION: Influenza virus with a deletion of the NS1 gene were highly attenuated in mice [PMID:9878611].
MUTATION: mutations eliminating expression of PB1F2 without afffecting the PB1 open reading frame were attenuating following intranasal inoculation [PMID:16873254].
MUTATION: NSs mutant virus is avirulent in mice [PMID:18225953].
shiga-like toxin 1 subunit B encoded within prophage CP-933V
MUTATION: map mutant is attenuated in calves [PMID:15528651].
MUTATION: Z3341 mutant is attenuated in calves [PMID:15528651].
shiga-like toxin 1 subunit A encoded within prophage CP-933V
MUTATION: Z0275 mutant is attenuated in calves [PMID:15528651].
MUTATION: sanA mutant is attenuated in calves [PMID:15528651].
MUTATION: mglA mutant is attenuated in calves [PMID:15731074].
galactose/methyl galaxtoside transporter ATP-binding protein
MUTATION: Z0390 mutant is attenuated in calves [PMID:15528651].
MUTATION: Z3496 mutant is attenuated in calves [PMID:15528651].
MUTATION: Z0469 mutant is attenuated in calves [PMID:15528651].
MUTATION: rdgC mutant is attenuated in calves [PMID:15528651].
MUTATION: Z0609 mutant is attenuated in calves [PMID:15528651].
MUTATION: evgS mutant is attenuated in calves [PMID:15731074].
hybrid sensory histidine kinase in two-component regulatory system with EvgA
MUTATION: yfhH mutant is attenuated in calves [PMID:15528651].
MUTATION: trxC mutant is attenuated in calves [PMID:15528651].
MUTATION: Z0990 mutant is attenuated in calves [PMID:15528651].
MUTATION: Z3950 mutant is attenuated in calves [PMID:15528651].
MUTATION: recD mutant is attenuated in calves [PMID:15731074].
MUTATION: kduI mutant is attenuated in calves [PMID:15528651].
MUTATION: z4200 (pkgA) mutant is attenuated in calves [PMID:15731074].
MUTATION: z3635 (yfdV) mutant is attenuated in calves [PMID:15731074].
MUTATION: z4282 mutant is attenuated in calves [PMID:15731074].
MUTATION: speA mutant is attenuated in calves [PMID:15731074].
MUTATION: Z4318 mutant is attenuated in calves [PMID:15528651].
MUTATION: pitB mutant is attenuated in calves [PMID:15731074].
MUTATION: Z1126 mutant is attenuated in calves [PMID:15528651].
MUTATION: z1129 mutant is attenuated in calves [PMID:15731074].
MUTATION: tdcE mutant is attenuated in calves [PMID:15731074].
MUTATION: Z1182 mutant is attenuated in calves [PMID:15528651].
MUTATION: Z1202 mutant is attenuated in calves [PMID:15528651].
MUTATION: trxB mutant is attenuated in calves [PMID:15731074].
MUTATION: Z1328 mutant is attenuated in calves [PMID:15528651].
MUTATION: ygeJ mutant is attenuated in calves [PMID:15528651].
MUTATION: ymcC mutant is attenuated in calves [PMID:15528651].
shiga-like toxin II B subunit encoded by bacteriophage BP-933W
MUTATION: ycdS mutant is attenuated in calves [PMID:15528651].
MUTATION: agaB mutant is attenuated in calves [PMID:15528651].
PTS system N-acetylgalactosamine-specific transporter subunit IIB
MUTATION: mdoC (ymdD) mutant is attenuated in calves [PMID:15731074].
MUTATION: ypjA mutant is attenuated in calves [PMID:15528651].
MUTATION: serA mutant is attenuated in calves [PMID:15731074].
MUTATION: z1829 mutant is attenuated in calves [PMID:15731074].
MUTATION: Z5946 mutant is attenuated in calves [PMID:15528651].
restriction modification enzyme S subunit
MUTATION: attenuated in mice and humans [PMID:18482721].
minor fimbrial subunit, D-mannose specific adhesin
MUTATION: fimE mutant is attenuated in calves [PMID:15731074].
MUTATION: yjhS mutant is attenuated in calves [PMID:15528651].
MUTATION: Z5886 mutant is attenuated in calves [PMID:15528651].
MUTATION: nrdD mutant is attenuated in calves [PMID:15731074].
anaerobic ribonucleoside triphosphate reductase
MUTATION: Z1930 mutant is attenuated in calves [PMID:15528651].
protease encoded within prophage CP-933X
MUTATION: yjeJ mutant is attenuated in calves [PMID:15528651].
MUTATION: yjcF mutant is attenuated in calves [PMID:15528651].
MUTATION: arp mutant is attenuated in calves [PMID:15528651].
MUTATION: Z5444 mutant is attenuated in calves [PMID:15528651].
MUTATION: ilvG mutant is attenuated in calves [PMID:15528651].
acetolactate synthase 2 catalytic subunit
MUTATION: narG mutant is attenuated in calves [PMID:15731074].
MUTATION: z2056 mutant is attenuated in calves [PMID:15731074].
MUTATION: z2142 mutant is attenuated in calves [PMID:15731074].
MUTATION: Z2144 mutant is attenuated in calves [PMID:15528651].
MUTATION: Z2149 mutant is attenuated in calves [PMID:15528651].
MUTATION: z2176 mutant is attenuated in calves [PMID:15731074].
MUTATION: ydeK mutant is attenuated in calves [PMID:15731074].
MUTATION: Z2203 mutation is attenuated in calves [PMID:15528651].
MUTATION: z2205 mutant is attenuated in calves [PMID:15731074].
MUTATION: z2207 mutant is attenuated in calves [PMID:15731074].
MUTATION: yddA mutant is attenuated in calves [PMID:15731074].
MUTATION: Z5214 mutant is attenuated in calves [PMID:15528651].
MUTATION: Z5212 mutant is attenuated in calves [PMID:15528651].
MUTATION: Z5131 mutant is attenuated in calves [PMID:15528651].
MUTATION: escC mutant is attenuated in calves [PMID:15528651].
MUTATION: z5121(st22) mutant is attenuated in calves [PMID:15731074].
MUTATION: escV mutant is attenuated in calves [PMID:15528651].
MUTATION: deletion of escN abolished pathogenicity in infant rabbits compared to wild-type EHEC [PMID:15731044].
MUTATION: sepQ mutant is attenuated in calves [PMID:15528651].
MUTATION: Z5114 (cesF) mutant is attenuated in calves [PMID:15528651].
MUTATION: tir deletion strains are unable to adhere to tissue in an in vitro organ culture [PMID:17474908].
MUTATION: attenuated in humans [PMID:8376594].
MUTATION: deletion of espA in STEC abolished ability to attach to HeLa cells and induce actin rearrangements [PMID:9786192].
MUTATION: espD deletion mutant of the enterohemorrhagic E. coli (EHEC) strain EDL933 had impaired attachment to HeLa cells [PMID:10456938].
MUTATION: deletion mutant attenuated in humans compared to wild-type EPEC [PMID:10816529].
MUTATION: espF EPEC mutant is deficient in its ability to disrupt electrical resistance across a polarized monolayer of intestinal epithelial cells, suggesting that EspF is an effector molecule required for disrupting intestinal epithelial barrier function [PMID:11238563].
MUTATION: yibD mutant is attenuated in calves [PMID:15528651].
MUTATION: rhsA mutant is attenuated in calves [PMID:15731074].
MUTATION: hrpA mutant is attenuated in calves [PMID:15528651].
MUTATION: Z2318 mutant is attenuated in calves [PMID:15528651].
MUTATION: dctA mutant is attenuated in calves [PMID:15528651].
MUTATION: Z2368 mutant is attenuated in calves [PMID:15528651].
MUTATION: chuA mutant unable to grow on iron-depleted medium containing heme [PMID:9157252].
MUTATION: yhiJ mutant is attenuated in calves [PMID:15528651].
MUTATION: Z3620 mutant is attenuated in calves [PMID:15528651].
MUTATION: ycjV mutant is attenuated in calves [PMID:15731074].
MUTATION: acnA mutant is attenuated in calves [PMID:15731074].
MUTATION: trpB mutant is attenuated in calves [PMID:15731074].
MUTATION: Z6010 mutant is attenuated in calves [PMID:15528651].
MUTATION: trkA mutant is attenuated in calves [PMID:15731074].
potassium transporter peripheral membrane protein
MUTATION: Z2702 mutant is attenuated in calves [PMID:15528651].
MUTATION: z2749 mutant is attenuated in calves [PMID:15731074].
MUTATION: z2751 mutant is attenuated in calves [PMID:15731074].
MUTATION: celF mutant is attenuated in calves [PMID:15528651].
MUTATION: cspC mutant is attenuated in calves [PMID:15528651].
MUTATION: Z2984 mutant is attenuated in calves [PMID:15528651].
serine acetlyltransferase of prophage CP-933T
MUTATION: sidA mutant is attenuated in calves [PMID:15528651].
DNA-binding transcriptional activator SdiA
MUTATION: Z3023 mutant is attenuated in calves [PMID:15528651].
MUTATION: Z3026 mutant is attenuated in calves [PMID:15528651].
MUTATION: z3062 mutant is attenuated in calves [PMID:15731074].
MUTATION: manB mutant is attenuated in calves [PMID:15528651].
MUTATION: manC mutant is attenuated in calves [PMID:15528651].
MUTATION: fcl mutant is attenuated in calves [PMID:15528651].
MUTATION: wbdP mutant is attenuated in calves [PMID:15528651].
MUTATION: per mutant is attenuated in calves [PMID:15528651].
MUTATION: pgl mutant exhibited a 15 to 30 fold defect in growth in vivo [PMID:19398547].
MUTATION: mutant attenuated in virulence after intravenous infection of mice [PMID:16177371].
MUTATION: deletion of bsh decreased resistance to bile, bacterial faecal carriage in guinea pigs and liver colonization in mice [PMID:12180927].
MUTATION: a gtcA mutant was attenuated in mice [PMID:11254558]
wall teichoic acid glycosylation protein GtcA
MUTATION: mogR deletion mutant has a 250-fold decrease in virulence in mice and has reduced capacity for cell-to-cell spread [PMID:15302931].
Other designations: hypothetical protein
MUTATION: mutant reduced invasion of Caco-2 cells compared to wild type [PMID:15155625].
two-component sensor histidine kinase CheA
MUTATION: mutant attenuated in mice, multiplication was significantly impaired [PMID:19246760].
MUTATION: lmo1269 (sipX) is attenuated in mice [PMID:14982622].
MUTATION: lmo1271 (sipZ) mutant is attenuated in mice [PMID:14982622].
MUTATION: mutant showed reduced capacity to persist in spleens and livers of infected mice [PMID:17021213].
MUTATION: mutant is strongly attenuated in mice, deletion led to abnormal cell division and loss of motility [PMID:12761132].
invasion associated secreted endopeptidase
MUTATION: attenuated in mice [PMID:7558297].
MUTATION: attenuated in mice [PMID:16790768].
bifunctional 3-deoxy-7-phosphoheptulonate synthase/chorismate mutase
MUTATION: mutant displayed 100 fold decrease in virulence in bacteria, also attenuated in mice [PMID:14762012].
MUTATION: VirR deletion severely decreased virulence in mice and invasion in cell culture [PMID:16102006].
MUTATION: attenuated in mice [PMID:17042784].
MUTATION: FbpA mutant attenuated in mice [PMID:15228540].
MUTATION: mutant attenuated in mice [PMID:15813732].
MUTATION: attenuated virulence in mice [PMID:8878044].
MUTATION: aut deletion mutants show reduced invasiveness and virulence in mice and guinea pigs [PMID:15009888].
MUTATION: pycA mutant unable to replicate in mammalian cells, attenuated in mice [PMID:20097852].
MUTATION: mutant displayed impaired adherence to various cell lines in vitro, and impaired virulence in mice [PMID:11849532].
MUTATION: mutant strain defective for growth, less virulent in animals by a factor of 300 [PMID:14564012].
MUTATION: deletion mutant showed reduced bacterial adherence to host cells, severely attenuated in mice [PMID:19818015].
peptide ABC transporter substrate-binding protein
MUTATION: mutant strain was avirulent in mice, eliminated in the liver, affected cell division [PMID:9987121].
MUTATION: deletion mutant attenuated in mice [PMID:16905535].
MUTATION: mutant was impaired in ability to survive in macrophage cells and was attenuated in mice [PMID:15758237].
MUTATION: attenuated in mice [PMID:1729245].
listeriolysin positive regulatory protein
MUTATION: mutant had attenuated virulence in mice, failed to grow in host tissues [PMID:1847723].
phosphatidylinositol-specific phospholipase c
MUTATION: mutant strain resulted in a 100-fold virulence defect in mice, prematurely killed host cell [PMID:11901168].
MUTATION: attenuated in mice [PMID:1311708].
MUTATION: mutant impaired in cell to cell spread, attenuated in maternal organs [PMID:15871123].
actin-assembly inducing protein precursor
MUTATION: deletion mutants showed reduced virulence in mice, escape from vacuole and cell-to-cell spread [PMID:7591052].
MUTATION: mutant strain impaired colonization in plant tissue [PMID:19357783].
MUTATION: mutant strain showed a restricted capacity to grow in bone-marrow-derived macrophages, and an attenuated virulence in mice [PMID:8885268].
MUTATION: mutant strains showed a significant reduction in adherence to several cell types, attenuated in mice [PMID:11251838].
MUTATION: mutant showed loss in virulence, reduced numbers of viable bacteria in both liver and spleen of mice [PMID:9862466].
MUTATION: mutant strain showed reduced bacterial escape from phagosomes of macrophages and attenuated virulence in mice [PMID:10760131].
MUTATION: attenuated in mice [PMID:16369036].
MUTATION: mutant avirulent in mice [PMID:16952950].
MUTATION: knockout inhibited growth in mMWB and reduced spread in epithelial cells [PMID:19181806].
MUTATION: impaired growth, avirulent in a murine model [PMID:11790730].
MUTATION: lmo0415 (pgdA) is attenuated in mice [PMID:17215377].
MUTATION: plc mutant is attenuated in mice [PMID:7746141].
MUTATION: virS mutant is attenuated in mice [PMID:8052128].
MUTATION: mutant attenuated in murine infection model [PMID:15664928].
branched-chain amino acid carrier protein
MUTATION: SpyM3_0013 mutant is attenuated in zebrafish [PMID:19223485].
MUTATION: F2 like fibronectin-binding protein mutant had attenuated attachment to to HEp-2 epithelial cells [PMID:14749329].
protein F2 like fibronectin-binding protein
MUTATION: slo mutant was attenuated in mice [PMID:11035749].
MUTATION: atmB mutant is attenuated in zebrafish [PMID:19223485].
MUTATION: SpyM3_0385 mutant is attenuated in zebrafish [PMID:19223485].
MUTATION: SpyM3_0386 mutant is attenuated in zebrafish [PMID:19223485].
MUTATION: salT mutant is attenuated in zebrafish [PMID:19223485].
MUTATION: emm3 mutant has reduced adherence to and internalization into HEp-2 cells compared to the wild type [PMID:14522456].
M protein trans-acting positive regulator, multi-gene activator
MUTATION: SpyM3_1795 mutant is attenuated in zebrafish [PMID:19223485].
MUTATION: hasA mutant is attenuated in zebrafish [PMID:19223485].
MUTATION: pbp1A mutant is attenuated in rats [PMID:10998175].
MUTATION: ciaR mutant had a significant decrease in intracellular survival within neutrophils, murine macrophages, and human BMEC [PMID:19114476].
MUTATION: lmb mutant has reduced invasion of human brain microvascular endothelial cells compared to the wildtype [PMID:17400016].
MUTATION: csrS mutant is attenuated in mice [PMID:15659687].
MUTATION: csrR mutant is attenuated in mice [PMID:15659687].
MUTATION: sodB mutant is extremely sensitive to killing by phagocytes compared to the wild-type, and causes only mild damage in infection of rabbit ileal loops [PMID:2404874].
MUTATION: dsbA mutants are less invasive to MK-2 cell monolayers compared to the wild-type [PMID:7761426].
MUTATION: aroA deletion mutants are attenuated in HeLa cells [PMID:8757833].
3-phosphoshikimate 1-carboxyvinyltransferase
MUTATION: phoP mutants were resolved more quickly than wild type in animal models, and are more susceptible to killing by PMNs [PMID:11207599].
DNA-binding transcriptional regulator PhoP
MUTATION: tonB mutant is able to invade epithelial cells but is incapable of cell to cell spread [PMID:11035742].
MUTATION: galU mutant is attenuated in cell to cell spread in He La cells [PMID:7528731].
MUTATION: yihE mutant is unable to cause keratoconjunctivitis in guinea pigs [PMID:15073317].
MUTATION: sitA mutant is attenuated in mice [PMID:19289511].
iron ABC transporter substrate-binding protein
MUTATION: vacJ mutants are incapable of intercellular spread of epithelial cells [PMID:8145644].
ABC transporter outer membrane lipoprotein
MUTATION: dksA mutants are able to invade cultured cell monlayers but are incapable of cell to cell spread [PMID:11500451].
RNA polymerase-binding transcription factor
MUTATION: surA mutant is able to infect epithelial cells but is incapable of cell to cell spread [PMID:20447864].
peptidyl-prolyl cis-trans isomerase SurA
MUTATION: aroD deletion led to attenuation in HeLa cells and monkeys [PMID:8356844].
MUTATION: mutant of the ompB locus (both the envZ and ompR genes) showed attenuated virulence in HeLa cells, and a weak response to a Serany test [PMID:2121709].
MUTATION: vacB mutants had attenuated invasion of MK2 cells compared to the wild-type strain [PMID:1400189].
MUTATION: guaAguaB mutants are attenuated in HeLa cells [PMID:8757833].
MUTATION: hfq deletion mutants are attenuated in guinea pig eye infection model (Sereny test) [PMID:20080057].
MUTATION: rfe mutant is attenuated in cell to cell spread in He La cells [PMID:7528731].
undecaprenyl-phosphate alpha-N-acetylglucosaminyl 1-phosphate transferase
MUTATION: sigA mutant is attenuated in rabbit ileal loop infection model [PMID:10768931].
MUTATION: iuc mutants are attenuated in chicken embryos and rabbit ileal loops [PMID:19130265].
MUTATION: mutants of the iuc locus and the aerobactin receptor, iutA were attenuated in chicken embryos [PMID:3028962].
MUTATION: envZ insertion mutant is able to invade cells but has decreased virulence due to the inability to survive intracellularly [PMID:2121709].
MUTATION: ompC mutants were attenuated in their ability to spread cell to cell and kill epithelial cells, and had a negative Sereny test [PMID:8359885].
MUTATION: miaA mutants had reduced ability to invade and spread in MK2 cell monolayers compared to the wildtype [PMID:9294434].
tRNA delta(2)-isopentenylpyrophosphate transferase
MUTATION: gbs1020 (CiaR) mutant had a significant decrease in intracellular survival within neutrophils, murine macrophages, and human BMEC [PMID:19114476].
MUTATION:cpsD mutant results in an unencapsulated strain which is avirulent in a neonatal rat model of sepsis compared to the wild type strain, and is also sensitive to killing by human phagocytes in vitro [PMID:8355611].
capsular polysaccharide chain length regulator/exporter
MUTATION: lmb mutant has reduced invasion of human brain microvascular endothelial cells compared to wildtype [PMID:17400016].
MUTATION: scpB mutant has significantly reduced invasion of HEp2 and A549 human cell lines [PMID:11953377].
MUTATION: gbs1402 (pefR) mutant is attenuated in mice [PMID:20421944].
MUTATION: gbs1477 (pilB) mutant had significantly reduced invasion of hBMECs [PMID:17041051].
MUTATION: Deletion of srr1(gbs1529) in NCTC 10/84 resulted in a significant decrease in adherence to and invasion of hBMECs [PMID:19392623].
MUTATION: iroA gene cluster mutants were unable to resist Lcn2 in mouse serum [PMID:17060628].
MUTATION: attenuated in chicks [PMID:18541653].
MUTATION: ycjM mutant is attenuated in chickens [PMID:15845486].
MUTATION: wecE mutant is attenuated in mice [PMID:12180926].
TDP-4-oxo-6-deoxy-D-glucose transaminase
MUTATION: focA deletion mutants were unable to bind to brain glycolipids [PMID:8098039].
MUTATION: fimF mutant is attenuated in mice [PMID:12180926].
MUTATION: fimD mutant is attenuated in mice [PMID:12180926].
MUTATION: fimC mutant is attenuated in mice [PMID:12180926].
MUTATION: fimI mutant is attenuated in mice [PMID:12180926].
MUTATION: fimB mutant is attenuated in mice [PMID:12180926].
MUTATION: manB mutant is attenuated in mice [PMID:12180926].
MUTATION: waaW mutant is attenuated in chickens [PMID:15845486].
UDP-galactose:(galactosyl) LPS alpha1,2-galactosyltransferase
MUTATION: hlyC is required for the acylation and therefore activation of the toxin hemolysin which has the ability to lyse several different types of cells [PMID:8793877].
MUTATION: attenuated in zebra fish [PMID:20019794].
MUTATION: attenuated to human neutrophils in vitro [PMID:7960108].
MUTATION: mutant papA in wild-type smooth strains do not mediate Gal-Gal adherence [PMID:1672263].
MUTATION: Sat elicits cytopathic activity that damages host tissue and may increase the ability of E. coli to propagate [PMID:12117966].
MUTATION: mutant attenuated in mice competition assay [PMID:11553558].
MUTATION: attenuated in mice [PMID:2973985].
MUTATION: kpsC mutant is attenuated in mice [PMID:12180926].
MUTATION: pyrD mutant is attenuated in mice [PMID:12180926].
MUTATION: phoU mutant is attenuated in mice [PMID:12180926].
MUTATION: colT is a collagenase that catalyzes the hydrolysis of collagen in host tissues [PMID:16701501].
MUTATION: cstA mutants have reduced epithelial cell invasion and reduced transepithelial migration of PMN compared to the wild type [PMID:15182677].
MUTATION: leuO mutant exhibited wild-type levels of epithelial invasion but highly reduced transepithelial migration of PMN [PMID:15182677].
MUTATION: tdcA mutant is less invasive of cultured epithelial cells and attenuated in mice [PMID:19812899].
MUTATION: invE mutants were unable to penetrate Henle-407 human intestinal cells and Madin-Darby canine kidney cells [PMID:1631083].
MUTATION: invH mutants are attenuated in calves [PMID:9529064].
MUTATION: invI mutants are defective for entry into cultured epithelial cells [PMID:7752894].
MUTATION: spaR mutant is severely impaired in entry to Henle-407 cells [PMID:8751894].
MUTATION: spaQ mutant is severely impaired in entry to Henle-407 cells [PMID:8751894].
MUTATION: spaO mutant is severely impaired in entry to Henle-407 cells [PMID:8751894].
MUTATION: invJ mutants are defective for entry into cultured epithelial cells [PMID:7752894].
MUTATION: spaP mutant is severely impaired in entry to Henle-407 cells [PMID:8751894].
MUTATION: spaS mutant was 30-fold reduced for invasion into HEp-2 cells when compared with the wild-type strain [PMID:10692170].
MUTATION: A SipC nucleation-deficient mutant, which maintained its effector translocation activity, had significantly reduced ability to induce actin cytoskeleton rearrangements, resulting in lower bacterial invasion into HeLa cells [PMID:15720547].
MUTATION: orgA mutants are attenuated in their ability to invade HEp-2 cells [PMID:10816487].
MUTATION: prgK mutants are attenuated in their ability to invade HEp-2 cells [PMID:10816487].
MUTATION: prgJ mutants are attenuated in their ability to invade HEp-2 cells [PMID:10816487].
MUTATION: waaP mutant is avirulent in mice [PMID:10899846].
MUTATION: fliC mutants were attenuated in orally inoculated chicks [PMID:11731137].
MUTATION: spiC mutant cannot survive within macrophages and is attenuated in mice [PMID:10406797].
MUTATION: sseC mutant is attenuated in mice [PMID:11159962].
MUTATION: sseD mutant is attenuated in mice [PMID:11159962].
MUTATION: ssaM mutant is attenuated in mice [PMID:15491354].
MUTATION: ssaV and aroC double mutants are attenuated in humans [PMID:19745519].
MUTATION: pcgL mutant is attenuated in pigs [PMID:17526851].
MUTATION: sigD mutant is less invasive than the wild type in both HEp-2 and CHO cell lines [PMID:9537377].
MUTATION: sigE mutant is less invasive than the wild type in both HEp-2 and CHO cell lines [PMID:9537377].
UTP--glucose-1-phosphate uridylyltransferase subunit GalU
lipid A biosynthesis (KDO)2-(lauroyl)-lipid IVA acyltransferase
MUTATION: rfc mutant is attenuated in invasion of T84 cell monolayer and adhesion to epithelial cells [PMID:11854195].
UDP-GlcNAc:undecaprenylphosphate GlcNAc-1-phosphate transferase
MUTATION: clpX deletion mutant is attenuated in mice [PMID:20375606].
ATP-dependent protease ATP-binding subunit ClpX
MUTATION: A quadruple-knockout strain (Delta sod15 Delta sodA1 Delta sodC Delta sodA2) was attenuated more than 40-fold upon intranasal challenge of mice compared to the wild type [PMID:18955476].
MUTATION: codY mutant is attenuated in mice [PMID:19651859].
MUTATION: sigB mutant is less virulent in mice than the parent strain [PMID:10960085].
MUTATION: An lpd mutant is highly attenuated in chickens [PMID:18342996].
dihydrolipoamide dehydrogenase (E3) component of pyruvate dehydrogenase complex
MUTATION: MGA_0674 mutant is attenuated in chickens [PMID:20515935].
MUTATION: MGA_1107 mutant is attenuated in chickens [PMID:20123709].
MUTATION: attenuated in murine model [PMID:9383163].
oligopeptide transport ATP-binding protein
oligopeptide transport system ATP-binding protein OppD homologue
phosphoribosylformylglycinamidine synthase II
MUTATION: SA1062 (stp1) mutant is attenuated in mice [PMID:20552019].
MUTATION: stk1 (SA1063) mutant is attenuated in mice [PMID:19395491].
peptide methionine sulfoxide reductase homolog
Other designations: methionine sulfoxide reductase A
MUTATION: mutant displayed reduced ability to colonize and reduced virulence in nematodes and rat endocarditis [PMID:19459977].
factor essential for expression of methicillin resistance
MUTATION: SA1262 (cvfC3) mutant is attenuated in silkworms [PMID:20347953].
MUTATION: attenuated in murine model [PMID:15664928].
MUTATION: SA1453 (cymR) mutant is attenuated in mice [PMID:20485570].
MUTATION: relA spoT deletion mutants are attenuated in mice [PMID:19701461].
bifunctional (p)ppGpp synthetase II/ guanosine-3',5'-bis pyrophosphate 3'-pyrophosphohydrolase
MUTATION: purH mutant is attenuated in mice [PMID:14742535].
AICAR formyltransferase; IMP cyclohydrolase
Other designations: bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase
MUTATION: hfq mutant is highly attenuated in mice after subcutaneous or intravenous injection and has attenuated survival in macrophages [PMID:19593436].
MUTATION: greA mutants are attenuated in mice [PMID:14742535].
MUTATION: pcm mutant is attenuated in mice [PMID:14742535].
protein-L-isoaspartate O-methyltransferase
MUTATION: nlpD mutant is attenuated in mice [PMID:19759820].
MUTATION: purK mutant is attenuated in mice [PMID:14742535].
Other designations: phosphoribosylaminoimidazole carboxylase ATPase subunit
MUTATION: y1136 mutant is attenuated in mice [PMID:14742535].
MUTATION: pgm mutant of Y. pestis is attenuated in mice [PMID:12009274].
MUTATION: ompX mutants are attenuated in their ability to attach to and invade HeLa cells [PMID:17768237].
MUTATION: y1436 mutant is attenuated in mice [PMID:14742535].
MUTATION: y1537 mutant is attenuated in mice [PMID:14742535].
MUTATION: y1718 mutant is attenuated in mice [PMID:14742535].
MUTATION: phoP mutants have a reduced ability to survive in J774 macrophage cell cultures and under conditions of low pH and oxidative stress in vitro. The mean lethal dose of the phoP mutant in mice was increased 75-fold in comparison with that of the wild-type strain [PMID:10816493].
MUTATION: mgtC mutants are defective in early intracellular survival in macrophages compared to wild type Y. pestis [PMID:16790745].
MUTATION: yfeAB mutant is attenuated when given subcutaneously to mice and is avirulent when given to mice intravenously [PMID:10231495].
attachment invasion locus protein precursor
MUTATION: lpxM (msbB) mutant is avirulent in mice and guinea pigs [PMID:17913308].
MUTATION: YchM mutant is attenuated in mice [PMID:14742535].
MUTATION: y2316 mutant is attenuated in mice [PMID:14742535].
MUTATION: ybtP mutant is avirulent in mouse bubonic plague model [PMID:10231486].
permease and ATP-binding protein of yersiniabactin-iron ABC transporter
MUTATION: irp2 mutants are unable to grow at 37 degrees in iron deficient media [PMID:7896707].
MUTATION: psn mutant is unable to grow on iron-deficient media at 37 degrees C [PMID:7896707].
pesticin/yersiniabactin outer membrane receptor
MUTATION: yadBC mutant is attenuated in mice and is less invasive of HeLa cells than the wild-type [PMID:18025093].
MUTATION: psaA mutants have a 100-fold reduced 50% lethal dose in mice [PMID:2164509].
pH 6 antigen precursor (antigen 4) (adhesin)
MUTATION: psaE mutants are attenuated in mice [PMID:2164509].
MUTATION: y3010 mutant is attenuated in mice [PMID:14742535].
MUTATION: smpB ssrA mutant is attenuated in mice [PMID:20065026].
MUTATION: dnaE mutant is attenuated in mice [PMID:14742535].
MUTATION: y3395 mutant is attenuated in mice [PMID:14742535].
MUTATION: y3719 mutant is attenuated in mice [PMID:14742535].
MUTATION: yapE mutant is attenuated in mice and has impaired colonization in bubonic plague model [PMID:18936182].
MUTATION: y3857 mutant is attenuated in mice [PMID:14742535].
MUTATION: dam mutant is attenuated in mice [PMID:16188402].
MUTATION: crp mutant is attenuated in mice [PMID:20086087].
MUTATION: caf1A mutants are attenuated in mice [PMID:14711524].
MUTATION: caf1M mutants are attenuated in mice [PMID:14711524].
MUTATION: The LD50 for the mouse of the yscH mutant was 10-fold higher than that of the parental strain indicating that YopR is involved in pathogenesis [PMID:8709853].
MUTATION: lcrF mutant is attenuated in mice [PMID:14742535].
MUTATION: lcrV mutants are avirulent in mice [PMID:7730287].
MUTATION: lcrH mutant is avirulent in mice [PMID:2707857].
MUTATION: yopB mutant is avirulent in mouse model, fails to elicit a cytotoxic response in cultured HeLa cells and is unable to inhibit phagocytosis by macrophage-like J774 cells [PMID:8918459].
MUTATION: yopD mutants are unable to induce cytotoxicity in HeLa cells [PMID:1937815].
MUTATION: yopM mutant is attenuated in mice compared to the wild type [PMID:2401564].
MUTATION: yopK mutant has an increased LD50 dose in mice, and infected mice died after 5 days as compared to mice infected with the wild type died after just 3 days [PMID:3002984].
MUTATION: yopE mutants are attenuated after oral or intraperitoneal infection in mice, but are not attenuated after intravenous infection in mice [PMID:2191183].
MUTATION: ypkA mutants of Y. pseudotuberculosis are attenuated in mice [PMID:8441468].
MUTATION: yopH mutants are unable to resist phagocytosis by J774 cells, while wild type Yersinia is able to resist phagocytosis [PMID:8809758].
MUTATION: pla mutant is attenuated in mice [PMID:1439793].
Yop secretion and targeting control protein
MUTATION: hemO mutant is attenuated in hamsters [PMID:19114124].
MUTATION: atxA mutant is avirulent in mice [PMID:12224521].
Other designations: transcriptional activator AtxA
MUTATION: pagA mutant is non-lethal in mice [PMID:1910002].
MUTATION: lef mutants are non-lethal in mice [PMID:1910002].
magnesium ion-transporting ATPase E1-E2 family protein
MUTATION: gltD encodes the small subunit of glutamate synthase. It is required for B. abortus growth as shown in signature-tagged transposon mutagenesis. It suggests that glutamate may serve as carbon and/or nitrogen sources during growth of B abortus [PMID:10858227].
MUTATION: The virB11 mutation experiment confirms that a complete VirB apparatus is required for their secretion [PMID:15312849].
MUTATION: Mutants with polar and nonpolar mutations introduced in irB10 showed different behaviors in mice and in the HeLa cell infection assay, suggesting that virB10 per se is necessary for the correct function of this type IV secretion apparatus [PMID:11260139]. A B. abortus virB10 mutant showed a decrease of intracellular live bacteria comparable to that of the wild-type strain until 4 h after infection, indicating that a functional VirB system is not required for the short-term survival of Brucella inside macrophages. At later time points, the number of live virB10 mutants progressively decreased. Hence, the Brucella virB10 strain did not replicate, but rather was killed. Although the virB10 mutants are capable of short-term survival, they can not evade long-term degradation through fusion with lysosomes [PMID:11260139]. B abortus virB1 and virB10 mutants are unable to persist in mouse spleens after i.p. inoculation, suggest that attenuation in the animal model is due to an inability of these strains to grow intracellularly [PMID:11260139]. A B abortus virB10 mutant lost the ability to multiply in HeLa cells and was not recovered from the spleens of infected BALBc mice [PMID:11260139]. The non polar virB10 mutant was able to block the acquisition of cathepsin D, but was not able to translocate to the replication compartment [PMID:11260139]. The virB10 non-polar mutants were capable of avoiding interactions with the endocytic pathway but , diverging to wild-type Brucella, were unable to reach the endoplasmic reticulum to establish their intracellular replication niche and seemed to be recycled to the cell surface [PMID:11260139].
MUTATION: Uptake in the presence or absence of Ca2 and Mg2 did not influence the subsequent intracellular survival of wild-type Brucella, whereas the decrease in the number of surviving virB9 mutant cells was delayed in the absence of Ca2 and Mg2. Possibly two types of adhesion molecules promoted uptake of Brucella, one being Ca2 and Mg2 dependent and the other not, and that both types participate in the uptake of wild-type bacteria but only the latter type participates in the uptake of the virB9 mutant [PMID:12414149]. Four independent mutants in virB5, virB9 or virB10 were highly attenuated in an in vitro infection model with human macrophages [PMID:12414149]. The intracellular fate of three virB mutants (virB2, virB4 and virB9) in HeLa cells by immunofluorescence was examined. The three VirB proteins are not necessary for penetration and the inhibition of phago-lysosomal fusion within non-professional phagocytes. Rather, the virB mutants are unable to reach the replicative niche and reside in a membrane -bound vacuole expressing the late endosomal marker, LAMP1, and the sec61beta protein from the ER membrane, proteins that are present in autophagic vesicles originating from the ER [PMID:12414149]. Attenuated non-polar virB2, virB4, virB8, virB9 and virB10 Brucella mutants are capable of penetrating cells as the same rate as the virulent wild-type Brucella, transit through EEA1 -positive early compartments and then localize in LAMP1-positive compartments at early times of infection [PMID:12414149].
MUTATION: virB8 mutant was attenuated by a mini-Tn5 transposon mutagenesis [PMID:12414149]. Attenuated non-polar virB2, virB4, virB8, virB9 and virB10 Brucella mutants are capable of penetrating cells as the same rate as the virulent wild-type Brucella, transit through EEA1-positive early compartments and then localize in LAMP1-positive compartments at early times of infection [PMID:12414149].
MUTATION: A comparison of the VirB8 and VirB5 contents after induction of the B suis wild type and of virB5 and virB12 mutants further confirmed that the virB5 and virB12 genes belong to the same operon [PMID:10510235]. Smooth strains of Brucella unable to replicate (ie, killed B suis or the avirulent mutant B suis virB5) exhibit delayed phagosome-lysosome fusion [PMID:10510235]. Polar mutations in the operon upstream of virB5 exert a greater effect on the expression of virB5 than they do on the expression of the downstream gene virB12. It indicates that in B abortus , regulatory elements other than the virB promoter may influence VirB12 protein levels [PMID:10510235]. Four independent mutants in virB5, virB9 or virB10 were highly attenuated in an in vitro infection model with human macrophages [PMID:10510235].
MUTATION: A mutant strain of B abortus that contains an in-frame deletion in virB4 is unable to replicate in macrophages and survives in mice [PMID:15135535]. ntracellular replication was inhibited in wild-type B abortus after introducing a plasmid expressing a mutant VirB4 altered in the NTP -binding region. VirB4 containing the intact NTP -binding region is essential for evasion of fusion with lysosomes (11988518). The ruffling associated with internalization of the virB4 mutant results in a more rapid uptake than for the wild-type strain. The virB4 mutant shows primarily small regions of phalloidin staining at the sites of binding. Macrophages incubated simultaneously with B abortus and the fluid-phase marker tetramethyl rhodamine isothiocyanate (TRITC)-dextran accumulate the marker in large vacuoles containing the wild-type strain, but little or no marker accumulates in phagosomes containing the virB4 mutant. Similarly, phase-contrast micrographs have shown the wild-type strain in large phase-transparent compartments, but the virB4 mutant is in much smaller compartments (14738898). Intracellular growth-defective virB4 mutant and attenuated vaccine strain S19 did not induce abortion [PMID:15135535]. The B abortus virB4 mutant was completely cleared from the spleens of mice after 4 weeks, while the pncA mutant showed a 1.5-log reduction of the number of bacteria isolated from spleens after 10 weeks. Splenomegaly was not observed at all in mice infected with virB4 mutant [PMID:15135535].
MUTATION: The B abortus virB3 gene is found to be essential for intracellular growth inside HeLa cells [PMID:12761078].
MUTATION: The Brucella abortus virB operon, encoding a type IV secretion system (T4SS), is required for intracellular replication and persistent infection in the mouse model. The products of the first two genes of the virB operon, virB1 and virB2, are predicted to be localized at the bacterial surface. Both mutants were shown to be nonpolar, as demonstrated by their ability to express the downstream gene virB5 during stationary phase of growth in vitro. Both VirB1 and VirB2 were essential for intracellular replication in J774 macrophages. The nonpolar virB2 mutant was unable to cause persistent infection in the mouse model, demonstrating the essential role of VirB2 in the function of the T4SS apparatus during infection [PMID:16113325]. Polar mutations in the virB1 to virB2 intergenic region or in virB2 reduced the detection of VirB5 to a greater extent than they did that of VirB12. A virB1 mutation also eliminates the transcription of virB12 in B suis [PMID:16113325].
MUTATION: The Brucella abortus virB operon, encoding a type IV secretion system (T4SS), is required for intracellular replication and persistent infection in the mouse model. The products of the first two genes of the virB operon, virB1 and virB2, are predicted to be localized at the bacterial surface. Both mutants were shown to be nonpolar, as demonstrated by their ability to express the downstream gene virB5 during stationary phase of growth in vitro. Both VirB1 and VirB2 were essential for intracellular replication in J774 macrophages. The nonpolar virB1 mutant persisted at wild-type levels, showing that the function of VirB1 is dispensable in the mouse model of persistent infection [PMID:16272371]. A B abortus polar virB1 mutant failed to replicate in HeLa cells, indicating that the virB operon plays a critical role in intracellular multiplication [PMID:16272371]. Polar mutations in the virB1 to virB2 intergenic region or in virB2 reduced the detection of VirB5 to a greater extent than they did that of VirB12. A virB1 mutation also eliminates the transcription of virB12 in B suis [PMID:16272371]. An infection assay with signature-tagged Brucella abortus mutants demonstrated that mutagenesis of the virB1 gene causes attenuation of virulence [PMID:16272371].
MUTATION: gnd is involved in pentose phosphate pathway. It is essential for intracellular growth inside HeLa cells as shown by its Brucella suis miniTn5Km2 transposon mutation analysis. The mutant is attenuated in the mouse model [PMID:12761078].
glycosyl transferase group 2 family protein
flagellar basal body P-ring biosynthesis protein FlgA
MUTATION: A mutant of Brucella suis bearing a Tn5 insertion in norD , the last gene of the operon norEFCBQD, encoding nitric oxide reductase, was unable to survive under anaerobic denitrifying conditions (more-than-5log reduction in viable counts). As a consequence of the norD mutation , NO might not be further reduced to N2O by the NO reductase and it could become toxic for the bacteria. The infection of resting macrophages showed that the norD mutant and the wild-type strain displayed similar rates of multiplication. On the contrary, activation of J774A.1 cells by LPS and IFN was accompanied by a more-thantenfold attenuation of the norD mutant at 48 h p. i. [PMID:16495577].
MUTATION: The narG gene encodes for an essential component of the dissimilatory nitrate reductase complex. This complex is encoded by the narGHIJ locus, which is present in the B suis genome together with the gene of the nitrite extrusion protein, narK. The narG mutant was unable to produce nitrite from nitrate [PMID:12438693]. A study with miniTn5 mutants of B. suis constitutively expressing gfp indicates that B. suis xx gene is required for intracellular multiplication in human macrophage THP-1 cells [PMID:12438693].
respiratory nitrate reductase subunit alpha
MUTATION: The transcription product of Brucella abortus oxyR binds to the B abortus catalase promoter region. A gene replacementdeletion Brucella oxyR mutant exhibits increased sensitivity to prolonged exposure to H2O2 and is unable to adapt to H2O2 in the environment [PMID:10986275].
MUTATION: The cydB and cydD mutants are also defective for the intracellular growth of B abortus and B suis, suggesting that functional cytochrome bd oxidase is required for growth in an intracellular environment [PMID:12761078].
ABC transporter ATP-binding protein CydD
MUTATION: cydB is a gene that is part of the cydAB operon encoding cytochrome bd oxidase , which catalyzes an alternate terminal electron transport step in bacterial respiration. Transposon (Tn5) mutagenesis of B abortus cydB was severely attenuated for intracellular survival. Unlike the virulent strain 2308, the Brucella cydB::Tn5 mutant was severely compromised for survival in the spleens of inoculated mice [PMID:11274104]. The cydB and cydD mutants are also defective for the intracellular growth of B abortus and B suis, suggesting that functional cytochrome bd oxidase is required for growth in an intracellular environment [PMID:11274104].
cytochrome d ubiquinol oxidase subunit II
MUTATION: The role of Phosphatidylcholine (PC) in Brucella abortus was examined by generating mutants in pcs (BApcs) and pmtA (BApmtA), which encode key enzymes of the two bacterial PC biosynthetic routes, the choline and methyl-transferase pathways. In rich medium, BApcs and the double mutant BApcspmtA but not BApmtA displayed reduced growth, increased phosphatidylethanolamine and no PC, showing that Pcs is essential for PC synthesis under these conditions. In minimal medium, the parental strain, BApcs and BApmtA showed reduced but significant amounts of PC suggesting that PmtA may also be functional Probing with phage Tb, antibiotics, polycations and serum demonstrated that all mutants had altered envelopes. In macrophages, BApcs and BApcspmtA showed reduced ability to evade fusion with lysosomes and establish a replication niche. In mice, BApcs showed attenuation only at early times after infection, BApmtA at later stages and BApcspmtA throughout. The results suggest that Pcs and PmtA have complementary roles in vivo related to nutrient availability and that PC and the membrane properties that depend on this typical eukaryotic phospholipid are essential for Brucella virulence [PMID:16882035].
polar differentiation response regulator
MUTATION: B suis ugpB mutant does not contain SP41 protein. Mutants lacking SP41 production are less invasive, but proliferate in HeLa cells. An isogenic DeltaugpB mutant showed a significant inhibitory effect on Brucella adherence and invasion of human cultured epithelial cells and this effect could be reversed by restoration of the ugpB on a plasmid. [PMID:16817909].
glycerol-3-phosphate ABC transporter periplasmic glycerol-3-phosphate-binding protein
MUTATION: UgpA is one of the attenuated Signature-Tagged Mutagenesis mutants of Brucella melitensis identified during the acute phase of infection in mice [PMID:14638795].
glycerol-3-phosphate ABC transporter permease
MUTATION: A study with miniTn5 mutants of B. suis constitutively expressing gfp indicates that B. suis gcvT gene is required for intracellular multiplication in human macrophage THP-1 cells [PMID:12438693].
glycine cleavage system aminomethyltransferase T
MUTATION: Brucella abortus zwf mutant via mini-Tn5Km2 transposon mutagenesis has intracellular growth defect inside HeLa cells and macrophages [PMID:12761078].
nickel ABC transporter nickel-binding protein
MUTATION: EryB is an erythritol phosphate dehydrogenase. The vaccine strain B abortus B19 is the only known B abortus isolate whose growth is inhibited by erythritol. The B abortus B19 strain is an eryCD double mutant. The defect in B19 was complemented in trans by plasmids containing the complete ery region and by plasmids with Tn1725 insertions in eryA, eryB and eryD. Plasmids with Tn1725 insertions in eryC were the only ones that failed to complement the Ery phenotype of B19 [PMID:10708387]. The B. suis eryB mutant by Tn5 transposon mutagenesis was attenuated in the human macrophage -like THP-1 cells. This mutant is sensitive to erythritol and mimics the erythritol sensitive response of the B19 strain [PMID:10708387].
MUTATION: The eryC gene encodes for enzyme Derythrulose-1-phosphate dehydrogenase. The vaccine strain B abortus B19 is the only known B abortus isolate whose growth is inhibited by erythritol. The B abortus B19 strain is an eryCD double mutant. The defect in B19 was complemented in trans by plasmids containing the complete ery region and by plasmids with Tn1725 insertions in eryA, eryB and eryD. Plasmids with Tn1725 insertions in eryC were the only ones that failed to complement the Ery phenotype of B19 [PMID:10708387]. Allelic exchange mutants in eryC of Brucella suis were erythritol sensitive in vitro with a MIC of 1 to 5 mM of erythritol. Their multiplication in macrophage-like cells was 50 to 90- fold reduced , but complementation of the mutant restored wild-type levels of intracellular multiplication and the capacity to use erythritol as a sole carbon source. In vivo, the eryC mutant colonized the spleens of infected BALBc mice to a significantly lower extent than the wild type and the complemented strain. Interestingly, eryC mutants that were in addition spontaneously erythritol tolerant nevertheless exhibited wild-type-like intramacrophagic and intramurine replication. In conclusion, erythritol was not an essential carbon source for the pathogen in the macrophage host cell but that the inactivation of the eryC gene significantly reduced the intramacrophagic and intramurine fitness of B suis [PMID:10708387].
MUTATION: A study with miniTn5 mutants of B. suis constitutively expressing gfp indicates that B. suis cobW gene is required for intracellular multiplication in human macrophage THP-1 cells [PMID:12438693].
cobalamin synthesis protein/P47K family protein
ABC transporter periplasmic substrate-binding protein
MUTATION: Brucella abortus znuA mutant via mini-Tn5Km2 transposon mutagenesis has intracellular growth defect inside HeLa cells [PMID:12761078]. High-affinity zinc uptake system protein mutant (znuA mutant) showed reduced growth in zinc chelated medium, and failed to replicate in HeLa cells and mouse bone marrow-derived macrophages. Transformation of znuA mutant with a shuttle vector pBBR1MCS-4 containing znuA gene restored the growth in zinc chelated medium and intracellular replication in HeLa cells and macrophages to a level comparable to that of wild-type strain. Bacterial internalization into HeLa cells and macrophages and co-localization with either late endosomes or lysosomes of znuA mutant were not different from those of wild-type strain. These results suggest that znuA does not contribute to intracellular trafficking of B abortus, but contributes to utilization of zinc required for intracellular growth [PMID:12761078].
zinc ABC transporter periplasmic zinc-binding protein
zinc ABC transporter ATP-binding protein
MUTATION: rpsA is a B. suis gene identified by signature-tagged mutagenesis [PMID:10678941].
MUTATION: The product of pheA gene is specifically dedicated to the biosynthesis of phenylalanine. The B. abortus pheA mutant with mini-Tn5 disruption displays nutritional defects in vitro. Experimental findings with the B abortus ilvD, trpB, and pheA mutants suggest that tryptophan and phenylalanine are available to the brucellae in their intracellular niche but that other amino acids (eg, leucine, isoleucine, or valine) are not. The pheA::miniTn5 mutant displayed attenuation in macrophages but not in mice [PMID:15271960].
MUTATION: Brucella pgm encodes the phosphoglucomutase. The B. abortus pgm mutant (B2211) lacks the O antigen. However, the core region of the mutant LPS migrated in Tricine-PAGE electrophoresis in a position that was indistinguishable from that of the wild type core. Although the exponential intracellular replication of the pgm mutant was delayed by approximately 20 h with respect to that of the wild type, the high number of recoverable bacteria at 48 h postinfection indicates that mutant strain B2211 replicates inside HeLa host cells [PMID:10992476]. B abortus phosphoglucomutase (pgm) insertional mutants were attenuated in vivo but not in vitro [PMID:10992476].
sulfite reductase (NADPH) hemoprotein subunit beta
MUTATION: B. suis pyrD mutation study indicated that pyrimidine synthesis pathway contributes to intracellular growth [PMID:12761078].
sensor histidine kinase/response regulator
MUTATION: B abortus bacA mutant exhibited decreased survival in macrophages and greatly accelerated clearance from experimentally infected mice compared to the virulent parental strain [PMID:10741969]. R meliloti bacA gene encodes a putative cytoplasmic membrane transport protein required for symbiosis [PMID:10741969]. The BacA protein is essential for the long-term survival of Sinorhizobium meliloti and Brucella abortus within acidic compartments in plant and animal cells , respectively. Mutation study showed that B. abortus BacA affects the distribution of LPS fatty acids, including a very-long-chain fatty acid thought to be unique to the alpha-proteobacteria[PMID:10741969].
MUTATION: A B. suis purF mutation experiment suggests that the purine biosynthesis pathway contributes to intracellular growth [PMID:12761078].
twin-arginine translocation pathway signal sequence domain-containing protein
glycosyl transferase group 4 family protein
MUTATION: No function has been assigned to the B. melitensis 16M wbkB gene either by homology search or functionally, because deletion of wbkB did not interfere with the O-antigen structure [PMID:11081580].
MUTATION: gmd may be involved in perosamine synthesis. It has been shown to be in LPS synthesis since its B. melitensis mutation induces rough phenotype [PMID:15099501].
MUTATION: A single mutation of PepN leads to a significant decrease in the growth rate, thus PepN seems to play a more prominent role than do the other proteases [PMID:12933870].
MUTATION: B. abortus purN gene is essential for intracellular growth in HeLa cells as shown from transposon mutagenesis study [PMID:12761078].
phosphoribosylglycinamide formyltransferase
MUTATION: A study with miniTn5 mutants of B. suis constitutively expressing gfp indicates that B. suis glnA gene is required for intracellular multiplication in human macrophage THP-1 cells [PMID:12438693].
MUTATION: The NtrY protein is a sensor of an ntr-related regulon which may be part of the glnALG operon. This mutant has a weakly attenuated phenotype (reduction of 1.2 log units versus the wild type at 48 h postinfection) which could be explained by a pleiotropic effect on the ntr regulon, since the ntrC mutant did not show such a phenotype [PMID:10678941].
MUTATION: ntrC encodes for a response regulator subfamily (NtrC). A B suis ntrC isogenic mutant was constructed which showed no significant differences in growth rates compared to the wild-type strain when grown at different temperatures in vitro. However, the mutant exhibited a reduction in metabolic activity in the presence of many amino acids. The mutation did not affect survival or multiplication of B suis in macrophages, but during the initial stages of infection in the murine brucellosis model, the ntrC mutant showed a reduced ability to multiply rapidly in splenic tissue [PMID:10373105].
DNA-directed RNA polymerase subunit alpha
MUTATION: A study with miniTn5 mutants of B. suis constitutively expressing gfp indicates that B. suis serB gene is required for intracellular multiplication in human macrophage THP-1 cells [PMID:12438693].
MUTATION: Brucella abortus pnc mutant via mini-Tn5Km2 transposon mutagenesis has intracellular growth defect inside HeLa cells [PMID:12761078]. Nicotinamidasepyrazinamidase mutant (pncA mutant) of Brucella abortus failed to replicate in HeLa cells, and showed a lower rate of intracellular replication than that of wild-type strain in macrophages [PMID:12761078]. The pncA mutant was not co-localizing with either late endosomes or lysosomes. The pncA mutant showed a 1.5-log reduction of the number of bacteria isolated from mouse spleens after 10 weeks [PMID:12761078]. It indicates that the mutant has reduced virulence in mice.
MUTATION: Brucella abortus pnc mutant via mini-Tn5Km2 transposon mutagenesis has intracellular growth defect inside HeLa cells [PMID:15135535]. Nicotinamidasepyrazinamidase mutant (pncA mutant) of Brucella abortus failed to replicate in HeLa cells, and showed a lower rate of intracellular replication than that of wild-type strain in macrophages [PMID:15135535]. The pncA mutant was not co-localizing with either late endosomes or lysosomes. The pncA mutant showed a 1.5-log reduction of the number of bacteria isolated from mouse spleens after 10 weeks [PMID:15135535]. It indicates that the mutant has reduced virulence in mice.
MUTATION: aspC encodes for an aminotransferase. B.abortus aspC mutant obtained from randomized miniTn5Km2 transposon mutagenesis showed decreased intracellular survival inside HeLa cells. So B. abortus aspC gene is essential for HeLa cell intracellular growth [PMID:12761078].
deoxyuridine 5'-triphosphate nucleotidohydrolase
phosphoribosylaminoimidazole carboxylase, catalytic subunit
MUTATION: pyc is one B. suis gene identified by signature-tagged mutagenesis. It is essential for survival and mulitplication in macrophages [PMID:10678941].
branched-chain amino acid ABC transporter permease
MUTATION: A study with miniTn5 mutants of B. suis constitutively expressing gfp indicates that B. suis lysA gene is required for intracellular multiplication in human macrophage THP-1 cells [PMID:12438693].
hypoxanthine-guanine phosphoribosyltransferase
imidazole glycerol phosphate synthase subunit HisF
MUTATION: The two-component BvrSBvrR system is essential for Brucella abortus virulence. Disruption of BvrSBvrR damages the outer membrane, thus contributing to the severe attenuation manifested by bvrS and bvrR mutants. The bvrS and bvrR mutants are avirulent in mice, show reduced invasiveness to epithelial cells and macrophages, and are incapable of inhibiting lysosome fusion and replicating intracellularly [PMID:12218183]. Mutations in the bvrR or bvrS genes hamper the penetration of B abortus in non-phagocytic cells and impairs intracellular trafficking and virulence. BvrRBvrS mutants do not recruit small GTPases of the Rho subfamily required for actin polymerization and penetration to cells. Dysfunction of the BvrRBvrS system alters the outer membrane permeability, the expression of several group 3 outer membrane proteins and the pattern of lipid A acylation. Constructs of virulent B abortus chimeras containing heterologous LPS from the bvrS(-) mutant demonstrated an altered permeability to cationic peptides similar to that of the BvrRBvrS mutants. It is hypothesized that the Brucella BvrRBvrS is a system devoted to the homeostasis of the outer membrane and, therefore in the interface for cell invasion and mounting the required structures for intracellular parasitism [PMID:12218183]. In contrast to S2308 and S19, bvrS and bvrR mutant strains poorly invade HeLa cells and are rapidly targeted to cathepsin D- containing compartments [PMID:12218183]. B abortus bvrS bvrR mutants display reduced invasiveness and virulence [PMID:12218183]. Brucella bvrS and bvrR null mutants are defective in several outer membrane proteins, mainly Omp3a (former Omp25) and Omp3b as well as in the structure of the LPS molecule, but the O chain seems to be intact [PMID:12218183]. Because bvrR and bvrS mutants are also altered in cell-surface hydrophobicity, permeability, and sensitivity to surface- targeted bactericidal peptides, it is proposed that BvrRBvrS controls cell envelope changes necessary to transit between extracellular and intracellular environments [PMID:12218183]. BvrR/BvrS mutants are avirulent in mice, show reduced invasiveness in cells, and are unable to inhibit lysosome fusion and to replicate intracellularly [PMID:12218183].
putative outer membrane virulence protein
putative secreted protein-tyrosine phosphatase
MUTATION: arcA mutant is attenuated in mice [PMID:14742535].
MUTATION: YPO1003 mutant is attenuated in mice [PMID:14742535].
MUTATION: YPO1179 mutant is attenuated in mice [PMID:14742535].
MUTATION: yadBC mutant (yadB is YPO1387) is attenuated in mice and is less invasive to HeLa cells than the wildtype [PMID:18025093].
MUTATION: yadBC (yadC is YPO1388) mutant is attenuated in mice and is less invasive of HeLa cells than the wild-type [PMID:18025093].
MUTATION: a Y. pestis ail deletion mutant was rapidly killed by sera from all mammals tested except mice [PMID:18025094].
pesticin/yersiniabactin receptor protein
lipoprotein inner membrane ABC transporter
MUTATION: YPO1994 mutant is attenuated in mice [PMID:14742535].
MUTATION: YPO2027 mutant is attenuated in mice [PMID:14742535].
MUTATION: slyA (rovA) mutant is attenuated in mice [PMID:16938880].
MUTATION: lpp deletion mutant is attenuated in mice [PMID:19737605].
MUTATION: YPO2471 mutant is attenuated in mice [PMID:14742535].
MUTATION: YPO2793 mutant is attenuated in mice [PMID:14742535].
MUTATION: guaBA operon mutant is highly attenuated in mice [PMID:20096773].
MUTATION: YPO2947 mutant is attenuated in mice [PMID:14742535].
MUTATION: YP03045 mutant is attenuated in mice [PMID:14742535].
phosphoribosylaminoimidazole carboxylase ATPase subunit
MUTATION: yadBC double mutant is less invasive of HeLa cells compared to the wild type and decreased virulence in bubonic plague in mice [PMID:18025093].
MUTATION: YPO3973 mutant is attenuated in mice [PMID:14742535].
MUTATION: mutant showed attenuated virulence in C3H/HeN mice [PMID:19997622].
recombination and DNA strand exchange inhibitor protein
MUTATION: sodA mutant showed complete attenuation in C3H/HeN mice compared with control strains [PMID:19040638].
superoxide dismutase [Mn] (General stress protein 24)(GSP24)
MUTATION: rel(Bbu) deletion mutant eliminated virulence in mice [PMID:16041012].
guanosine-3',5'-bis(diphosphate) 3'-pyrophosphohydrolase
MUTATION: deletion severely impaired mutant's ability to persist and induce disease in murine tissues [PMID:19266024].
MUTATION: bmtA mutant attenuated in mice [PMID:19218460].
MUTATION: mutant not infectious in murine model [PMID:20815822].
MUTATION: deletion mutant unable to infect mice or ticks [PMID:19754308]
MUTATION: mutant not infectious in mice, showed decreased motility [PMID:20444101].
MUTATION: BMEI0066 deletion mutant fails to replicated in murine macrophages and is rapidly cleared from the spleens of experimentally infected BALB/c mice [PMID:19742243].
phosphoenolpyruvate-protein phosphotransferase PTSP
high-affinity branched-chain amino acid transport system permease livH
phosphoribosylaminoimidazole carboxylase catalytic subunit
lipopolysaccharide core biosynthesis mannosyltransferase LPCC
carbamoyl phosphate synthase small subunit
acetolactate synthase 3 catalytic subunit
molybdenum cofactor biosynthesis protein A
arginine/ornithine-binding periplasmic protein precursor
undecaprenyl-phosphate alpha-N-acetylglucosaminyltransferase
thiol:disulfide interchange protein DsbA
c-di-GMP phosphodiesterase A-related protein
MUTATION: B abortus bacA mutant exhibited decreased survival in macrophages and greatly accelerated clearance from experimentally infected mice compared to the virulent parental strain [PMID:12270820]. R meliloti bacA gene encodes a putative cytoplasmic membrane transport protein required for symbiosis [PMID:12270820]. The BacA protein is essential for the long-term survival of Sinorhizobium meliloti and Brucella abortus within acidic compartments in plant and animal cells , respectively. Mutation study showed that B. abortus BacA affects the distribution of LPS fatty acids, including a very-long-chain fatty acid thought to be unique to the alpha-proteobacteria[PMID:12270820].
maltose ABC transporter ATP-binding protein
thiol:disulfide interchange protein CYCY precursor
MUTATION: Brucella pgm encodes the phosphoglucomutase. The B. abortus pgm mutant (B2211) lacks the O antigen. However, the core region of the mutant LPS migrated in Tricine-PAGE electrophoresis in a position that was indistinguishable from that of the wild type core. Although the exponential intracellular replication of the pgm mutant was delayed by approximately 20 h with respect to that of the wild type, the high number of recoverable bacteria at 48 h postinfection indicates that mutant strain B2211 replicates inside HeLa host cells [PMID:12525425]. B abortus phosphoglucomutase (pgm) insertional mutants were attenuated in vivo but not in vitro [PMID:12525425].
MUTATION: The two-component BvrSBvrR system is essential for Brucella abortus virulence. Disruption of BvrSBvrR damages the outer membrane, thus contributing to the severe attenuation manifested by bvrS and bvrR mutants. The bvrS and bvrR mutants are avirulent in mice, show reduced invasiveness to epithelial cells and macrophages, and are incapable of inhibiting lysosome fusion and replicating intracellularly [PMID:11401996]. Mutations in the bvrR or bvrS genes hamper the penetration of B abortus in non-phagocytic cells and impairs intracellular trafficking and virulence. BvrRBvrS mutants do not recruit small GTPases of the Rho subfamily required for actin polymerization and penetration to cells. Dysfunction of the BvrRBvrS system alters the outer membrane permeability, the expression of several group 3 outer membrane proteins and the pattern of lipid A acylation. Constructs of virulent B abortus chimeras containing heterologous LPS from the bvrS(-) mutant demonstrated an altered permeability to cationic peptides similar to that of the BvrRBvrS mutants. It is hypothesized that the Brucella BvrRBvrS is a system devoted to the homeostasis of the outer membrane and, therefore in the interface for cell invasion and mounting the required structures for intracellular parasitism [PMID:11401996]. In contrast to S2308 and S19, bvrS and bvrR mutant strains poorly invade HeLa cells and are rapidly targeted to cathepsin D- containing compartments [PMID:11401996]. B abortus bvrS bvrR mutants display reduced invasiveness and virulence [PMID:11401996]. Brucella bvrS and bvrR null mutants are defective in several outer membrane proteins, mainly Omp3a (former Omp25) and Omp3b as well as in the structure of the LPS molecule, but the O chain seems to be intact [PMID:11401996]. Because bvrR and bvrS mutants are also altered in cell-surface hydrophobicity, permeability, and sensitivity to surface- targeted bactericidal peptides, it is proposed that BvrRBvrS controls cell envelope changes necessary to transit between extracellular and intracellular environments [PMID:11401996]. BvrR/BvrS mutants are avirulent in mice, show reduced invasiveness in cells, and are unable to inhibit lysosome fusion and to replicate intracellularly [PMID:11401996].
MUTATION: The Brucella abortus virB operon, encoding a type IV secretion system (T4SS), is required for intracellular replication and persistent infection in the mouse model. The products of the first two genes of the virB operon, virB1 and virB2, are predicted to be localized at the bacterial surface. Both mutants were shown to be nonpolar, as demonstrated by their ability to express the downstream gene virB5 during stationary phase of growth in vitro. Both VirB1 and VirB2 were essential for intracellular replication in J774 macrophages. The nonpolar virB1 mutant persisted at wild-type levels, showing that the function of VirB1 is dispensable in the mouse model of persistent infection [PMID:15322008]. A B abortus polar virB1 mutant failed to replicate in HeLa cells, indicating that the virB operon plays a critical role in intracellular multiplication [PMID:15322008]. Polar mutations in the virB1 to virB2 intergenic region or in virB2 reduced the detection of VirB5 to a greater extent than they did that of VirB12. A virB1 mutation also eliminates the transcription of virB12 in B suis [PMID:15322008]. An infection assay with signature-tagged Brucella abortus mutants demonstrated that mutagenesis of the virB1 gene causes attenuation of virulence [PMID:15322008].
attachment mediating protein VIRB1-like protein
MUTATION: The Brucella abortus virB operon, encoding a type IV secretion system (T4SS), is required for intracellular replication and persistent infection in the mouse model. The products of the first two genes of the virB operon, virB1 and virB2, are predicted to be localized at the bacterial surface. Both mutants were shown to be nonpolar, as demonstrated by their ability to express the downstream gene virB5 during stationary phase of growth in vitro. Both VirB1 and VirB2 were essential for intracellular replication in J774 macrophages. The nonpolar virB2 mutant was unable to cause persistent infection in the mouse model, demonstrating the essential role of VirB2 in the function of the T4SS apparatus during infection [PMID:15322008]. Polar mutations in the virB1 to virB2 intergenic region or in virB2 reduced the detection of VirB5 to a greater extent than they did that of VirB12. A virB1 mutation also eliminates the transcription of virB12 in B suis [PMID:15322008].
MUTATION: A mutant strain of B abortus that contains an in-frame deletion in virB4 is unable to replicate in macrophages and survives in mice [PMID:11988518]. ntracellular replication was inhibited in wild-type B abortus after introducing a plasmid expressing a mutant VirB4 altered in the NTP -binding region. VirB4 containing the intact NTP -binding region is essential for evasion of fusion with lysosomes (11988518). The ruffling associated with internalization of the virB4 mutant results in a more rapid uptake than for the wild-type strain. The virB4 mutant shows primarily small regions of phalloidin staining at the sites of binding. Macrophages incubated simultaneously with B abortus and the fluid-phase marker tetramethyl rhodamine isothiocyanate (TRITC)-dextran accumulate the marker in large vacuoles containing the wild-type strain, but little or no marker accumulates in phagosomes containing the virB4 mutant. Similarly, phase-contrast micrographs have shown the wild-type strain in large phase-transparent compartments, but the virB4 mutant is in much smaller compartments (14738898). Intracellular growth-defective virB4 mutant and attenuated vaccine strain S19 did not induce abortion [PMID:11988518]. The B abortus virB4 mutant was completely cleared from the spleens of mice after 4 weeks, while the pncA mutant showed a 1.5-log reduction of the number of bacteria isolated from spleens after 10 weeks. Splenomegaly was not observed at all in mice infected with virB4 mutant [PMID:11988518].
MUTATION: A comparison of the VirB8 and VirB5 contents after induction of the B suis wild type and of virB5 and virB12 mutants further confirmed that the virB5 and virB12 genes belong to the same operon [PMID:12595417]. Smooth strains of Brucella unable to replicate (ie, killed B suis or the avirulent mutant B suis virB5) exhibit delayed phagosome-lysosome fusion [PMID:12595417]. Polar mutations in the operon upstream of virB5 exert a greater effect on the expression of virB5 than they do on the expression of the downstream gene virB12. It indicates that in B abortus , regulatory elements other than the virB promoter may influence VirB12 protein levels [PMID:12595417]. Four independent mutants in virB5, virB9 or virB10 were highly attenuated in an in vitro infection model with human macrophages [PMID:12595417].
MUTATION: virB8 mutant was attenuated by a mini-Tn5 transposon mutagenesis [PMID:10678941]. Attenuated non-polar virB2, virB4, virB8, virB9 and virB10 Brucella mutants are capable of penetrating cells as the same rate as the virulent wild-type Brucella, transit through EEA1-positive early compartments and then localize in LAMP1-positive compartments at early times of infection [PMID:10678941].
MUTATION: Uptake in the presence or absence of Ca2 and Mg2 did not influence the subsequent intracellular survival of wild-type Brucella, whereas the decrease in the number of surviving virB9 mutant cells was delayed in the absence of Ca2 and Mg2. Possibly two types of adhesion molecules promoted uptake of Brucella, one being Ca2 and Mg2 dependent and the other not, and that both types participate in the uptake of wild-type bacteria but only the latter type participates in the uptake of the virB9 mutant [PMID:11349069]. Four independent mutants in virB5, virB9 or virB10 were highly attenuated in an in vitro infection model with human macrophages [PMID:11349069]. The intracellular fate of three virB mutants (virB2, virB4 and virB9) in HeLa cells by immunofluorescence was examined. The three VirB proteins are not necessary for penetration and the inhibition of phago-lysosomal fusion within non-professional phagocytes. Rather, the virB mutants are unable to reach the replicative niche and reside in a membrane -bound vacuole expressing the late endosomal marker, LAMP1, and the sec61beta protein from the ER membrane, proteins that are present in autophagic vesicles originating from the ER [PMID:11349069]. Attenuated non-polar virB2, virB4, virB8, virB9 and virB10 Brucella mutants are capable of penetrating cells as the same rate as the virulent wild-type Brucella, transit through EEA1 -positive early compartments and then localize in LAMP1-positive compartments at early times of infection [PMID:11349069].
MUTATION: Mutants with polar and nonpolar mutations introduced in irB10 showed different behaviors in mice and in the HeLa cell infection assay, suggesting that virB10 per se is necessary for the correct function of this type IV secretion apparatus [PMID:11401996]. A B. abortus virB10 mutant showed a decrease of intracellular live bacteria comparable to that of the wild-type strain until 4 h after infection, indicating that a functional VirB system is not required for the short-term survival of Brucella inside macrophages. At later time points, the number of live virB10 mutants progressively decreased. Hence, the Brucella virB10 strain did not replicate, but rather was killed. Although the virB10 mutants are capable of short-term survival, they can not evade long-term degradation through fusion with lysosomes [PMID:11401996]. B abortus virB1 and virB10 mutants are unable to persist in mouse spleens after i.p. inoculation, suggest that attenuation in the animal model is due to an inability of these strains to grow intracellularly [PMID:11401996]. A B abortus virB10 mutant lost the ability to multiply in HeLa cells and was not recovered from the spleens of infected BALBc mice [PMID:11401996]. The non polar virB10 mutant was able to block the acquisition of cathepsin D, but was not able to translocate to the replication compartment [PMID:11401996]. The virB10 non-polar mutants were capable of avoiding interactions with the endocytic pathway but , diverging to wild-type Brucella, were unable to reach the endoplasmic reticulum to establish their intracellular replication niche and seemed to be recycled to the cell surface [PMID:11401996].
MUTATION: FtcR is required in B melitensis 16M for the transcription of the fliF gene during vegetative and intracellular growth, and for the production of the two structural flagellar components FlgE and FliC during vegetative growth. A ftcR mutant has the same virulence phenotype as previously found with structural flagellar mutants. In HeLa cells and bovine macrophages, no attenuation of the ftcR mutant was observed compared to the WT parental strain. In BALB/c mice, the ftcR mutant was not attenuated after 1 week of infection but was attenuated after 4 weeks of infection. FtcR acts as a flagellar master regulator in B melitensis and perhaps in other related alpha-proteobacteria [PMID:17056750].
high-affinity zinc uptake system ATP-binding protein ZNUC
MUTATION: Brucella abortus znuA mutant via mini-Tn5Km2 transposon mutagenesis has intracellular growth defect inside HeLa cells [PMID:15472468]. High-affinity zinc uptake system protein mutant (znuA mutant) showed reduced growth in zinc chelated medium, and failed to replicate in HeLa cells and mouse bone marrow-derived macrophages. Transformation of znuA mutant with a shuttle vector pBBR1MCS-4 containing znuA gene restored the growth in zinc chelated medium and intracellular replication in HeLa cells and macrophages to a level comparable to that of wild-type strain. Bacterial internalization into HeLa cells and macrophages and co-localization with either late endosomes or lysosomes of znuA mutant were not different from those of wild-type strain. These results suggest that znuA does not contribute to intracellular trafficking of B abortus, but contributes to utilization of zinc required for intracellular growth [PMID:15472468].
high-affinity zinc uptake system protein ZNUA
ribosome biogenesis GTP-binding protein YsxC
ribose ABC transporter ATP-binding protein
MUTATION: The eryC gene encodes for enzyme Derythrulose-1-phosphate dehydrogenase. The vaccine strain B abortus B19 is the only known B abortus isolate whose growth is inhibited by erythritol. The B abortus B19 strain is an eryCD double mutant. The defect in B19 was complemented in trans by plasmids containing the complete ery region and by plasmids with Tn1725 insertions in eryA, eryB and eryD. Plasmids with Tn1725 insertions in eryC were the only ones that failed to complement the Ery phenotype of B19 [PMID:16177356]. Allelic exchange mutants in eryC of Brucella suis were erythritol sensitive in vitro with a MIC of 1 to 5 mM of erythritol. Their multiplication in macrophage-like cells was 50 to 90- fold reduced , but complementation of the mutant restored wild-type levels of intracellular multiplication and the capacity to use erythritol as a sole carbon source. In vivo, the eryC mutant colonized the spleens of infected BALBc mice to a significantly lower extent than the wild type and the complemented strain. Interestingly, eryC mutants that were in addition spontaneously erythritol tolerant nevertheless exhibited wild-type-like intramacrophagic and intramurine replication. In conclusion, erythritol was not an essential carbon source for the pathogen in the macrophage host cell but that the inactivation of the eryC gene significantly reduced the intramacrophagic and intramurine fitness of B suis [PMID:16177356].
MUTATION: EryB is an erythritol phosphate dehydrogenase. The vaccine strain B abortus B19 is the only known B abortus isolate whose growth is inhibited by erythritol. The B abortus B19 strain is an eryCD double mutant. The defect in B19 was complemented in trans by plasmids containing the complete ery region and by plasmids with Tn1725 insertions in eryA, eryB and eryD. Plasmids with Tn1725 insertions in eryC were the only ones that failed to complement the Ery phenotype of B19 [PMID:16177356]. The B. suis eryB mutant by Tn5 transposon mutagenesis was attenuated in the human macrophage -like THP-1 cells. This mutant is sensitive to erythritol and mimics the erythritol sensitive response of the B19 strain [PMID:16177356].
nickel-binding periplasmic protein precursor
sugar phosphate isomerase/epimerase IolE
iron(III)-binding periplasmic protein precursor
SN-glycerol-3-phosphate transport system permease UGPA
spermidine/putrescine-binding periplasmic protein
ribonucleotide reductase stimulatory protein
HAD superfamily protein involved in N-acetyl-glucosamine catabolism
pyruvate dehydrogenase complex repressor
bactoprenol glucosyl transferase / bactoprenol apolipoprotein N-acyltransferase
MUTATION: brnQ mutant is attenuated in killing C. elegans [PMID:17307944].
branched-chain amino acid ABC transporter
MUTATION: EF0376 mutant is attenuated in killing C. elegans [PMID:17307944].
MUTATION: EF0382 mutant is attenuated in killing C. elegans [PMID:17307944].
MUTATION: EF0737 mutant is attenuated in killing C. elegans [PMID:17307944].
MUTATION: EF0861 mutant is attenuated in killing C. elegans [PMID:17307944].
MUTATION: bopD mutant has delayed colonization in murine intestinal tract [PMID:16834772].
LacI family sugar-binding transcriptional regulator
MUTATION: bps (srtC) mutant is attenuated in mice [PMID:17785477].
MUTATION: EF1302 mutant is attenuated in killing C. elegans [PMID:17307944].
MUTATION: EF1513 mutant is attenuated in killing C. elegans [PMID:17307944].
MUTATION: EF1542 mutant is attenuated in killing C. elegans [PMID:17307944].
MUTATION: recQ-1 mutant is attenuated in killing C. elegans and is attenuated in mice [PMID:17307944].
MUTATION: psr mutant is attenuated in killing C. elegans [PMID:17307944].
MUTATION: thyA mutant is attenuated in killing C. elegans [PMID:17307944].
MUTATION: EF1590 mutant is attenuated in killing C. elegans and is attenuated in mice [PMID:17307944].
protease synthase and sporulation negative regulatory protein pai 1
MUTATION: phrB mutant is attenuated in killing C. elegans and is attenuated in mice [PMID:17307944].
MUTATION: scrB mutant is avirulent in C. elegans and attenuated in mice [PMID:17307944]. MUTATION: scrB-1 mutant is attenuated in killing C. elegans and is attenuated in mice [PMID:17307944].
MUTATION: scrR-1 mutant is attenuated in killing C. elegans [PMID:17307944].
MUTATION: EF1623 mutant is attenuated in killing C. elegans [PMID:17307944].
MUTATION: purL mutant is attenuated in mice [PMID:9780263].
MUTATION: EF1792 mutant is attenuated in killing C. elegans [PMID:17307944].
MUTATION: fsrB (agrBfs) mutant is attenuated in killing C. elegans and is attenuated in mice [PMID:17307944].
MUTATION: map mutant is attenuated in killing C. elegans [PMID:17307944].
MUTATION: cpsI mutant is rapidly cleared from murine cutaneous infection sites compared to the wild type [PMID:11830672].
MUTATION: EF2591 mutant is attenuated in killing C. elegans [PMID:17307944].
MUTATION: EF2598 mutant is attenuated in killing C. elegans [PMID:17307944].
PTS system beta-glucoside-specific transporter subunit IIABC
MUTATION: EF2675 mutant is attenuated in killing C. elegans [PMID:17307944].
MUTATION: EF2957 mutant is attenuated in killing C. elegans [PMID:17307944].
hexapeptide repeat-containing acetyltransferase
MUTATION: srtA mutant is attenuated in murine urinary tract infection model [PMID:20696830].
MUTATION: EF3314 deletion mutant is attenuated in attachment to HeLa cells, survival within macrophages and in a C. elegans killing model [PMID:19856273].
MUTATION: asa1 deletion mutant has reduced adherence to macrophages, and an AS negative strain had decreased survival in macrophages compared to a AS positive strain [PMID:10948103].
MUTATION: ftsZ mutant had a significantly lower growth rate than wild-type bacteria and frequently appeared as filamentous forms displaying incomplete cell division septa. The latter phenotype correlated with a deficiency in generating infectious foci on a per-genome basis compared to wild-type organisms in vero cells [PMID:19114492].
Mxi-Spa secretion machinery protein Spa33
Mxi-Spa secretion machinery protein Spa32
Mxi-Spa secretion machinery protein Spa15
MUTATION: Upon infection of ileal loops in rabbits, the ospG mutant induced a stronger inflammatory response than the wild-type strain, indicating that OspG negatively controls the host innate response induced by S. flexneri upon invasion of the epithelium [PMID:16162672].
MUTATION: ospF mutants had reduced PMN transepithelial migration when compared to wild-type infection, PMN transepithelial migration is necessary for virulence of Shigella [PMID:16988276].
MUTATION: sen deletion mutant elicited lower rises in mucosal short-circuit current than the wild type, suggesting that the senA/ospD3 gene encodes an enterotoxin of Shigella [PMID:7591128].
MUTATION: ospC1 mutants had reduced PMN transepithelial migration when compared to wild-type infection, PMN transepithelial migration is necessary for virulence of Shigella [PMID:16988276].
MUTATION: ospB mutants had reduced PMN transepithelial migration when compared to wild-type infection, PMN transepithelial migration is necessary for virulence of Shigella [PMID:19017275].
MUTATION: mxiN mutants were unable to invade HeLa cells [PMID:12864857].
Mxi-Spa secretion machinery protein MxiN
Mxi-Spa secretion machinery protein MxiM
Mxi-Spa secretion machinery protein MxiK
Mxi-Spa secretion machinery protein MxiJ
Mxi-Spa secretion machinery protein MxiA
IpgC, cytoplasmic chaperone for IpaB and IpaC
MUTATION: ipgB2 mutant had entry into polarized cells reduced by 70% compared to the wild-type [PMID:18316224].
MUTATION: The invasiveness of the ipgB1 mutant was decreased to less than 50% of the wild-type level (100%) in a gentamicin protection or plaque forming assay [PMID:15849186].
secreted by the Mxi-Spa machinery, function unknown
invasion plasmid antigen, secreted by the Mxi-Spa secretion machinery
IpaC, secreted by the Mxi-Spa secretion machinery, required for entry into epithelial cells
IpaB, secreted by the Mxi-Spa secretion machinery, required for entry into epithelial cells
MUTATION: phoN2/apy mutant is attenuated for growth in HeLa and Caco-2 cells [PMID:16452446].
PhoN2 (Apy), periplasmic phosphatase, apyrase, ATP diphosphohydrolase
Mxi-Spa secretion machinery protein MxiH
Mxi-Spa secretion machinery protein MxiI
MUTATION: bfpA deletion mutant of EPEC was less virulent in humans than the wild-type EPEC [PMID:9641917].
MUTATION: bfpB mutant EPEC is unable to form BFP which is a major virulence factor of EPEC [PMID:8932312].
MUTATION: bfpE mutant strain of EPEC fails to form detectable BFP and fails to carry out autoaggregation and localized adherence to HEp-2 epithelial cells in tissue culture [PMID:11443077].
MUTATION: bfpF mutant colonized the human intestine but was about 200-fold less virulent than the wild-type EPEC [PMID:9641917].
MUTATION: mutation in bfpP blocks BFP biogenesis and localized adherence to host cells by EPEC [PMID:10762251].
MUTATION: bfpT (perA) disruption mutant of EPEC was less virulent in humans than the wild-type EPEC [PMID:9641917].
MUTATION: yopP mutant is attenuated in mice [PMID:10216859].
MUTATION: lcrV mutant is attenuated in mice [PMID:10216859].
MUTATION: yscR mutant is attenuated in mice [PMID:10216859].
MUTATION: yscU mutant is attenuated in mice [PMID:10216859].
MUTATION: virG mutant is attenuated in mice [PMID:10216859].
MUTATION: virF mutant is attenuated in mice [PMID:10216859].
MUTATION: yscC mutant is attenuated in mice [PMID:10216859].
MUTATION: yscL mutant is attenuated in mice [PMID:10216859].
MUTATION: sycH mutant is attenuated in mice [PMID:12654794].
MUTATION: yadA mutant is attenuated in mice [PMID:12654794].
MUTATION: purN mutant is attenuated in chickens and mice [PMID:12933901].
MUTATION: dsbB mutant is attenuated in mice [PMID:10873488].
MUTATION: PM0081 mutant is attenuated in chickens [PMID:12933901].
MUTATION: dcaA mutant is attenuated in chickens and mice [PMID:12933901].
MUTATION: guaA mutant is attenuated in mice [PMID:10873488].
MUTATION: ponC mutant is attenuated in chickens [PMID:12933901].
MUTATION: purF mutant is attenuated in mice [PMID:10873488].
MUTATION: pyrF mutant is attenuated in chickens [PMID:12933901].
Other designations: orotidine 5'-phosphate decarboxylase
MUTATION: PM0855 mutant is attenuated in chickens and mice [PMID:12933901].
MUTATION: PM1069 mutant is attenuated in chickens [PMID:12933901].
MUTATION: dam mutant is attenauted in mice [PMID:12904568].
MUTATION: PM1294 mutant is attenuated in chickens and mice [PMID:12933901].
MUTATION: deoC mutant is attenuated in chickens [PMID:12933901].
MUTATION: atpG mutant is attenuated in mice [PMID:10873488].
MUTATION: gmhA mutants have reduced epithelial cell invasion and reduced transepithelial migration of PMN compared to the wild type [PMID:15182677].
pathogenicity island 2 secreted effector protein
surface presentation of antigens protein
MUTATION: STM0016 mutant is attenuated in mice [PMID:16518469].
MUTATION: STM0030 mutant is attenuated in mice [PMID:16518469].
MUTATION: STM0036 mutant is attenuated in pigs [PMID:17526851].
MUTATION: A surA mutant (BRD1115) is attenuated in BALB/c mice [PMID:10678914].
MUTATION: dgt mutant is attenuated in mice [PMID:16518469].
deoxyguanosinetriphosphate triphosphohydrolase
MUTATION: yagS mutant is attenuated in mice [PMID:16518469].
MUTATION: STM0298 mutant is attenuated in mice [PMID:16518469].
MUTATION: safA mutant is attenuated in pigs [PMID:17526851].
MUTATION: dinP mutant is attenuated in mice [PMID:16518469].
MUTATION: STM0328 mutant is attenuated in pigs [PMID:17526851].
MUTATION: stbD mutant is attenuated in pigs [PMID:17526851].
MUTATION: stbC mutant is attenuated in pigs [PMID:17526851].
MUTATION: yaiU mutant is attenuated in pigs [PMID:17526851].
MUTATION: sbcD mutant is attenuated in pigs [PMID:17526851].
MUTATION: STM0438 mutant is attenuated in pigs [PMID:17526851].
MUTATION: cyoB mutant is attenuated in mice [PMID:16518469].
cytochrome o ubiquinol oxidase subunit I
MUTATION: clpP mutant is attenuated in mice [PMID:7618105].
MUTATION: lon mutant is attenuated in mice [PMID:12496146].
MUTATION: ybaJ mutant is attenuated in pigs [PMID:17526851].
MUTATION: gip mutant is attenuated in mice [PMID:16518469].
MUTATION: STM0520 mutant is attenuated in mice [PMID:16518469].
MUTATION: allD mutant is attenuated in mice [PMID:16518469].
MUTATION: fimA mutants are attenuated in mice and swine [PMID:14573666].
MUTATION: fimH mutants were impaired in binding and internalization of HeLa cells [PMID:17379714].
MUTATION: fimW mutant is attenuated in mice [PMID:16518469].
MUTATION: STM0557 mutant is attenuated in pigs [PMID:17526851].
MUTATION: rfbl mutant is attenuated in pigs [PMID:17526851].
MUTATION: nfnB mutant is attenuated in mice [PMID:16518469].
MUTATION: fepA mutant is attenuated in pigs [PMID:17526851].
MUTATION: citC mutant is attenuated in pigs [PMID:17526851].
MUTATION: dpiA mutant is attenuated in pigs [PMID:17526851].
MUTATION: cspE mutant is attenuated in mice [PMID:16518469].
MUTATION: hscC mutant is attenuated in pigs [PMID:17526851].
MUTATION: STM0723 mutant is attenuated in mice [PMID:16518469].
polysaccharide/polyol phosphate ABC transporter ATPase
MUTATION: A tolA mutant is attenuated in mice [PMID:19118362].
cell envelope integrity inner membrane protein TolA
MUTATION: STM0765 mutant is attenuated in pigs [PMID:17526851].
MUTATION: slrP mutant is attenuated in mice [PMID:10569754].
MUTATION: ybhM mutant is attenuated in pigs [PMID:17526851].
MUTATION: mdfA mutant is attenuated in pigs [PMID:17526851].
MUTATION: pflA mutant is attenuated in pigs [PMID:17526851].
pyruvate formate lyase-activating enzyme 1
MUTATION: STM0972 mutant is attenuated in mice [PMID:16518469].
MUTATION: focA mutant is attenuated in mice [PMID:16518469].
MUTATION: STM1002 mutant is attenuated in mice [PMID:16518469].
MUTATION: sseI mutant is attenuated in mice [PMID:16518469].
required for maintaining a long-term systemic infection
Other designations: secreted effector protein
MUTATION: pyrD mutant is attenuated in pigs [PMID:17526851].
MUTATION: ycbG mutant is attenuated in mice [PMID:16518469].
MUTATION: pipA mutants have reduced epithelial cell invasion and reduced transepithelial migration of PMN compared to the wild type [PMID:15182677].
MUTATION: pipC mutant is attenuated in pigs [PMID:17526851].
MUTATION: sopB mutants induce significantly less fluid accumulation in bovine ligated ileal loops than the wild-type [PMID:12065528].
MUTATION: pipD mutant is attenuated in mice [PMID:16518469].
MUTATION: copS mutant is attenuated in mice [PMID:16518469].
MUTATION: csgF mutant is attenuated in mice [PMID:16518469].
MUTATION: csgD mutant is attenuated in mice [PMID:16518469].
DNA-binding transcriptional regulator CsgD
MUTATION: csgC mutant is attenuated in mice [PMID:16518469].
MUTATION: solA mutant is attenuated in mice [PMID:16518469].
MUTATION: sifA mutants are attenuated in mice and don't induce Salmonella-produced filaments in epithelial cells [PMID:8861213].
MUTATION: pagC mutant is attenuated in mice [PMID:16518469].
virulence membrane protein PAGC precursor
MUTATION: yeaJ mutant is attenuated in mice [PMID:16518469].
MUTATION: ydjA mutant is attenuated in pigs [PMID:17526851].
PTS system N,N'-diacetylchitobiose-specific transporter subunit IIB
MUTATION: celF mutant is attenuated in pigs [PMID:17526851].
phospho-beta-glucosidase/cellobiose-6-phosphate hydrolase
MUTATION: nlpC mutant is attenuated in mice [PMID:16518469].
MUTATION: ydiK mutant is attenuated in mice [PMID:16518469].
MUTATION: ssrB mutant is attenuated in pigs [PMID:17526851].
MUTATION: ssrA mutant is attenuated in pigs [PMID:17526851].
MUTATION: ssaB mutant is attenuated in pigs [PMID:17526851].
MUTATION: ssaC mutant is attenuated in murine macrophages [PMID:16113260].
MUTATION: ssaD mutant is attenuated in pigs [PMID:17526851].
MUTATION: ssaE mutant is attenuated in mice [PMID:16518469].
MUTATION: sseB mutant is attenuated in mice [PMID:16518469].
MUTATION: sseE mutant is defective for replication in murine macrophages [PMID:16113260].
MUTATION: sseF mutant is defective for replication in murine macrophages [PMID:16113260].
MUTATION: sseG mutant has a defect in replication in murine macrophages [PMID:16113260].
MUTATION: ssaG mutant is attenuated in pigs [PMID:17526851].
type III secretion system apparatus protein
MUTATION: ssaJ mutant is attenuated in pigs [PMID:17526851].
needle complex inner membrane lipoprotein
MUTATION: ssaK mutant is attenuated in pigs [PMID:17526851].
MUTATION: ssaL mutant is attenuated in pigs [PMID:17526851].
MUTATION: ssaN mutant is attenuated in mice [PMID:16518469].
MUTATION: ssaQ mutant is attenuated in pigs [PMID:17526851].
MUTATION: ssaR mutant is attenuated in pigs [PMID:17526851].
MUTATION: ssaS mutant is attenuated in pigs [PMID:17526851].
type III secretion system apparatus protein SsaS
MUTATION: ssaU mutant is attenuated in mice [PMID:16518469].
MUTATION: slyA mutant is attenuated in mice [PMID:8290552].
MUTATION: ydgF mutant is attenuated in mice [PMID:16518469].
MUTATION: STM1527 mutant is attenuated in pigs [PMID:17526851].
MUTATION: STM1549 mutant is attenuated in mice [PMID:16518469].
MUTATION: yddX mutant is attenuated in mice [PMID:16518469].
MUTATION: nmpC (ompD) mutant is attenuated in swine [PMID:17296750].
MUTATION: STM1583 mutant is attenuated in mice [PMID:16518469].
MUTATION: sseJ mutants are defective in intracellular replication in cultured epithelial cells and are attenuated in mice [PMID:16177296].
Other designations: secreted effector protein SseJ
MUTATION: ynaF mutant is attenuated in pigs [PMID:17526851].
MUTATION: STM1668 mutant is attenuated in pigs [PMID:17526851].
MUTATION: STM1669 mutant is attenuated in mice [PMID:16518469].
MUTATION: yciH mutant is attenuated in mice [PMID:16518469].
MUTATION: yciF mutant is attenuated in pigs [PMID:17526851].
MUTATION: hns mutant is attenuated in pigs [PMID:17526851].
global DNA-binding transcriptional dual regulator H-NS
MUTATION: fadD mutant is attenuated in mice [PMID:16518469].
MUTATION: cspC mutant is attenuated in mice [PMID:16518469].
MUTATION: sopE2 mutant has reduced ability to invade HeLa cells compared to wild-type [PMID:10735884].
MUTATION: pagO mutant is attenuated in pigs [PMID:17526851].
MUTATION: STM1864 mutant is attenuated in pigs [PMID:17526851].
MUTATION: pagK mutant is attenuated in pigs [PMID:17526851].
MUTATION: znuABC mutant is attenuated in mice [PMID:21219981].
high-affinity zinc transporter periplasmic protein
high-affinity zinc transporter membrane protein
MUTATION: A ruvB mutant is attenuated in mice [PMID:20670908].
MUTATION: STM1934 mutant is attenuated in mice [PMID:16518469].
MUTATION: sirA mutant is defective for intracellular replication, invasion of epithelial cells and defective in murine macrophages [PMID:16113260].
MUTATION: fliQ mutant is attenuated in mice [PMID:7618105].
MUTATION: yeeI mutant is attenuated in pigs [PMID:17526851].
MUTATION: sopA mutants induce significantly less fluid accumulation in bovine ligated ileal loops than the wild-type [PMID:12065528].
MUTATION: udg mutant is attenuated in mice [PMID:16518469].
MUTATION: rfbP mutant is attenuated in mice [PMID:16518469].
undecaprenol-phosphate galactosephosphotransferase/O-antigen transferase
MUTATION: rfbK mutant is attenuated in pigs [PMID:17526851].
MUTATION: rfbM mutant is attenuated in mice [PMID:7618105].
MUTATION: rfbN mutant is attenuated in pigs [PMID:17526851].
MUTATION: rfbH mutant is attenuated in pigs [PMID:17526851].
MUTATION: rfbI mutant is attenuated in pigs [PMID:17526851].
CDP-6-deoxy-delta-3,4-glucoseen reductase
MUTATION: rfbC mutant is attenuated in mice [PMID:16518469].
MUTATION: rfbA mutant is attenuated in mice [PMID:16518469].
MUTATION: rfbD mutant is attenuated in mice [PMID:7618105].
MUTATION: rfbB mutant is attenuated in mice [PMID:7618105].
MUTATION: galF mutant is attenuated in mice [PMID:16518469].
UTP--glucose-1-phosphate uridylyltransferase subunit GalF
MUTATION: wcaM mutant is attenuated in mice [PMID:16518469].
MUTATION: wcaE mutant is attenuated in pigs [PMID:17526851].
MUTATION: yegQ mutant is attenuated in mice [PMID:16518469].
MUTATION: STM2137 mutant is attenuated in mice [PMID:16518469].
MUTATION: stcD mutant is attenuated in mice [PMID:16518469].
MUTATION: stcC mutant is attenuated in mice [PMID:16518469].
MUTATION: bglX mutant is attenuated in mice [PMID:16518469].
periplasmic beta-D-glucoside glucohydrolase
MUTATION: yeiA mutant is attenuated in mice [PMID:16518469].
MUTATION: STM2197 mutant is attenuated in mice [PMID:16518469].
MUTATION: STM2243 mutant is attenuated in pigs [PMID:17526851].
MUTATION: STM2245 mutant is attenuated in pigs [PMID:17526851].
MUTATION: A gyrA-cpxA-rpoB Salmonella Typhimurium mutant was attenuated in pigs [PMID:15542179].
MUTATION: STM2373 mutant is attenuated in mice [PMID:16518469].
MUTATION: ppk mutant is attenuated in pigs [PMID:17526851].
MUTATION: STM2503 mutant is attenuated in pigs [PMID:17526851].
MUTATION: shdA mutants exhibit a shedding defect in mice [PMID:12540539].
MUTATION: ratB mutant are unable to colonize the cecum in mice, but are still able to colonize the eyer's patches, mesenteric lymph nodes, and spleen of mice [PMID:12540539].
MUTATION: cadB mutant is attenuated in pigs [PMID:17526851].
MUTATION: STM2574 mutant is attenuated in pigs [PMID:17526851].
MUTATION: yfhL mutant is attenuated in mice [PMID:16518469].
MUTATION: STM2585 mutant is attenuated in mice [PMID:16518469].
MUTATION: clpB mutant is attenuated in pigs [PMID:17526851].
MUTATION: STM2680 mutant is attenuated in mice [PMID:16518469].
MUTATION: STM2689 (bapA) mutant strain showed a significantly lower colonization rate at the intestinal cell barrier and consequently a decreased efficiency for organ invasion compared with the wild-type strain in mice [PMID:16313619].
MUTATION: fljA mutant is attenuated in pigs [PMID:17526851].
MUTATION: mig-14 mutants are cleared by mice compared to the wild type which is fatal to mice in the doses given [PMID:11083839].
MUTATION: ygaE mutant is attenuated in mice [PMID:16518469].
MUTATION: hilC mutants have decreased invasion of HEp-2 cells compared to the wild type [PMID:10320584].
MUTATION: orgB mutants are attenuated in their ability to invade HEp-2 cells [PMID:10816487].
MUTATION: prgI mutants are attenuated in their ability to invade HEp-2 cells [PMID:10816487].
MUTATION: prgH mutants are attenuated in their ability to invade HEp-2 cells [PMID:10816487].
MUTATION: hilD mutants have decreased invasion of HEp-2 cells compared to the wild type [PMID:10320584].
MUTATION: hilA mutants have reduced ability to invade HEp-2 cells and to colonize murine Peyer’s patches [PMID:10456944].
MUTATION: sptP mutants have reduced epithelial cell invasion and reduced transepithelial migration of PMN compared to the wild type. Competition experiments indicate that sptP mutants fail to colonize the spleen of mice when coinoculated with wild-type S. enterica [PMID:15182677].
protein tyrosine phosphatase/GTPase activating protein
MUTATION: sipA mutants have a decreased invasion of MDCK cells as compared to the wild type [PMID:19046340].
MUTATION: sicA mutants are unable to invade cultured epithelial cells [PMID:7608068].
surface presentation of antigens protein SpaS
surface presentation of antigens protein SpaP
surface presentation of antigens protein SpaO
MUTATION: invC mutants are attenuated in chicks infected orally but not intraperitoneally [PMID:9087319].
MUTATION: In the absence of InvB, the ΔsopB ΔsopE2 strain was severely defective in its ability to invade cultured intestinal cells, indicating that InvB is required for the translocation of SopE into host cells [PMID:14645290].
MUTATION: invA mutants are attenuated in chicks infected orally but not intraperitoneally [PMID:9087319].
MUTATION: invG mutants have reduced ability to enter into cultured epithelial cells [PMID:7997169].
MUTATION: invF mutants have reduced ability to enter into cultured epithelial cells [PMID:7997169].
needle complex outer membrane lipoprotein precursor
MUTATION: sopD mutants induce significantly less fluid accumulation in bovine ligated ileal loops than the wild-type [PMID:12065528].
MUTATION: barA mutant is inefficient in invasion of HEp-2 epithelial cells [PMID:16113260].
MUTATION: kdul mutant is attenuated in pigs [PMID:17526851].
MUTATION: STM3036 mutant is attenuated in mice [PMID:16518469].
MUTATION: STM3128 mutant is attenuated in mice [PMID:16518469].
MUTATION: STM3192 mutant is attenuated in mice [PMID:16518469].
DNA-binding transcriptional activator TdcA
MUTATION: sspA mutants are not able to cause lethal infection in calves, however these mutants are still able to cause diarrhea in calves [PMID:10816458].
MUTATION: fkpA mutant exhibited a reduced ability to survive intracellularly in J774.A1 cells [PMID:9009347].
FKBP-type peptidyl-prolyl cis-trans isomerase
MUTATION: slyD mutant is attenuated in pigs [PMID:17526851].
MUTATION: crp deletion mutants are attenuated in mice [PMID:3291452].
MUTATION: Lack of Dam methylation causes severe attenuation in animal models. Defects in virulence in dam mutants include such as impaired expression and secretion of invasion proteins, reduced cytotoxicity on M cells , inefficient colonization of Peyer’s patches and mesenteric lymph nodes, sensitivity to components of innate immunity, envelope instability and changes in LPS expression [PMID:19762965].
MUTATION: envZ mutant is attenuated in mice [PMID:7618105].
MUTATION: STM3602 mutant is attenuated in pigs [PMID:17526851].
MUTATION: yiaO mutant is attenuated in mice [PMID:16518469].
periplasmic dicarboxylate-binding protein
MUTATION: STM3690 mutant is attenuated in mice [PMID:16518469].
MUTATION: yibD mutant is attenuated in mice [PMID:16518469].
MUTATION: rfaK mutant is attenuated in pigs [PMID:17526851].
MUTATION: rfaZ mutant is attenuated in mice [PMID:16518469].
lipopolysaccharide core biosynthesis protein
MUTATION: rfaB mutant is attenuated in pigs [PMID:17526851].
MUTATION: rfaG mutant is attenuated in pigs [PMID:17526851].
MUTATION: sugR mutant is attenuated in pigs [PMID:17526851].
MUTATION: rhuM mutant has diminished capacity to invade cultured epithelial cells compared to the wild type [PMID:15182677].
MUTATION: misL mutant is attenuated in mice [PMID:15948960].
MUTATION: marT mutant is attenuated in mice [PMID:16518469].
MUTATION: mgtC mutant is attenuated in pigs [PMID:17526851].
MUTATION: ibpA mutant is attenuated in mice [PMID:16518469].
MUTATION: torD mutant is attenuated in mice [PMID:16518469].
MUTATION: An atpA mutant is attenuated in mice [PMID:19649318].
MUTATION: STM3907 mutant is attenuated in mice [PMID:16518469].
MUTATION: ppiC mutant is attenuated in mice [PMID:16518469].
MUTATION: trxA mutant is attenuated in mice [PMID:19884329].
MUTATION: wecE mutant is attenuated in pigs [PMID:17526851].
MUTATION: yigF mutant is attenuated in pigs [PMID:17526851].
MUTATION: yigG mutant is attenuated in mice [PMID:16518469].
MUTATION: STM3980 mutant is attenuated in mice [PMID:16518469].
MUTATION: cpxA mutants are attenuated in mice [PMID:15271926].
MUTATION: yneB mutant is attenuated in mice [PMID:16518469].
autoinducer-2 (AI-2) modifying protein LsrF
MUTATION: yneC mutant is attenuated in mice [PMID:16518469].
autoinducer-2 (AI-2) modifying protein LsrG
DNA-directed RNA polymerase subunit beta
MUTATION: STM4155 mutant is attenuated in mice [PMID:16518469].
MUTATION: STM4158 mutant is attenuated in mice [PMID:16518469].
MUTATION: yjaG mutant is attenuated in mice [PMID:16518469].
MUTATION: purD mutant is attenuated in mice [PMID:7618105].
MUTATION: metA mutant is attenuated in mice [PMID:16518469].
MUTATION: STM4198 mutant is attenuated in pigs [PMID:17526851].
MUTATION: STM4206 mutant is attenuated in mice [PMID:16518469].
MUTATION: STM4260 mutant is attenuated in mice [PMID:16518469].
MUTATION: STM4261 mutant is attenuated in mice [PMID:16518469].
MUTATION: yjdB mutant is attenuated in mice [PMID:16518469].
MUTATION: STM4316 mutant is attenuated in pigs [PMID:17526851].
MUTATION: phoN mutant is attenuated in mice [PMID:16518469].
MUTATION: yjeJ mutant is attenuated in mice [PMID:16518469].
MUTATION: A poxA mutant is attenuated in mice [PMID:9826331].
MUTATION: STM4433 mutant is attenuated in pigs [PMID:17526851].
MUTATION: idnK mutant is attenuated in mice [PMID:16518469].
MUTATION: sthA mutant is attenuated in mice [PMID:16518469].
MUTATION: PSLT072 mutant is attenuated in mice [PMID:16518469].
MUTATION: spvR mutant is attenuated in mice [PMID:7618105].
MUTATION: spvB mutants are attenuated in mice [PMID:11260464]. TOXIN: spvB encodes an ADP-ribosylating enzyme that uses actin as a substrate and depolymerizes actin filaments when expressed in CHO cells [PMID:11260464].
MUTATION: spvA mutant is attenuated in mice [PMID:7618105].
MUTATION: The spvBC-bearing plasmid was capable of replacing all of the spv genes, as well as the entire virulence plasmid, of serovar Typhimurium for causing systemic infection in BALB/c mice after subcutaneous, but not oral, inoculation. A point mutation in the spvBC plasmid preventing translation but not transcription of spvC eliminated the ability of the plasmid to confer virulence [PMID:11443102].
MUTATION: spvD mutant is attenuated in mice [PMID:7618105].
MUTATION: pefC mutants are attenuated in mice [PMID:8557375].
MUTATION: rck mutants reduces serum resistance and eukaryotic cell invasion [PMID:8675302].
Other designations: occlusion-derived virus envelope protein
MUTATION: traT mutants have altered membrane permeability and are sensitive to hydrophobic antibiotics [PMID:3323837].
conjugal transfer surface exclusion protein TraT
Other designations: type III secretion system protein
MUTATION: knock out mutant showed growth inhibition in yeast and mammalian cells [PMID:18830244].
MUTATION: Higher doses of VGF- virus than WT virus were required for intracranial lethality in mice and for production of skin lesions in rabbits. Thus, expression of the VGF gene is important to the virulence of vaccinia virus [PMID:3339716].
similar to viral growth factor (C11R vaccinia virus Copenhagen)
Other designations: CPXV021 protein or CPXV VGF protein
tegument protein; phosphorylates nuclear egress lamina protein; mediates phosphorylation of HDAC1 and HDAC2 and other cellular and viral proteins
Other designations: serine/threonine protein kinase US3
contains a RING finger; disrupts ND10; proteasome-dependent degradation of several cellular proteins
Other designations: ubiquitin E3 ligase ICP0
MUTATION: A thymidine kinase-deficient mutant (B8-D53) showed no detectable thymidine kinase-inducing activity and was attenuated in calves [PMID:2994602].
modulates transactivating tegument protein VP16; RNA-binding protein
Other designations: tegument protein VP13/14
MUTATION: Strain A of the virus has a mutation in the glycoprotein E gene, and is avirulent in calves [PMID:8023552]. MUTATION: the Za strain of BHV1 is attenuated by a deletion of the gE gene and is used as a live attenuated vaccine [PMID:8023552].
type 1 membrane protein; contains a signal peptide; complexed with envelope glycoprotein I to form an Fc-receptor
Other designations: envelope glycoprotein E
MUTATION: deletion of ORF10 reduced viral titers and the extent of cutaneous lesions significantly in SCIDhu skin xenografts in vivo [PMID:16537591].
Other designations: transactivating tegument protein VP16
MUTATION: An E mutant is attenuated in hamsters [PMID:18463152].
MUTATION: The L gene from the attenuated Edmonston strain replaced the L protein of a virulent clinical isolate IC-B of the measles virus and grown in Vero cells. The recombinant viruses had had growth disadvantage in CD150-positive lymphoid B95a cells compared to the wild type IC-B [PMID:16306593].
large subunit of RNA dependent RNA polymerase (RdRp); RNA synthesis, capping, and polyadenylation
Other designations: large polymerase protein
MUTATION: The M gene from the attenuated Edmonston strain replaced the M protein of a virulent clinical isolate IC-B of the measles virus and grown in Vero cells. The recombinant viruses had had growth disadvantage in CD150-positive lymphoid B95a cells compared to the wild type IC-B [PMID:16306593].
hydrophobic protein on inner leaflet of membrane; inhibits transcription
MUTATION: V and C protein mutants (encoded by the P gene) are attenuated in Rhesus monkeys [PMID:18385234].
subunit of RNA dependent RNA polymerase (RdRp); chaperone for Measles virus nucleocapsid protein
Other designations: C protein|V protein|phosphoprotein
Other designations: nonstructural protein 1
Other designations: nonstructural protein 2
MUTATION: A glycoprotein G deletion in bovine respiratory syncytial virus(rBRSV) and recombinant rBRSV was attenuated in calves [PMID:12414977].
Other designations: attachment glycoprotein
MUTATION: A mutation in the non-virion protein of IHNV causes attenuated growth in rainbow trout [PMID:15047826].
MUTATION: The N protein of the virulent Nishigahara strain was placed in the background of the avirulent Ni-CE rabies virus to create a chimeric rabies virus. The chimera killed mice after intracereberal inoculation, compared to the Ni-CE strain which is avirulent in mice [PMID:17010466].
MUTATION: The P protein of the virulent NIshigahara strain was placed in the background of the avirulent Ni-CE rabies virus to create a chimeric rabies virus. The chimera killed mice after intracereberal inoculation, compared to the Ni-CE strain which is avirulent in mice [PMID:1489854].
MUTATION: The M protein of the virulent NIshigahara strain was placed in the background of the avirulent Ni-CE rabies virus to create a chimeric rabies virus. The chimera killed mice after intracereberal inoculation, compared to the Ni-CE strain which is avirulent in mice [PMID:17010466].
MUTATION: G protein from the virulent Nishigahara strain was recombined with the RC-HL genome an attenuated rabies virus. The chimeric virus killed mice when given by intracerebral inoculation. The RC-HL rabies virus normally is attenuated in mice, and therefore the G protein can be considered a virulence factor of rabies virus [PMID:11533176].
MUTATION: A SIV nef mutant is attenuated in rhesus monkeys [PMID:1470917].
MUTATION: Although the T2-minus recombinant myxoma virus grew normally in tissue culture, upon infection of susceptible rabbits the viral disease was observed to be significantly attenuated [PMID:1651597].
MUTATION: Feline immunodeficiency virus (FIV) made defective in the accessory gene ORF-A were previously shown to be greatly attenuated in its ability to replicate in lymphocytes but to grow normally or near normally in other cell types [PMID:15680433].
MUTATION: A vif mutant in feline immunodeficiency virus was attenuated in cats [PMID:10891409].
MUTATION: toxB mutants had attenuated adherence to Caco-2 cells [PMID:11598035].
MUTATION: espP mutant is attenuated in calves [PMID:17451446].
MUTATION: VCA0688 mutant is attenuated in mice [PMID:11952899].
MUTATION: VCA0910 mutant is attenuated in mice [PMID:11952899].
MUTATION: VCA0006 mutant is attenuated in mice [PMID:11952899].
MUTATION: VCA0903 mutant is attenuated in mice [PMID:11952899].
MUTATION: VCA0896 mutant is attenuated in mice [PMID:11952899].
MUTATION: VCA0600 mutant is attenuated in mice [PMID:11952899].
MUTATION: VCA0578 mutant is attenuated in mice [PMID:11952899].
MUTATION: VCA0530 mutant is attenuated in mice [PMID:11952899].
MUTATION: VCA0583 mutant is attenuated in mice [PMID:11952899].
MUTATION: VCA0930 mutant is attenuated in mice [PMID:11952899].
MUTATION: VC0028 mutant was attenuated in mice [PMID:11952899].
MUTATION: cyaA mutant is attenuated in mice [PMID:11952899].
MUTATION: VC2426 (pilD/vcpD) mutant is attenuated in mice [PMID:9781884].
MUTATION: VC2433 mutant is attenuated in mice [PMID:11952899].
cyclic 3',5'-adenosine monophosphate phosphodiesterase
MUTATION: tolC mutant is deficient in intestinal colonization of mice [PMID:11402016].
MUTATION: VC2437 mutant is attenuated in mice [PMID:11952899].
MUTATION: barA mutant is attenuated in mice [PMID:11952899].
MUTATION: VC2455 mutant is attenuated in mice [PMID:11952899].
MUTATION: acpS mutant is attenuated in mice [PMID:11952899].
MUTATION: recO mutant is attenuated in mice [PMID:11952899].
MUTATION: carB mutant is attenuated in mice [PMID:11952899].
carbamoyl phosphate synthase large subunit
MUTATION: VC2390 mutant is attenuated in mice [PMID:11952899].
MUTATION: aceF mutant is attenuated in mice [PMID:11952899].
MUTATION: VC2295 mutant is attenuated in mice [PMID:11952899].
Na(+)-translocating NADH-quinone reductase subunit A
MUTATION: VC2320 mutant is attenuated in mice [PMID:11952899].
MUTATION: VC2290 mutant is attenuated in mice [PMID:11952899].
Na(+)-translocating NADH-quinone reductase subunit F
MUTATION: VC2291 mutant is attenuated in mice [PMID:11952899].
Na(+)-translocating NADH-quinone reductase subunit E
MUTATION: VC2206 (flgP) mutant is defective in intestinal colonization of mice [PMID:17981980].
MUTATION: fur mutant is attenuated in mice [PMID:11952899].
MUTATION: fabG mutant is attenuated in mice [PMID:11952899].
MUTATION: VC2030 mutant is attenuated in mice [PMID:11952899].
MUTATION: aphA mutant is attenuated in mice [PMID:11489126].
histone deacetylase/AcuC/AphA family protein
MUTATION: VC2052 mutant is attenuated in mice [PMID:11952899].
cytochrome c-type biogenesis protein CcmF
MUTATION: VC2067 mutant is attenuated in mice [PMID:11952899].
MUTATION: tolB mutant is attenuated in mice [PMID:11952899].
MUTATION: VC1887 mutant is attenuated in mice [PMID:11952899].
MUTATION: VC1771 mutant is attenuated in mice [PMID:11952899].
MUTATION: mukB mutant is attenuated in mice [PMID:11952899].
MUTATION: VC1715 mutant is attenuated in mice [PMID:11952899].
MUTATION: VC1716 mutant is attenuated in mice [PMID:11952899].
MUTATION: VC1639 mutant is attenuated in mice [PMID:11952899].
MUTATION: VC1675 mutant is attenuated in mice [PMID:11952899].
MUTATION: galM mutant is attenuated in mice [PMID:11952899].
MUTATION: VC1595 mutant is attenuated in mice [PMID:11952899].
MUTATION: VC0257 mutant is attenuated in mice [PMID:11952899].
MUTATION: VC0965 mutant is attenuated in mice [PMID:11952899].
MUTATION: VC1004 mutant is attenuated in mice [PMID:11952899].
MUTATION: VC1012 mutant is attenuated in mice [PMID:11952899].
MUTATION: VC0251 mutant is attenuated in mice [PMID:11952899].
acyl protein synthase/acyl-CoA reductase RfbN
MUTATION: rfbL mutant is attenuated in mice [PMID:11952899].
MUTATION: VC0250 mutant is attenuated in mice [PMID:11952899].
MUTATION: luxO mutant is defective in colonization of infant mouse intestine [PMID:11854465].
MUTATION: VC1075 mutant is attenuated in mice [PMID:11952899].
MUTATION: VC1098 mutant is attenuated in mice [PMID:11952899].
MUTATION: VC0051 mutant is attenuated in mice [PMID:11952899].
MUTATION: VC0032 mutant is attenuated in mice [PMID:11952899].
MUTATION: VC0036 mutant is attenuated in mice [PMID:11952899].
MUTATION: tcpP mutant is attenuated in mice [PMID:11952899].
toxin co-regulated pilus biosynthesis protein P
MUTATION: VC0828 mutant is attenuated in mice [PMID:11952899].
MUTATION: VC0831 mutant is attenuated in mice [PMID:11952899].
toxin co-regulated pilus biosynthesis outer membrane protein C
MUTATION: VC0835 mutant is attenuated in mice [PMID:11952899].
toxin co-regulated pilus biosynthesis protein T
MUTATION: tcpE mutant is attenuated in mice [PMID:11952899].
toxin co-regulated pilus biosynthesis protein E
MUTATION: tcpF mutant is attenuated in mice [PMID:11952899].
toxin co-regulated pilus biosynthesis protein F
MUTATION: VC0869 mutant is attenuated in mice [PMID:11952899].
MUTATION: VC0247 mutant is attenuated in mice [PMID:11952899].
lipopolysaccharide/O-antigen transport protein
MUTATION: VC0244 mutant is attenuated in mice [PMID:11952899].
MUTATION: VC1162 mutant is attenuated in mice [PMID:11952899].
MUTATION: VC1173 mutant is attenuated in mice [PMID:11952899].
MUTATION: VC0192 mutant is attenuated in mice [PMID:11952899].
MUTATION: VC0212 mutant is attenuated in mice [PMID:11952899].
MUTATION: VC0242 mutant is attenuated in mice [PMID:11952899].
MUTATION: VC0243 mutant is attenuated in mice [PMID:11952899].
MUTATION: VC0239 mutant is attenuated in mice [PMID:11952899].
MUTATION: VC1380 mutant is attenuated in mice [PMID:11952899].
MUTATION: VC0238 mutant is attenuated in mice [PMID:11952899].
hexapaptide repeat-containing transferase
MUTATION: VC0260 mutant is attenuated in mice [PMID:11952899].
MUTATION: hfq mutant fails to colonize the suckling mouse intestine [PMID:15225327].
MUTATION: VC0459 mutant is attenuated in mice [PMID:11952899].
MUTATION: VC0468 mutant is attenuated in mice [PMID:11952899].
MUTATION: VC2506 mutant is attenuated in mice [PMID:11952899].
MUTATION: sspA mutant is attenuated in mice [PMID:11952899].
MUTATION: VC0259 mutant is attenuated in mice [PMID:11952899].
lipopolysaccharide biosynthesis protein RfbV
MUTATION: VC0485 mutant is attenuated in mice [PMID:11952899].
MUTATION: VC0125 mutant is attenuated in mice [PMID:11952899].
MUTATION: VC0596 mutant is attenuated in mice [PMID:11952899].
MUTATION: VC0639 mutant is attenuated in mice [PMID:11952899].
MUTATION: VC0647 mutant is attenuated in mice [PMID:11952899].
MUTATION: VC2544 mutant is attenuated in mice [PMID:11952899].
MUTATION: VC2347 mutant is attenuated in mice [PMID:11952899].
MUTATION: VC2660 mutant is attenuated in mice [PMID:11952899].
MUTATION: VC0724 mutant is attenuated in mice [PMID:11952899].
MUTATION: phoU mutant is attenuated in mice [PMID:11952899].
MUTATION: VC0523 mutant is attenuated in mice [PMID:11952899].
glycerol-3-phosphate acyltransferase PlsY
MUTATION: VC0095 mutant is attenuated in mice [PMID:11952899].
MUTATION: VC0132 mutant is attenuated in mice [PMID:11952899].
MUTATION: spaC (DIP2010) mutant has diminished adherence to human pharyngeal epithelial cells [PMID:17376076].
MUTATION: spaB (DIP2011) mutant has diminished adherence to human pharyngeal epithelial cells [PMID:17376076].
MUTATION: Inactivation of the aroA gene highly attenuates B. bronchiseptica, severely impairing its ability to colonize and survive in the respiratory tract of mice [PMID:12009288].
MUTATION: A dnt mutant in Bordetella Bronchiseptica was attenuated in guinea pigs [PMID:3182989].
MUTATION: A double mutant strain of Bordetella Bronchiseptica lacking adenylate cyclase(cyaA gene) and type III secretion(bscN gene) is attenuated in mice [PMID:17452472].
bifunctional hemolysin-adenylate cyclase
MUTATION: attenuated in mice [PMID:16495546].
MUTATION: mutant was 30% to 40% less efficient at adhering to CHO cells and to human HeLa cells compared to parent [PMID:1988935].
MUTATION: cyaC mutant had toxin activities less than 1% of the wild type [PMID:1987161].
cyclolysin-activating lysine-acyltransferase
MUTATION: mutant strain was unable to multiply as fast and is avirulent in murine respiratory models [PMID:1614333].
MUTATION: attenuated in infant mice [PMID:11348687].
MUTATION: tonB exb double mutant is attenuated in mice [PMID:10722583].
siderophore-mediated iron transport protein
MUTATION: tonB exbB double mutant is attenuated in mice [PMID:10722583].
MotA/TolQ/ExbB proton channel family protein
MUTATION: deletion mutant displayed a significant defect in respiratory tract colonization in mice [PMID:15155640].
MUTATION: deletion mutant avirulent in the infant mouse model [PMID:2877614].
MUTATION: deletion mutant showed significantly reduced ability to colonize in the trachea of a mouse respiratory infection model [PMID:1350044].
MUTATION: lpxL1 deficient mutant displayed defect in infection of human macrophages [PMID:17967899].
lipid A biosynthesis lauroyl acyltransferase
MUTATION: TcfA mutation reduced bacteria by 10 fold compared to parent strain [PMID:7476158].
MUTATION: deletion mutant attenuated in mice [PMID:18762220].
MUTATION: mutant showed reduced colonization in mice compared to wild-type [PMID:11348687].
MUTATION: mutant displayed reduced virulence, and lost ability to express some Bvg+-phase factors [PMID:9194696].
MUTATION: mutant strain showed growth inhibition and reduced colonization [PMID:9573202].
virulence factors transcription regulator
MUTATION: FhaB mutation abolished bacterial adhesion to Chinese Hamster Ovary cells [PMID:8415678].
MUTATION: deletion mutant showed a decrease in cytotoxicity and secretion of proteins in vitro as well as reduced colonization in the trachea of a rat infection model [PMID:9663681].
MUTATION: FimD mutant strain showed reduced colonization in the lungs and trachea of mice [PMID:11348687].
MUTATION: mutation strongly reduced binding to CHO cells [PMID:8415678].
MUTATION: fauA mutant is attenuated in mice [PMID:17724074].
MUTATION: Viruses lacking UL41 (vhs) are attenuated in mice [PMID:10729135].
Other designations: tegument host shutoff protein
MUTATION: A thymidine kinase-deficient (UL23) mutant was found to be attenuated in mice [PMID:212476].
tegument serine/threonine protein kinase
MUTATION: ICP0 null HSV-1 mutant is avirulent in mice [PMID:16764725].
MUTATION: ICP34.5 mutant virus is avirulent in mice [PMID:12663769].
virion protein; inhibits stress-induced translational arrest; related to eIF2 phosphatase regulatory subunit GADD34; binds protein phosphatase 1 to form a holoenzyme capable of dephosphorylating eIF2-alpha
Other designations: neurovirulence protein ICP34.5
possibly envelope-associated; interacts with cytokeratin 18
MUTATION: A HSV-1 strain with mutatinos in the gD gene is attenuated for virulence in mice [PMID:18243431].
type 1 membrane protein; contains a signal peptide; binds cell surface receptors
Other designations: envelope glycoprotein D|envelope glycoprotein J
dsRNA-binding protein; antagonizes PKR; inhibits stress-induced translational arrest
Other designations: tegument protein US11
type 1 membrane protein; contains a signal peptide; complexed with envelope glycoprotein E to form an Fc-receptor
Other designations: envelope glycoprotein I
MUTATION: An HSV-1 gE (US8) deletion strain is attenuated in mice [PMID:18562543].
MUTATION: A UL29 mutant is attenuated in mice [PMID:8289372].
Other designations: single-stranded DNA-binding protein
MUTATION: A M. avium relA mutant is attenuated in calves and goats [PMID:21565243].
MUTATION: ugd mutant had defects in intracellular survival in macrophages [PMID:16790745].
MUTATION: psn (fyuA) mutant is unable to grow on iron-deficient media at 37 degrees C [PMID:7896707].
MUTATION: lpxM (msbB) mutant is attenuated in mice and guinea pigs [PMID:17913308].
MUTATION: lcrH (sycD) mutant is avirulent in mice [PMID:2707857].
putative Yop negative regulation/targeting component YopD
putative cytotoxic effector protein YopT
putative protein-tyrosine phosphatase Yop effector YopH
MUTATION: yopK (yopQ) mutant has an increased LD50 dose in mice, and infected mice died after 5 days as compared to mice infected with the wild type died after just 3 days [PMID:3002984].
putative virulence determinant protein YopQ
putative targeted effector protein kinase YpkA
putative type III secretion protein YscH
putative outer membrane virulence protein YopE
MUTATION: ymt mutants are unable to block X. cheopsis fleas and have low survival rates in the flea gut [PMID:11976454].
MUTATION: mutant strain showed reduction in motility, attenuated in mice [PMID:16213668].
MUTATION: deletion mutant avirulent in mice [PMID:9791184].
MUTATION: a recQ mutant was attenuated in mice [PMID:11254558]
MUTATION: attenuated in mice [PMID:14638794].
MUTATION: a gtca mutant showed diminished ability to invade intestinal epithelial cells, was attenuated in mice [PMID:11254558].
cell wall teichoic acid glycosylation protein GtcA
MUTATION: virulence of a agrA mutant was attenuated in a mouse [PMID:12874326].
MUTATION: attenuated virulence in spleens of mice [PMID:12940983].
MUTATION: mutant strain showed reduced bacterial escape from phagosomes of macrophages and virulence in mice [PMID:10760131].
MUTATION: mutant attenuated in mice, impaired cell to cell spread in host cells [PMID:19451247].
MUTATION: sigB mutant is less virulent in mice than the parental strain [PMID:10960085].
MUTATION: fpuA (GBAA4766) mutant is attenuated in mice [PMID:20487286].
MUTATION: GBAA0552 mutant is attenuated in mice [PMID:19768119].
MUTATION: phnX (GBAA1340) mutant is attenuated in mice [PMID:19768119].
MUTATION: lef mutant is non-lethal in mice [PMID:1910002].
MUTATION: BAS4929 (ccpA) mutant is attenuated in mice [PMID:20971911].
MUTATION: mprF mutant is attenuated in mice [PMID:11342591].
MUTATION: virB4 mutant is attenuated in the capacity to grow in co-culture with, invade into, or survive within endothelial cells [PMID:15049812].
MUTATION: pacC mutant is attenuated in mice [PMID:15686555].
similar to S54308 DNA binding protein - Emericella nidulans
MUTATION: skn7 deletion mutant is attenuated in mice [PMID:19693686].
MUTATION: CgAtg11 mutant is killed more efficiently by macrophages than the wildtype [PMID:19811500].
MUTATION: cnb1 mutant is attenuated in mice [PMID:20100876].
MUTATION: crz1 mutant is attenuated in mice [PMID:20100876].
MUTATION: Two Hantaan virus strains, clone 1 (cl-1), which is virulent in newborn mice, and its attenuated mutant (mu11E10), were used to examine the pathogenesis of Hantaan virus infection in a mouse model and identify virus factors relating to virulence. After subcutaneous inoculation of newborn BALB/c mice, cl-1 caused fatal disease with high viral multiplication in peripheral organs, but mu11E10 produced nonfatal infection with a low level of virus multiplication. Sequence comparison detected a single deduced amino acid change (cl-1 Ile to mu11E10 Thr) at amino acid number 515 in glycoprotein G1. In mouse brain microvascular endothelial cells in vitro, viruses possessing a cl-1-derived M segment grew more rapidly than viruses containing a mu11E10-derived M segment. These results suggest that the single amino acid change in the glycoprotein alters peripheral growth, which affects invasion of the central nervous system in mice [PMID:10982372].
MUTATION: A UL41 mutant is highly attenuated in mice [PMID:20448414].
MUTATION: A UL50 mutant is attenuated in pigs [PMID:9228681].
MUTATION: A gp50+gp63 deletion mutant in Pseudorabies virus was attenuated in pigs [PMID:8178562].
Other designations: tegument protein UL21
MUTATION: A gp50 null mutant is attenuated in pigs [PMID:8178562].
type 2 membrane protein; tegument-associated; localizes envelope proteins
Other designations: membrane protein US9
MUTATION: a thymidine kinase PRV mutant is attenuated in pigs [PMID:12488067]. MUTATION: A UL23 mutant, in combination with mutations in glycoproteins G and E, is attenuated in raccoons [PMID:12488067].
MUTATION: US3 mutant is attenuated in pigs [PMID:7975253].
MUTATION: yopM mutant has attenuated colonization of mouse tissues [PMID:20368345].
MUTATION: yscU mutant is attenuated in mice [PMID:11292689].
MUTATION: yscH mutant is attenuated in mice [PMID:11292689].
yscH, yopR, lcrP; type III secretion protein
MUTATION: yopH mutant is attenuated in mice [PMID:12542470].
yopH; protein-tyrosine phosphatase Yop effector
MUTATION: cls mutant is attenuated in mice [PMID:11292689].
MUTATION: ddhC mutant is attenuated in mice [PMID:11292689].
MUTATION: gmd mutant is attenuated in mice [PMID:11292689].
MUTATION: ksgA mutant is attenuated in mice [PMID:11292689].
MUTATION: A phoP mutant in Yersinia pseudotuberculosis (Yptb) was attenuated in mice [PMID:17194509].
MUTATION: wzx mutant is attenuated in mice [PMID:11292689].
MUTATION: hfq mutant is attenuated in mice [PMID:20231416].
MUTATION: ldsA (lpg0742) mutant is attenuated in mouse macrophages [PMID:16997951].
MUTATION: cpxR mutant is attenuated in mouse macrophages [PMID:16997951].
MUTATION: mip mutants are approximately 50- to 100-fold less infective for A. castellanii and for human mononuclear phagocytes in vitro compared with their isogenic Mip-positive parental strains [PMID:7591108].
macrophage infectivity potentiator (Mip)
MUTATION: lpg1905 mutant is attenuated in macrophages and human alveolar cells [PMID:17388784].
ectonucleoside triphosphate diphosphohydrolase I
MUTATION: sidJ (lpg2155) mutant is attenuated in macrophages [PMID:17101649].
MUTATION: icmX mutant is attenuated in guinea pigs [PMID:10393970].
intracellular multiplication protein IcmX
MUTATION: enhC mutant is attenuated in mouse macrophages [PMID:18549456].
MUTATION: dotB mutant is attenuated in guinea pigs [PMID:10393970].
MUTATION: dotA mutant is unable to replicate in mouse macrophages [PMID:16997951].
defect in organelle trafficking protein DotA
MUTATION: feoB mutant is attenuated in human macrophages [PMID:12228295].
MUTATION: ptsP mutant is attenuated in guinea pigs [PMID:11447151].
phosphoenolpyruvate protein phosphotransferase PtsP
MUTATION: icmG mutant is attenuated in guinea pigs [PMID:10393970].
MUTATION: icmB mutant is attenuated in guinea pigs [PMID:10393970].
MUTATION: rpoS mutant is defective in intracellular replication in its protozoan host [PMID:19218380].
stationary phase specific sigma factor RpoS
MUTATION: djlA mutant is attenuated in mouse macrophages [PMID:16997951].
MUTATION: rtxA mutant is attenuated in mice and does not replicate as well as the wild type in monocytes [PMID:11119544].
structural toxin protein (hemagglutinin/hemolysin) RtxA
MUTATION: BMAA0739 (tssE) is attenuated in hamsters [PMID:17555434].
MUTATION: BMAA0743 (tssB) mutant is attenuated in hamsters [PMID:17555434].
MUTATION: virG mutant is avirulent in hamsters [PMID:15377793].
MUTATION: BMAA0742 (hcp1) mutant is attenuated in hamsters [PMID:17555434].
MUTATION: boaA (BMAA0649) mutant has reduced adherence to human epithelial cell lines, specifically HEp2 (laryngeal cells) and A549 (type II pneumocytes), as well as to cultures of normal human bronchial epithelium (NHBE) compared to the wild type [PMID:20920184].
MUTATION: BMAA0740 (tssD) mutant is attenuated in hamsters [PMID:17555434].
MUTATION: BPSL1039 mutant is attenuated in mice [PMID:17189432].
MUTATION: BPSL1263 (cdpA) mutant has a 3-fold reduction in invasion of human lung epithelial cells and a 6-fold reduction in cytotoxicity on human macrophage cells [PMID:20194589].
MUTATION: lipB mutant is attenuated in mice [PMID:16714590].
MUTATION: hisF mutant is attenuated in mice and has intracellular growth defects [PMID:16714590].
MUTATION: wcbN mutant is attenuated in mice [PMID:17189432].
D-glycero-d-manno-heptose 1,7-bisphosphate phosphatase
MUTATION: BPSL2825 mutant is attenuated in mice [PMID:16714590].
MUTATION: BPSL0634 mutant is attenuated in mice [PMID:17189432].
MUTATION: Inactivation of gene BPSL1528 leads to impaired actin tail formation, reduced intracellular survival, and high-grade attenuation of virulence in mice [PMID:16714590].
MUTATION: aroB mutant is attenuated in mice [PMID:17189432].
MUTATION: trpG mutant is attenuated in mice [PMID:17189432].
MUTATION: purM mutant is avirulent in mice [PMID:20404077].
MUTATION: purN mutant is attenuated in mice [PMID:16714590].
MUTATION: wcbB mutant is attenuated in mice [PMID:17189432].
capsular polysaccharide glycosyltransferase biosynthesis protein
MUTATION: wcbC mutation is attenuated in mice [PMID:11119486].
capsular polysaccharide biosynthesis/export protein
MUTATION: nth mutant is attenuated in mice [PMID:17189432].
MUTATION: BPSLO872 (mviN) mutant displayed an increased LD50 value in the hamster infection model and a loss of the ability to invade human lung epithelial cells [PMID:17110975].
MUTATION: BPSL0395 mutant is attenuated in mice [PMID:16714590].
MUTATION: wzm mutant is attenuated in mice [PMID:17189432].
capsular polysaccharide export ABC transporter transmembrane protein
MUTATION: ilvI mutant is attenuated in mice [PMID:12183585].
MUTATION: fliC mutant is attenuated in mice [PMID:12654773].
MUTATION: wcbD mutant is attenuated in mice [PMID:17189432].
capsule polysaccharide export ABC transporter transmembrane protein
MUTATION: BPSL3147 mutant is attenuated in mice [PMID:17189432].
MUTATION: serC mutant is attenuated in mice [PMID:16997946].
MUTATION: recA mutant is attenuated in mice [PMID:17189432].
MUTATION: BPSL1876 mutant is attenuated in mice [PMID:16988221].
MUTATION: boaB (BPSL1705) mutant has reduced attachment to respiratory cells, and a boaA boaB double mutant was attenuated in murine macrophages [PMID:20920184].
MUTATION: leuB mutant is attenuated in mice [PMID:17189432].
MUTATION: BPSS1509 mutant is attenuated in mice [PMID:16714590].
MUTATION: sctU mutant is attenuated in hamsters [PMID:15621426].
MUTATION: BPSS2074 (lpfA) mutant is attenuated in hamsters [PMID:16987331].
senescence marker protein-30 (SMP-30) family protein
MUTATION: bipD mutant was attenuated in mice [PMID:16714590].
MUTATION: BPSS1539 mutant is attenuated in mice [PMID:16714590].
MUTATION: bopE mutant is attenuated in mice [PMID:15289563].
MUTATION: bsaZ mutant is attenuated in mouse macrophages [PMID:12410823].
MUTATION: BPSS0067 mutant is attenuated in mice [PMID:16988221].
MUTATION: BPSS2053 mutant had reduced microbial adherence to human epithelial cells [PMID:18927621].
MUTATION: pmll mutant is attenuated in mice [PMID:15060030].
MUTATION: plaB mutant is attenuated in guinea pigs [PMID:20153694].
MUTATION: rtxA mutant is attenuated in mice and doesn't grow as well in monocytes as the wild type [PMID:11119544].
MUTATION: flaA mutant is less invasive of HL-60 cells than the wild type [PMID:11254565].
MUTATION: fur mutant has attenuated intracellular growth within U937 cell monolayers [PMID:12228295].
MUTATION: sdhA mutant is attenuated in mouse macrophages [PMID:17124169].
defect in organelle trafficking protein DotB (ATPase)
MUTATION: iraA mutant is attenuated in guinea pigs [PMID:10678909].
MUTATION: lvgA mutant is attenuated in guinea pigs [PMID:12704109].
MUTATION: rpoS mutant has defective intracellular replication in its protozoan host [PMID:19218380].
MUTATION: fur mutant is attenuated in growth within U937 cell monolayers[PMID:8975903].
MUTATION: sodC mutant is attenuated in mice [PMID:19577637].
MUTATION: sopE mutant is attenuated in mice [PMID:19577637].
MUTATION: FTT0054 mutant is attenuated in mouse spleen [PMID:17389372].
MUTATION: sodB mutant is attenuated in mice [PMID:16923916].
MUTATION: a sthA mutant was attenuated for infection in a mouse lung [PMID:17420240]
soluble pyridine nucleotide transhydrogenase
MUTATION: a sucC mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: sucB mutant is attenuated in mouse spleen [PMID:17389372].
dihydrolipoamide succinyltransferase component of 2-oxoglutarate dehydrogenase complex
MUTATION: a sucD mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: ksgA mutant is attenuated in mouse spleen [PMID:17389372].
MUTATION: surA mutant is attenuated in mouse spleen [PMID:17389372].
MUTATION: a FTT0105c mutant was attenuated for infection of a mouse lung [PMID:17420240]
MUTATION: a tet mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a glgB mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION; FTT0134 mutant is attenuated in mouse spleen [PMID:17389372].
MUTATION: a tig mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a FTT1441 mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a lon mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: lpnB mutant is attenuated in mouse spleen [PMID:17389372].
MUTATION: FTT1489 mutant is attenuated in mouse spleen [PMID:17389372].
MUTATION: a FTT1400c mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a FTT0975 mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a isftu1 mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a metlQ mutant was attenuated for infection in a mouse lung [PMID:17420240]
D-methionine ABC transporter permease/substrate-binding protein
MUTATION: a glpe mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a aroG mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a aspC1 mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: cdd mutant is attenuated in mouse spleen [PMID:17389372].
MUTATION: a bioD mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a bioC mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a bipA mutant was attenuated for infection in a mouse lung [PMID:17420240]
GTP binding translational elongation factor Tu and G family protein
MUTATION: a glgC mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: bioB mutant is attenuated in mouse spleen [PMID:17389372].
MUTATION: a capB mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a bioF mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: trpG mutant is attenuated in mouse spleen [PMID:17389372].
MUTATION: a FTT0708 mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: FTT0685c mutant is attenuated in mouse spleen [PMID:17389372].
MUTATION: FTT0667 mutant is attenuated in mouse spleen [PMID:17389372].
MUTATION: FTT0645c mutant is attenuated in mouse spleen [PMID:17389372].
MUTATION: carA mutant is attenuated in mouse spleen [PMID:17389372].
MUTATION: FTT1633c mutant is attenuated in mouse spleen [PMID:17389372].
MUTATION: FTT1640c mutant is attenuated in mouse spleen [PMID:17389372].
MUTATION: a FTT1314c mutant was attenuated for infection in a mouse lung [PMID:17420240]
Type IV pili fiber building block protein
MUTATION: a FTT1611 mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: FTT1334c mutant is attenuated in mouse spleen [PMID:17389372].
MUTATION: FTT0615c mutant is attenuated in mice [PMID:17389372].
MUTATION: FTT0589 mutant is attenuated in mouse spleen [PMID:17389372].
MUTATION: FTT0584 mutant is severely attenuated in mice [PMID:17389372].
MUTATION: an iglA mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: prfC mutant is attenuated in mouse spleen [PMID:17389372].
MUTATION: a FTT1117c mutant was attenuated for infection in a mouse lung [PMID:17420240]
isochorismatase hydrolase family protein
MUTATION: mtn mutant is attenuated in mouse spleen [PMID:17389372].
5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
MUTATION: a FTT1103 mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a FTT1102 mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a rpsU mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: cadA mutant is attenuated in mouse spleen [PMID:17389372].
MUTATION: a yibK mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: pcs mutant is attenuated in mouse spleen [PMID:17389372].
MUTATION: ruvB mutant is attenuated in mouse spleen [PMID:17389372].
MUTATION: FTT0295 mutant is attenuated in mouse spleen [PMID:17389372].
MUTATION: pdpA mutant is attenuated in mouse spleen [PMID:17389372].
MUTATION: pdpB mutant is attenuated in mouse spleen [PMID:17389372].
MUTATION: pdxY mutant is attenuated in mouse spleen [PMID:17389372].
MUTATION: FTT0256c mutant is attenuated in mice [PMID:17389372].
MUTATION: a FTT0209c mutant was attenuated for infection in a mouse lung [PMID:17420240]
periplasmic solute binding family protein
MUTATION: pgm mutant is attenuated in mouse spleen [PMID:17389372].
MUTATION: FTT0509c mutant is attenuated in mouse spleen [PMID:17389372].
MUTATION: sdhC mutant is attenuated in mouse spleen [PMID:17389372].
MUTATION: FTT0455c mutant is attenuated in mouse spleen [PMID:17389372].
dolichyl-phosphate-mannose-protein mannosyltransferase family protein
MUTATION: a parB mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: FTT0453c mutant is attenuated in mouse spleen [PMID:17389372].
MUTATION: a FTT0443 mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: FTT0398c mutant is mildly attenuated in mice [PMID:17389372].
MUTATION: FTT0399c mutant is attenuated in mouse spleen [PMID:17389372].
MUTATION: pcp mutant is attenuated in mouse spleen [PMID:17389372].
MUTATION: FTT1258 mutant is attenuated in mouse spleen [PMID:17389372].
MUTATION: htpG mutant is strongly attenuated in mice [PMID:17389372].
MUTATION: a deaD mutant was attenuated for infection in a mosue lung [PMID:17420240]
MUTATION: dedA1 mutant is attenuated in mouse spleen [PMID:17389372].
MUTATION: deoB mutant is attenuated in mouse spleen [PMID:17389372].
MUTATION: a deoD mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a fumA mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: cca mutant is attenuated in mouse spleen [PMID:17389372].
MUTATION: dsbB mutant is attenuated in mouse spleen [PMID:17389372].
MUTATION: gcvH mutant is attenuated in mouse spleen [PMID:17389372].
MUTATION: a elbB mutant was attenuated for infection in a mouse lung [PMID:17420240]
isoprenoid biosynthesis protein with amidotransferase-like domain
MUTATION: an iglB mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: xerC mutant is attenuated in mouse spleen [PMID:17389372].
MUTATION: galE mutant is attenuated in mouse spleen [PMID:17389372].
MUTATION: an iglC mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: rluC mutant is attenuated in mouse spleen [PMID:17389372].
ribosomal large subunit pseudouridine synthase C
MUTATION: a rluB mutant was attenuated for infection in a mouse lung [PMID:17420240]
ribosomal large subunit pseudouridine synthase B
MUTATION: ribB mutant is attenuated in mouse spleen [PMID:17389372].
MUTATION: ribA mutant is attenuated in mouse spleen [PMID:17389372].
riboflavin biosynthesis protein ribA/GTP-cyclohydrolase II
MUTATION: relA mutant is attenuated in mouse spleen [PMID:17389372].
MUTATION: recB mutant is attenuated in mouse spleen [PMID:17389372].
MUTATION: a recA mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: rbfA mutant is attenuated in mouse spleen [PMID:17389372].
MUTATION: qseC mutant is attenuated in mouse spleen [PMID:17389372].
MUTATION: pyrH mutant is attenuated in mouse spleen [PMID:17389372].
MUTATION: pyrF mutant is attenuated in mouse spleen [PMID:17389372].
MUTATION: pyrD mutant is attenuated in mouse spleen [PMID:17389372].
MUTATION: pyrB mutant is attenuated in mouse spleen [PMID:17389372].
MUTATION: putA mutant is attenuated in mouse spleen [PMID:17389372].
bifunctional proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase
MUTATION: purN mutant is attenuated in mouse spleen [PMID:17389372].
MUTATION: purM mutant is attenuated in mouse spleen [PMID:17389372].
MUTATION: purL mutant is attenuated in mouse spleen [PMID:17389372].
MUTATION: purH mutant is attenuated in mouse spleen [PMID:17389372].
MUTATION: purF mutant is attenuated in mouse spleen [PMID:17389372].
MUTATION: purE mutant is attenuated in mouse spleen [PMID:17389372].
phosphoribosylaminoimidazole carboxylase catalyic subunit
MUTATION: FTT1151c mutant is attenuated in mouse spleen [PMID:17389372].
MUTATION: a FTT0918 mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a FTT0910 mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: FTT0905 mutant is attenuated in mouse spleen [PMID:17389372].
MUTATION: FTT0903 mutant is attenuated in mouse spleen [PMID:17389372].
MUTATION: a secE mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: FTT0891 mutant is attenuated in mouse spleen [PMID:17389372].
MUTATION: a FTT0881c mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: FTT1129c mutant is attenuated in mouse spleen [PMID:17389372].
MUTATION: a FTT0843 mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a FTT1747 mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: apt mutant is attenuated in mouse spleen [PMID:17389372].
MUTATION: phoH mutant is attenuated in mouse spleen [PMID:17389372].
MUTATION: a FTT0901 mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a lpxB mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: FTT0800 mutant is attenuated in mouse spleen [PMID:17389372].
MUTATION: FTT0799 mutant is attenuated in mouse spleen [PMID:17389372].
glycosyl transferases group 1 family protein
MUTATION: FTT0798 mutant is attenuated in mice [PMID:17389372].
MUTATION: FTT0793 mutant is attenuated in mouse spleen [PMID:17389372].
MUTATION: FTT0790 mutant is attenuated in mouse spleen [PMID:17389372].
MUTATION: FTT0797 mutant is attenuated in mouse spleen [PMID:17389372].
MUTATION: a FTT0807 mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a FTT0759 mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: FTT0792 mutant is attenuated in mouse spleen [PMID:17389372].
MUTATION: FTT0748 mutant is strongly attenuated in mice [PMID:17389372].
MUTATION: fadD1 mutant is attenuated in mouse spleen [PMID:17389372].
MUTATIONO: a fadB/acbP mutant was attenuated for infection in a mouse lung [PMID:17420240]
bifunctional 3-hydroxacyl-CoA dehydrogenase/acyl-CoA-binding protein
MUTATION: a feoB mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a cphB mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: cphA mutant is attenuated in mouse spleen [PMID:17389372].
MUTATION: a uvrA mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: cyoB mutant is attenuated in mouse spleen [PMID:17389372].
MUTATION: a cyoC mutant was attenuated for infection in a mouse lung [PMID:17420240]
cytochrome O ubiquinol oxidase subunit III
MUTATION: cyoD mutant is attenuated in mice [PMID:17389372].
cytochrome O ubiquinol oxidase subunit IV
MUTATION: folD mutant is attenuated in mouse spleen [PMID:17389372].
bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/5,10-methylene-tetrahydrofolate cyclohydrolase
MUTATION: a wbtA mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a FTT1416c mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a rpsA mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a rpoA2 mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a rpmJ mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a rpmA mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a rplY mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: rplW mutant is attenuated in mouse spleen [PMID:17389372].
MUTATION: a rplT mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a fopA mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: rplQ mutant is attenuated in mouse spleen [PMID:17389372].
MUTATION: rplD mutant is attenuated in mouse spleen [PMID:17389372].
MUTATION: FTT1048c mutant is mildly attenuated in mice [PMID:17389372].
MUTATION: FTT1047c mutant is attenuated in mouse spleen [PMID:17389372].
MUTATION: a FTT1015 mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a secA mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: wbtD mutant is attenuated in mouse spleen [PMID:17389372].
MUTATION: a wbtF mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: wbtG mutant is attenuated in mouse spleen [PMID:17389372].
MUTATION: wbtH mutant is attenuated in mouse spleen [PMID:17389372].
MUTATION: a katG mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: xasA mutant is attenuated in mouse spleen [PMID:17389372].
glutamate:gamma-aminobutyric acid antiporter family protein
MUTATION: xerD mutant is attenuated in mouse spleen [PMID:17389372].
MUTATION: FTT0028c mutant is attenuated in mice [PMID:17389372].
MUTATION: a FTT0029c mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: FTT0057 mutant is attenuated in mouse spleen [PMID:17389372].
MUTATION: FTT0053 mutant is attenuated in mouse spleen [PMID:17389372].
MUTATION: FTT0056c mutant is attenuated in mouse spleen [PMID:17389372].
MUTATION: a yegQ mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a FTT0101 mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: yfdH mutant is attenuated in mouse spleen [PMID:17389372].
MUTATION: a FTT1152 mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a ppiC mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: lolD mutant is attenuated in mouse spleen [PMID:17389372].
lipoprotein releasing system ABC transporter ATP-binding protein
MUTATION: FTT1238c mutant is attenuated in mouse spleen [PMID:17389372].
MUTATION: FTT1239 mutant is attenuated in mouse spleen [PMID:17389372].
MUTATION: FTT1236 mutant is attenuated in mouse spleen [PMID:17389372].
MUTATION: FTT1237 mutant is attenuated in mouse spleen [PMID:17389372].
MUTATION: a FTT1221 mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a FTTt19 mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: manB mutant is attenuated in mouse spleen [PMID:17389372].
MUTATION: a FTTr07 mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: lysA mutant is attenuated in mice [PMID:17389372].
MUTATION: ispA mutant is attenuated in mouse spleen [PMID:17389372].
MUTATION: bioA mutant is attenuated in mouse spleen [PMID:17389372].
adenosylmethionine-8-amino-7-oxononanoate aminotransferase
MUTATION: emrA1 mutant is attenuated in mouse spleen [PMID:17389372].
MUTATION: a clpP mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a capC mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a FTT1676 mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: sdaC1 mutant is attenuated in mouse spleen [PMID:17389372].
MUTATION: a yjjK mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a hflK mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a hflX mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: hisS mutant is attenuated in mouse spleen [PMID:17389372].
MUTATION: a FTT0968c mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a minD mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: FTT0945 mutant is attenuated in mouse spleen [PMID:17389372].
MUTATION: FTT0944 mutant is attenuated in mouse spleen [PMID:17389372].
MUTATION: a FTT0941c mutant was attenuated for infection in a mouse lung[PMID:17420240]
MUTATION: FTT0940c mutant is attenuated in mouse spleen [PMID:17389372].
MUTATION: FTT0928c mutant is attenuated in mouse spleen [PMID:17389372].
MUTATION: a minC mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: ampD mutant is attenuated in mouse spleen [PMID:17389372].
MUTATION: FTT1490 mutant is attenuated in mouse spleen [PMID:17389372].
MUTATION: gcvP1 mutant is attenuated in mouse spleen [PMID:17389372].
MUTATION: a clpX mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a clpB mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: gcvT mutant is attenuated in mouse spleen [PMID:17389372].
MUTATION: FTT0165c mutant is attenuated in mouse spleen [PMID:17389372].
MUTATION: a aspC2 mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a glpX mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: PEP1 mutants had a significantly reduced in vivo colonization of broiler chicks [PMID:19349427]
amino acid ABC transporter permease PEB1
MUTATION: PEB1 mutants had a significantly reduced in vivo colonization of broiler chicks [PMID:19349427]
MUTATION: PEB1 mutants had a significantly reduced in vivo colinization of broiler chickens [PMID:19349427]
amino acid ABC transporter ATP-binding protein PEB1
MUTATION: adherence of deletion mutants of jlpA to HEp-2 epithelial cells was reduced compared with that of parental C. jejuni [PMID:11251839]
MUTATION: reduce ability to adhere to human epithelial Caco-2 cells [PMID:15184581].
MUTATION: A thymidine-kinase mutant is attenuated in chickens [PMID:12021870].
MUTATION: A UL0 mutant mutant was attenuated in chickens [PMID:14645915].
MUTATION: a UL47 mutant is attenuated in chickens [PMID:17325345].
plays a role in APEC complement resistance; similar to protein family HMM PF05818
Other designations: conjugal transfer surface exclusion protein TraT
MUTATION: The divergent Pka2 catalytic subunit was found to regulate mating, haploid fruiting, and virulence factor production in serotype D strains [PMID:14871933].
MUTATION: gcn5 mutant is avirulent in mice [PMID:20581290].
MUTATION: acs1 mutant is attenuated in mice [PMID:18673460].
MUTATION: sec6 RNAi mutant strains of C. neoformans were defective in a number of virulence factors and demonstrated attenuated virulence in mice [PMID:19210702].
MUTATION: kin1 mutant is attenuated in mice [PMID:19151325].
MUTATION: ccr4 mutant is attenuated in mice [PMID:17646356].
ccr4-not transcription complex, subunit 7
MUTATION: This gene (USX1) encodes the previously identified UDP-xylose synthase. We demonstrated that it is necessary for both capsule xylosylation and C. neoformans virulence [PMID:12139628].
MUTATION: cps1 mutant is attenuated in C. elegans killing assay [PMID:17545316].
MUTATION: ras1 mutant is avirulent in rabbit model of cryptococcal meningitis [PMID:10792722].
MUTATION: snf1 mutant is attenuated in mice [PMID:18673460].
MUTATION: apt1 mutant is attenuated in mouse inhalation model of cryptococcosis [PMID:19949048].
MUTATION: Deletion of XRN1 impairs uni- and bisexual mating [PMID:25267175].
MUTATION: This gene, HEM15, is predicted to encode a ferrochelatase that catalyses the final step in haem biosynthesis from highly photoreactive porphyrins. HEM15 is regulated by light and the mutants are photosensitive and exhibit reduced virulence [PMID:20488877].
MUTATION: The Δall1 mutants of two serotypes produced a shorter exo-PS with less branching and structural complexity than the parental strains;Δall1 mutant strains manifested differences in epitope expression and significant resistance to phagocytosis [PMID:18955480][PMID:18955480].
MUTATION: ura5 mutant is attenuated in mice [PMID:1541525].
orotidine monophosphate pyrophosphorylase (URA5)
MUTATION: Analysis of cell wall composition of the AGS1 deletion mutant demonstrated complete loss of alpha glucan accompanied by a compensatory increase in chitin/chitosan and a redistribution of beta glucan between cell wall fractions. The mutants were unable to growing mouse model of infection, but caused death in nematodes [PMID:17244196].
MUTATION: gcs1 mutant is attenuated in mice [PMID:17664261].
MUTATION: mpf3 mutant is attenuated in mice [PMID:15765146].
MUTATION: prgB mutant is attenuated in rabbit model of endocarditis [PMID:18955479].
MUTATION: P13K mutant is attenuated in invasion of H69 cells [PMID:15133042].
phosphatidylinositol 3-kinase; PI3ka plus PI3Kc domains
MUTATION: parasites with blocked expression of kerp1 are attenuated in causing liver abscesses in hamsters [PMID:17711481].
lysine and glutamic acid-rich protein 1 (KERP1)
MUTATION: Ehap-a gene was silenced resulting in a nonvirulent phenotype in hamsters [PMID:18493998].
MUTATION: P36p-deficient Plasmodium berghei is attenuated in mice [PMID:17604034].
Other designations: outer membrane protein P2
deoxyadenosyl-methyltransferase; DNA adenine methyltransferase; M.HindIV
Other designations: DNA adenine methylase
MUTATION: lgtC mutant is attenuated in infant rat model [PMID:8855319].
UDP-galactose--lipooligosaccharide galactosyltransferase
MUTATION: lic3A mutant is attenuated in chinchilla [PMID:12855765].
CMP-Neu5Ac--lipooligosaccharide alpha 2-3 sialyltransferase
Other designations: RNA polymerase sigma factor RpoE
MUTATION: pgmB mutant is had reduced adherence and invasion of human bronchial epithelial cells (16HBE14) [PMID:10931302].
MUTATION: hbpA mutant is attenuated in mice [PMID:18212083].
Other designations: heme-binding protein A
MUTATION: ktkE mutant has attenuated virulence in interperitoneal infection in infant rats [PMID:7927766].
MUTATION: licD mutant is more rapidly cleared in mouse pulmonary infection than the wild type [PMID:18347044].
MUTATION: siaB mutant is attenuated in chinchillas [PMID:12855765].
CMP-N-acetylneuraminic acid synthetase; CMP-NeuNAc synthetase; CMP-sialic acid synthetase
Other designations: acylneuraminate cytidylyltransferase
MUTATION: ptsI is attenuated in mice [PMID:12949188].
Other designations: phosphoenolpyruvate-protein phosphotransferase
MUTATION: pabaA mutant is attenauted in mice [PMID:10931287].
MUTATION: areA mutant has delayed onset of pulmonary aspergillosis in mice compared to the wild type [PMID:9669338].
MUTATION: sidD mutant is attenuated in D. melanogaster [PMID:20370364].
MUTATION: crzA mutant is attenuated in mice [PMID:18298443].
MUTATION: gliP mutant is attenuated in mice immunosuppressed by hydrocortisone [PMID:17601876].
MUTATION: fos-1 is attenuated in mice [PMID:12146755].
sensor histidine kinase/response regulator Fos-1/TcsA
MUTATION: cpcA mutant is attenauted in mice [PMID:15101984].
MUTATION: laeA mutant is attenuated in mice [PMID:16151250].
MUTATION: gpaB mutant is almost avirulent in a low-dose murine inhalation model [PMID:15322014].
MUTATION: zafA mutant is attenuated in a murine model of invasive aspergillosis [PMID:17542914].
MUTATION: pes1 mutant is attenuated in Galleria mellonella model system [PMID:16759234].
MUTATION: kre2 (afmnt1) mutant is attenuated in mice [PMID:18708564].
MUTATION: cnaA mutant is attenuated in mice [PMID:16835453].
MUTATION: rhbA mutant is attenuated in mice [PMID:12704156].
MUTATION: rasB mutant is attenuated in mice [PMID:16339716].
MUTATION: pyrG mutant is avirulent in mice [PMID:8926121].
orotidine 5'-phosphate decarboxylase PyrG
MUTATION: alb1 mutant is attenauted in mice [PMID:9620950].
conidial pigment polyketide synthase PksP/Alb1
MUTATION: acuM mutant is attenuated in G. mellonella and murine models of invasive aspergillosis [PMID:21062375].
MUTATION: pkaC1 mutant is almost avirulent in a low-dose murine inhalation model [PMID:15322014].
cAMP-dependent protein kinase catalytic subunit PkaC1
MUTATION: sidA mutant is attenuated in D. melanogaster [PMID:20370364].
MUTATION: T. cruzi isolates that express and shed higher amounts of trans-sialidase are more virulent in mice [PMID:15181573].
MUTATION: smeZ mutant is attenuated in zebrafish [PMID:19223485].
MUTATION: In a murine skin infection model, an insertion mutation in the response regulator gene, trxR (M5005_Spy_1305), led to a significant reduction in lesion size, lesion severity, and lethality [PMID:18678666].
MUTATION: grab mutant is attenuated in mice when injected intraperitoneally [PMID:10336419].
protein G-related alpha 2M-binding protein
MUTATION: ccpA mutant is attenuated in mice [PMID:20333240].
MUTATION: covS mutant has reduced capacity to bind to epithelial cell layers [PMID:20507231].
MUTATION: oppA mutant caused less mortality and tissue damage than the wild-type strain when inoculated into BALB/c mice via an air pouch [PMID:15845494].
MUTATION: perR mutant is attenuated in mouse air sac model [PMID:12183543].
M protein trans-acting positive regulator (Mga)
MUTATION: sap3 mutant is attenuated in mice and guinea pigs [PMID:9284116].
MUTATION: The deletion of the CaTEC1 gene attenuates virulence of C. albicans in a systemic model of murine candidiasis [PMID:11069668].
potential TEA/ATTS domain protein; similar to TEA/ATTS domain of S. cerevisiae TEC1 (YBR083W) regulator of Ty1 expression
Other designations: potential TEA/ATTS type DNA binding protein
MUTATION: cnb1 mutants are attenuated in mice [PMID:12796287].
MUTATION: mnt1p mutant has reduced ability to adhere to human buccal epithelial cells and to rat vaginal epithelial cells, and is attenuated in guinea pig and mouse models of systemic candidosis [PMID:9636208].
mannosyltransferase similar to S. cerevisiae KTR1p
MUTATION: IRO1 mutant is attenuated in mice [PMID:16237272].
potential transcription factor; version of putative iron utilization gene IRO1 with an N terminal extension; IRO1 rescues S. cerevisiae aft1 (YGL071W) mutant although not structurally similar; 3' half is deleted in CAI4 strain
Other designations: putative transcription factor
MUTATION: csf4 (UTR2) mutant has reduction in adherence to mammalian cells and attenuated virulence in an immunocompetent mouse model of disseminated candidiasis [PMID:15042589].
MUTATION: pde2 mutant is attenuated in mice [PMID:17614954].
similar to S. cerevisiae PDE2 (YOR360C) cAMP phosphodiesterase; same as cosmid orf Ca49C10.20c
MUTATION: CaTPS2 mutant is attenuated in a mouse model of systemic infection [PMID:11895938].
trehalose-6-phosphate phosphatase; similar to S. cerevisiae TPS2 (YDR074W) involved in stress response
MUTATION: vma7 null mutant is avirulent in a mouse model of systemic candidiasis [PMID:15870472].
MUTATION: hog1 mutant is attenuated in mice [PMID:10322006].
MAP kinase involved in osmoregulation; identified by functional complementation of S. cerevisiae hog1 (YLR113W) deletion mutant.
Other designations: likely protein kinase
MUTATION: gna1 null mutant is significantly attenuated in mice [PMID:10878139].
potential glucosamine phosphate N-acetyl tranferase (GNAT family) similar to S. cerevisiae GNA1 (YFL017C) involved in UDP-N-acetylglucosamine synthesis
Other designations: potential glucosamine phosphate N-acetyl tranferase (GNAT family)
MUTATION: disruption of INT1 gene in C. albicans suppressed hyphal growth, adhesion to epithelial cells, and virulence in mice [PMID:9478896].
Integrin-like protein; potential pleckstrin homology domain; similar to S. cerevisiae BUD4
Other designations: integrin-like protein
MUTATION: CST20 mutant cells were less virulent in a mouse model for systemic candidiasis [PMID:8917571].
likely signal transduction kinase; can functionally substitute for S. cerevisiae STE20 (YHL007C) kinase involved in pheromone response pathway
Other designations: likely signal transduction kinase
MUTATION: vps4 mutant is greatly attenuated for virulence in a mouse model of disseminated candidiasis [PMID:18814053].
likely AAA ATPase similar to S. cerevisiae VPS4 (YPR173C) AAA ATPase involved in vacuolar sorting
Other designations: potential vacuolar sorting ATPase
MUTATION: pmr1 mutant was severely attenuated in virulence in a murine model of systemic infection [PMID:15843378].
MUTATION: C. albicans KRE5 homozygous mutant strains exhibit a 50% reduction in adhesion to human epithelial cells and are completely avirulent in a mouse model of systemic infection [PMID:15590817].
similar to S. pombe stress-induced UDP-glucose-glycoprotein glucosyltransferase gpt1 (SPBPJ4664.06); similar to S. cerevisiae KRE5 (YOR336W) involved in beta-1,6 glucan biosynthesis
Other designations: potential glycoprotein glucosyltransferase
MUTATION: ker1 mutant had attenuated virulence in systemic mouse infections [PMID:15289560].
MUTATION: pmt2 mutant has attenuated virulence in a mouse model of hematogenously disseminated candidiasis (HDC) [PMID:16040968].
similar to dolichyl-P-mannose:protein mannosyltransferase involved in mannosylation of serine and threonine residues
MUTATION: sod5 mutant is attenuated in mice [PMID:14617819].
one of three potential Cu/Zn superoxide dismutase genes similar to N. crassa NCU03013.1; weak similarity to S. cerevisiae SOD1 (YJR104C); contains potential signal peptide
Other designations: potential secreted Cu/Zn superoxide dismutase
MUTATION: spt3 mutant is avirulent in mice [PMID:12072450].
MUTATION: alo1 mutant is attenuated in mice [PMID:11349062].
MUTATION: pmt5 mutant was less virulent in engineered human oral mucosa (EHOM) and in a mouse model of hematogenously disseminated candidiasis (HDC) [PMID:16040968].
similar to dolichyl-P-mannose:protein mannosyltransferase involved in mannosylation of serine and threonine residues; second orf similar to PMT1
MUTATION: a sap4/sap5/sap6 null mutant is attenuated in guinea pigs and mice [PMID:9284116].
MUTATION: cmp1 (CNA1)mutant is strongly attenuated in mice [PMID:12933882].
similar to calcineurin-like protein serine/threonine protein phosphatase
MUTATION: rim8 mutant is attenuated in a mouse model of hematogenously disseminated systemic candidiasis [PMID:10992507].
positive regulator of alkaline-induced genes via proteolysis of RIM101 transcription factor; contains potential Arrestin domains; similar to S. cerevisiae RIM8 (YGL045W) Regulator of IME2
Other designations: positive regulator of alkaline-induced genes
MUTATION: hgc1 (CLN3) mutant is has markedly reduced virulence in the kidneys of systemically infected mice [PMID:15071502].
similar to S. cerevisiae cyclin-dependent protein kinase CLN2 (YPL256C) involved in re-entry into mitotic cell cycle after pheromone arrest
MUTATION: tup1 mutant is significantly reduced in the ability to invade and injure endothelial cells [PMID:10816502].
transcriptional repressor of filamentous growth; similar to S. cerevisiae TUP1 (YCR084C); eight potential WD domains
Other designations: transcriptional repressor of filamentous growth
MUTATION: CNA mutant is attenuated in mice [PMID:12753189].
potential calcineurin-like protein serine/threonine protein phosphatase
MUTATION: chs7 mutant had reduced virulence and a high clearance rate in mice [PMID:16079341].
MUTATION: sap1 mutant is attenuated in mice and guinea pigs [PMID:9284116].
MUTATION: fkh2 mutant are unable to damage human epithelial or endothelial cells in vitro [PMID:12455696].
potential forkhead-like transcription factor similar to S. cerevisiae FKH2 (YNL068C) involved in pseudohyphal growth
Other designations: potential forkhead-like transcriptional regulator
MUTATION: NOT5 mutant had reduced adherence to epithelial cells and has attenuated virulence in mice [PMID:14500538].
one of two genes similar to S. cerevisiae NOT3 (YIL038C) and NOT5 (YPR072W) components of the cytoplasmic mRNA deadenylase and CCR4-NOT transcription factor complex
Other designations: potential mRNA deadenylase and CCR4-NOT complex subunit Not5p
MUTATION: cdc10 mutant is attenuated in mice [PMID:12819094].
MUTATION: ash1p mutant is attenuated for virulence in a mouse model of disseminated candidiasis [PMID:12446785].
GATA-type Zn finger protein that asymmetrically localizes to daughter cell nucleus and to growing hyphal tips
MUTATION: Homozygous pmt1 mutants were avirulent in a mouse model of systemic infection, while heterozygous PMT1/pmt1 strains showed reduced virulence [PMID:9694829].
MUTATION: skn7 mutant is mildly attenuated in mice [PMID:15039366].
HSF-type DNA binding and Response regulator receiver domains similar to S. cerevisiae SKN1 (YHR206W) involved in osmotic stress response
Other designations: potential HSF-type DNA binding transcription factor
MUTATION: sit1(ARN1) mutant was defective in infection of a reconstituted human epithelium as a model for human oral mucosa [PMID:12183576].
ferrichrome-type siderophore transporter transcriptionally regulated in response to iron; similar to S. cerevisiae ARN1 (YHL040C)
Other designations: ferrichrome-type siderophore transporter
MUTATION: RHO1 mutant is unable to colonize murine kidneys and cause disease in mice [PMID:12702298].
Ras-like GTP-binding protein; PKC1 pathway; regulatory subunit of GSC1 glucan synthase; can functionally substitute for S. cerevisiae RHO1 (YPR165W)
Other designations: Ras family GTP-binding protein Rho1p
MUTATION: disruption of the CEK1 gene adversely affects the growth of serum-induced mycelial colonies and attenuates virulence in a mouse model for systemic candidiasis [PMID:9596738].
MAP kinase-like orf; aka CEK1; one of two protein kinase genes similar to S. cerevisiae MAP kinases FUS3 (YBL016W) and KSS1 (YGR040W) involved in pheromone signal transduction
MUTATION: deletion of one or both copies of LIG4 resulted in attenuation of virulence in a murine model of candidiasis [PMID:11119499].
ATP-dependent DNA ligase implicated in dsDNA break repair via nonhomologous end-joining
Other designations: dsDNA break repair ligase
MUTATION: yvh1 has attenuated virulence in mice [PMID:16000712].
potential dual specificity phosphatase similar to S. cerevisiae YVH1 (YIR026C) nitrogen starvation-induced tyrosine phosphatase
Other designations: potential dual specificity phosphatase
MUTATION: rim101 mutant is attenuated in a mouse model of hematogenously disseminated systemic candidiasis [PMID:10992507].
proteolytically activated regulator of alkaline-induced filamentation; zinc finger protein similar to S. cerevisiae RIM101 (YHL027W) transcriptional activator needed for entry into meiosis
Other designations: proteolytically activated regulator of alkaline-induced filamentation
MUTATION: camp65 mutants are attenuated in mice [PMID:17217426].
Mannoprotein MP65; similar to S. cerevisiae soluble cell wall protein SCW10 (YMR305C) glucosidase involved in conjugation with cellular fusion; match to COG5309, Exo-beta-1,3-glucanase (Carbohydrate transport and metabolism)
Other designations: potential glycosyl hydrolase
MUTATION: mit1(SUR1) mutant was less virulent during both the acute and chronic phases of systemic infection in mice [PMID:15347680].
mannosylation of inositolphosphorylceramide
MUTATION: pmt4 mutant is attenuated in mice [PMID:15659169].
MUTATION: mad2 mutant is attenuated in mice [PMID:12100546].
MUTATION: sap7 mutant is attenuated in an intravenous model of systemic candidiasis in mice [PMID:16177393].
MUTATION: pld1(SPO14) mutants are unable to survive in internal organs after intravenous challenge, and are not lethal for immunodeficient mice after oral challenge [PMID:15552646].
Phospholipase D:required for commitment to meiosis
MUTATION: an irs4 null mutant strain was associated with attenuated mortality, diminished tissue burdens, less extensive infections, impaired C. albicans hyphal formation and decreased kidney damage in mice [PMID:16151204].
similar to S. cerevisiae IRS4p involved in chromatin silencing at rDNA loci
MUTATION: CaNAG6 mutant is attenuated in mice [PMID:12076781].
similar to S. cerevisiae SEY1 involved in vesicular traffic in stressed cells; similarity in the N-terminal region to human interferon-induced guanylate binding protein GBP1
MUTATION: CaNAG4 mutant is attenuated in mice [PMID:12076781].
potential transporter similar to S. cerevisiae TPO3 (YPR156C) and TPO2 (YGR138C) plasma membrane polyamine transporters
Other designations: potential polyamine transporter
MUTATION: ace2 mutant is virulent in a mouse model [PMID:15255906].
potential zinc finger protein similar to S. cerevisiae ACE2 (YLR131C) cell cycle-specific transcriptional regulator of CUP1
Other designations: potential zinc finger transcription factor
MUTATION: a DAC1/NAG1/HXK1(NAG5) mutant is highly attenuated in a murine systemic candidiasis model and was less adherent to human buccal epithelial cells in vitro [PMID:11705974].
N-acetylglucosamine kinase; recognizes glucose and mannose as substrates; similar to S. cerevisiae HXK1 (YFR053C)
Other designations: N-acetylglucosamine kinase
MUTATION: a DAC1/NAG1/HXK1 mutant is highly attenuated in a murine systemic candidiasis model and was less adherent to human buccal epithelial cells in vitro [PMID:11705974].
C. albicans glucosamine-6-phosphate deaminase (EC 3.5.99.6)
MUTATION: CaNAG3 mutant is attenuated in mice [PMID:12076781].
MUTATION: Candida albicans mutants lacking ICL1 are markedly less virulent in mice than the wild type [PMID:11452311].
isocitrate lyase capable of functionally substituting for S. cerevisiae ICL1 (YER065C); gluconeogenesis
MUTATION: Mice inoculated with 10(6) CFU of the tps1/tps1 mutant did not show visible symptoms of infection 16 days after inoculation, while those similarly inoculated with wild-type cells were dead 12 days after inoculation [PMID:9683476].
trehalose-6-phosphate synthase cloned by functional complementation of a S. cerevisiae tps1 (YBR126C) mutant
MUTATION: spa2Delta exhibited no virulence in the mouse systemic candidiasis model [PMID:12940995].
MUTATION: csh3 (SHR3) mutant is attenuated is avirulent in mice [PMID:14756779].
Protein required for amino acid permeases
MUTATION: CaYHB1 mutant is still lethal in mice but has reduced virulence compared to the wild type [PMID:15189992].
one of three likely flavohemoproteins similar to S. pombe SPAC869.02c and S. cerevisiae YHB1 (YGR234W) NADPH-dependent flavohemoglobin implicated in the oxidative stress response
Other designations: likely flavohemoglobin
MUTATION: gpi7 mutant is attenuated for virulence in mice and has reduced survival in the gastrointestinal environment of mice [PMID:11994163].
N terminal fragment of fungal cell wall-specific GPI anchor synthesis protein Gpi7p; similar to of S. cerevisiae LAS21 (YJL062W); truncation due to end of contig, other end of GPI7 is at end of contig19-10020, CaP19.60
Other designations: fungal cell wall GPI anchor synthesis protein Gpi7p fragment
MUTATION: cdc11 mutant is attenuated in mice [PMID:12819094].
Septin, component of 10nm filaments of mother-bud neck
MUTATION: sit4 mutant is attenuated in mice [PMID:14731272].
calcineurin-like phosphoesterase similar to S. cerevisiae SIT4 (YDL047W) type 2A-related protein phosphatase
Other designations: potential type 2A-related protein phosphatase
MUTATION: PEX2 RNA silenced mutant of the bloodstream form rapidly dies [PMID:12077356].
Other designations: Iron transport protein
Other designations: osmolarity response regulator
energy transducer; uptake of iron, cyanocobalimin; sensitivity to phages, colicins
protein secreted by the Mxi-Spa secretion machinery
transcriptional activator required for tanscription of the ipa, mxi, and spa operons
secreted by the Mxi-Spa machinery; modulates entry of bacteria into epithelial cells
secreted by the Mxi-Spa machinery; required for entry of bacteria into epithelial cells
secreted by the Mxi-Spa secretion machinery; required for entry into epithelial cells
component of the Mxi-Spa secretion machinery, contains one transmembrane segment
component of the Mxi-Spa secretion machinery
lipoprotein, component of the Mxi-Spa secretion machinery
putative component of the Mxi-Spa secretion machinery
lipoprotein; component of the Mxi-Spa secretion machinery
similar to transcriptional activators of the AraC family
outermembrane protein of the secretin family; component of the Mxi-Spa secretion machinery
secreted by and putative component of the Mxi-Spa secretion machinery; similar to YopN (secreted by the type III secretion machinery of Yersinia enterocoltica)
innermembrane protein; component of the Mxi-Spa secretion machinery
component of the Mxi-Spa secretion machinery; putative ATPase
secreted by and component of the Mxi-Spa machinery
secreted by the Mxi-Spa secretion machinery
Other designations: invasion plasmid antigen
required for proper localization of IcsA (VirG) at the surface of bacteria
probably secreted by the Mxi-Spa secretion machinery
member of the AraC family of transcriptional activators; required for transcription of virB and icsA
MUTATION: ospE mutants had attenuated adhesion to HeLa cells than the wild-type [PMID:19489119].
SenA; probably secreted by the Mxi-Spa secretion machinery
probably secreted by the Mxi-Spa machinery
MUTATION: hlyA mutant is attenuated in calves [PMID:15731074].
MUTATION: pepX mutant is attenuated in rats [PMID:10998175].
MUTATION: cydA mutant is attenuated in rats [PMID:15813741].
cytochrome d ubiquinol oxidase, subunit II
MUTATION: murF mutant is attenuated in rats [PMID:10998175].
UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase
MUTATION: C protein alpha antigen mutant is attenuated in mice [PMID:9371832].
MUTATION: carB mutant is attenuated in rats [PMID:10998175].
MUTATION: scpB mutant had significantly reduced invasion of HEp2 and A549 human cell lines [PMID:11953377].
MUTATION: lepA mutant is attenuated in rats [PMID:10998175].
MUTATION: scrB mutant is attenuated in rats [PMID:10998175].
MUTATION: rpoE mutant is attenuated in rats [PMID:16513739].
DNA-directed RNA polymerase subunit delta
MUTATION: An isogenic strain bearing a kanamycin insertion in mtaR (cpsY) was attenuated for survival in a neonatal-rat model of sepsis and grew poorly in human plasma [PMID:14594832].
MUTATION: pepN mutant is attenuated in rats [PMID:10998175].
MUTATION: cylE mutant has decreased invasion of lung epithelial cells [PMID:11807693].
MUTATION: guaA mutant is attenuated in rats [PMID:10998175].
MUTATION: lgt mutant has a significant reduction in adherence to human endothelial cells of fetal origin [PMID:19383708].
prolipoprotein diacylglyceryl transferase
MUTATION: aroC mutant is attenuated in mice [PMID:19323044].
MUTATION: pabB mutant is attenuated in mice [PMID:19121696].
MUTATION: sctU mutant is attenuated in mice [PMID:15621426].
MUTATION: BopA mutant was attenuated in mice [PMID:16714590].
Other designations: EEV maturation protein
Other designations: IMV heparin binding surface protein
Other designations: contains mutT-like motif of NTP-phosphohydrolase for DNA repair
MUTATION: C12L mutant is attenuated in BALB/c mice when infected intranasally [PMID:12388820].
Other designations: serine protease inhibitor-like SPI-1
MUTATION: VVDeltaE3L mutant is apathogenic in mice [PMID:11134298].
Other designations: double-strand RNA-binding protein
MUTATION: Deletion of N1L results in attenuation in culture and in intracranially infected mice [PMID:20441222].
Other designations: putative virulence factor
Other designations: putative alpha aminitin-sensitive protein
Other designations: EEV membrane glycoprotein
Other designations: soluble interferon-gamma receptor-like protein
Other designations: IEV and EEV membrane glycoprotein
Other designations: IEV transmembrane phosphoprotein
MUTATION: Vaccinia virus lacking the A46R gene was attenuated in a murine intranasal model [PMID:15767367].
MUTATION: Reassortant viruses with the RRV VP4 entered cultured mouse cholangiocytes more efficiently than did those with UK VP4 [PMID:21191030].
VirG; outermembrane protein exposed to the bacterial surface by a C-terminal autotransporter domain and involved in the movement of intracellular bacteria by binding to N-WASP
SopA; outermembrane protease of the OmpP family, involved in cleavage of surface exposed IcsA
Other designations: outer membrane protease
secreted by the Mxi-Spa machinery, modulates entry of bacteria into epithelial cells
outermembrane protein of the secretin family, component of the Mxi-Spa secretion machinery
secreted by and putative component of the Mxi-Spa secretion machinery, similar to YopN (secreted by the type III secretion machinery of Yersinia enterocoltica)
innermembrane protein, component of the Mxi-Spa secretion machinery
component of the Mxi-Spa secretion machinery, putative ATPase
secreted by the Mxi-Spa machinery, required for entry of bacteria into epithelial cells
secreted by the Mxi-Spa secretion machinery, required for entry into epithelial cells
MUTATION: ipaH mutant is attenuated in mice [PMID:17214743].
secreted by the Mxi-Spa secretion machinery, function unknown
Iron transport protein, periplasmic-binding protein
protein histidine kinase/phosphatase sensor for OmpR, modulates expression of ompF and ompC
Other designations: osmolarity sensor protein
response regulator (sensor, EnvZ) affecting transcription of ompC and ompF: outer membrane protein synthesis
Other designations: RNA-binding protein Hfq
MUTATION: A pgk mutant is attenuated in mice [PMID:20194591].
nitrite/sulfite reductase ferredoxin subunit
glyoxalase/bleomycin resistance protein/dioxygenase
MUTATION: a manAB double mutant is attenuated in mice [PMID:16790778].
PAS/histidine kinase/ATPase domain-containing protein
sensor, EnvZ; outer membrane protein synthesis
MUTATION: shuA mutant was attenuated in HeLa cells subjected to an iron chelator, DIP to produce iron deficient conditions, suggesting that shuA plays a role in virulence in iron deficient conditions [PMID:16856494].
MUTATION: iroN mutant was attenuated in HeLa cells subjected to an iron chelator, DIP to produce iron deficient conditions, suggesting that iroN plays a role in virulence in iron deficient conditions [PMID:16856494].
binding-protein dependent transport system inner membrane protein
aspartate carbamoyltransferase catalytic subunit
type IV secretion system protein VirB3-like protein
cytochrome bd ubiquinol oxidase subunit II
MUTATION: interruption of the eatA gene retarded fluid accumulation in the rabbit ileal loop model, suggesting that this autotransporter contributes to the virulence of ETEC [PMID:14977988].
secreted autotransporter serine protease EatA
MUTATION: Deletion of UIS3 in Plasmodium yoelii provided attenuation and full protection in mice [PMID:17624848].
surface exclusion protein; similar to GenBank Accession Number AAW58918
iron-related glycotransferase; similar to NP_753168
iron-related ABC transporter protein; similar to GenBank Accession Number AAN76099
iron-related ferric enterochelin esterase; similar to GenBank Accession Number AAN76100
iron-related siderophore receptor; similar to GenBank Accession Number AAN76093
Other designations: outer membrane receptor FepA
aerobactin biosynthesis protein; similar to GenBank Accession Number CAA53707
N-hydroxylysine acetylase; aerobactin biosynthesis protein; similar to GenBank Accession Number CAH64815
aerobactin biosynthesis protein; similar to GenBank Accession Number CAH64814
L-lysine 6-monooxigenase; similar to GenBank Accession Number CAE55773
ferric aerobactin receptor; similar to GenBank Accession Number CAE55774
MUTATION: A genetically attenuated parasite (GAP) with a mutation in the FabB/FabF gene is attenuated in mice by arresting in the late liver stage [PMID:21669394].
3-oxoacyl-acyl-carrier protein synthase I/II
MUTATION: beta toxin null mutants are attenuated in rabbit ileal loop model of disease [PMID:18078439].
MUTATION: recA mutant is attenuated in mice [PMID:9383163].
MUTATION: femA mutant is attenuated in mice [PMID:9383163].
MUTATION: Targeted deletion of SAP1 in the rodent malaria parasite Plasmodium yoelii generated mutant parasites that traverse and invade hepatocytes normally but cannot initiate liver-stage development in vitro and in vivo [PMID:18466298].
Record to support submission of GeneRIFs for a gene not in Gene (Plasmodium yoelii yoelii str. 17XNL).
MUTATION: a FTL_0837 mutant was attenuated for infection in a mouse lung [PMID:17420240]
D-methionine binding transport protein, ABC transporter, membrane and periplasmic protein
MUTATION: a FTL_0846 mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a FTL_1528 mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a FTL_1096 mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a FTL_1097 mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a FTL_1867 mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a FTL_1672 mutant was attenuated for infection of a mouse lung [PMID:17420240]
MUTATION: a FTL_1678 mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a FTL_0892 mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a FTL_0894 mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a FTL_0899 mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a FTL_0903 mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a FTL_0483 mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a FTL_0485 mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a FTL_1134 mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a FTL_1030 mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a FTL_0768 mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a FTL_0584 mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a FTL_0421 mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a FTL_0428 mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a FTL_0430 mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a FTL_0439 mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a FTL_0950 mutant was attenuated for infection in a mouse lung[PMID:17420240]
MUTATION: a FTL_0960 mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a FTL_0616 mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a FTL_0617 mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a FTL_0009 mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a FTL_0010 mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a FTL_0012 mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a secE mutant was attenuated for infection of a mouse lung [PMID:17420240]
MUTATION: a FTL_0663 mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a FTL_1233 mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a FTL_1240 mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a FTL_1225 mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a FTL_0645 mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a FTL_0723 mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a FTL_1419 mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a FTL_0803 mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: A guaA mutant is highly attenuated in mice [PMID:19368784].
MUTATION: a FTL_1075 mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a FTL_0111 mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a FTL_0112 mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a FTL_0113 mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a FTL_0133 mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a FTL_1354 mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a FTL_1554 mutant was attenuated for infection in a mouse lung [PMID:17420240]
cytochrome O ubiquinol oxidase, subunit III
MUTATION: a FTL_1601 mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a FTL_1273 mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a FTL_1274 mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a FTL_1275 mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a FTL_1936 mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a FTL_1622 mutant was attenuated for infection in a mouse lung [PMID:17420240]
multidrug transporter (tetracycline resistance protein)
MUTATION: a FTL_1623 mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a FTL_1458 mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a FTL_R0003 mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a FTL_1504 mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a FTL_1266 mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a FTL_0928 mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a FTL_0514 mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a FTL_0519 mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a FTL_0520 mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a FTL_0094 mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a FTL_1414 mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a FTL_1415 mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a FTL_1416 mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a FTL_1832 mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a FTL_1461 mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a FTL_1473 mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a FTL_1474 mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a FTL_1475 mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a tRNA-Ile1 mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a FTL_0382 mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a FTL_0387 mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: A purMCD mutant in Francisela tularensis was attenuated in mice [PMID:16861631].
MUTATION: a FTL_1947 mutant was attenuated for infection in a mouse lung [PMID:17420240]
putative ABC transporter ATP-binding protein
MUTATION: a FTL_1328 mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a FTL_0073 mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a FTL_0525 mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a FTL_0540 mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a FTL_0337 mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a FTL_1392 mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a FTL_1393 mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: A FTL0552 mutant in Francisella tularensis was attenuated in mice [PMID:18613792].
MUTATION: a FTL_0589 mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a FTL_0592 mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a FTL_0597 mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: a FTL_0789 mutant was attenuated for infection in a mouse lung [PMID:17420240]
MUTATION: attenuated in mice [PMID:11349064].
MUTATION: deletion mutant was significantly less invasive in human brain microvascular endothelial cells (BMECs) than the parent strain (E. coli K1) [PMID:11237832].
MUTATION: traJ mutants of E. coli K1 are attenuated in rat pups and macrophages [PMID:14688129].
MUTATION: cpe knockout mutant is avirulent in rabbit ileal loop model [PMID:10476029].
MUTATION: yhiE mutant is attenuated in causing keratoconjunctivitis in guinea pigs [PMID:15073317].
MUTATION: Mutation of plasmid gene ORF3 (comB3) reduced adherence/invasion of INT407 cells to approximately 1/3 of wild type strain 81-176 [PMID:10899834].
MUTATION: mvfR (pho34B12) mutant is attenuated in burned mouse model [PMID:9371831].
MUTATION: exoU mutant is avirulent in Dictyostelium discoideum, a genetically tractable eukaryotic organism [PMID:11867744].
MUTATION: flhB mutant is attenuated in Drosophila melanogaster and in mice [PMID:18591226].
MUTATION: PA14_38610 mutant is attenuated in Drosophila melanogaster and in mice [PMID:18591226].
MUTATION: PA14_37650 mutant is attenuated in Drosophila melanogaster and in mice [PMID:18591226].
MUTATION: pscJ mutant is attenuated in Dictyostelium discoideum, a genetically tractable eukaryotic organism [PMID:11867744].
MUTATION: PA14_33610 (pvdI) mutant is attenuated in Drosophila melanogaster and in mice [PMID:18591226].
MUTATION: gacA mutant is attenuated in burned mouse model [PMID:9371831].
MUTATION: kerV (PA14_41070) mutant is attenuated in mice [PMID:19779606].
MUTATION: prpR mutant is attenuated in mice and Drosophila melanogaster [PMID:18591226].
MUTATION: toxA mutant is attenuated in burned mouse model [PMID:7604262].
MUTATION: pilF mutant is attenuated in Drosophila melanogaster and in mice [PMID:18591226].
MUTATION: tpnA mutant is attenuated in Drosophila melanogaster and in mice [PMID:18591226].
MUTATION: prpL mutant is attenuated in rats [PMID:11500408].
Pvds-regulated endoprotease, lysyl class
MUTATION: lasR mutant is avirulent in Dictyostelium discoideum [PMID:11867744].
MUTATION: katA mutant is attenuated in Drosophila melanogaster and in mice [PMID:15972537].
MUTATION: PA14_03120 (hudR) mutant is attenuated in Drosophila melanogaster and in mice [PMID:18591226].
MUTATION: PA14_03530 mutant is attenuated in Drosophila melanogaster and in mice [PMID:18591226].
MUTATION: PA14_04850 mutant is attenuated in Drosophila melanogaster and in mice [PMID:18591226].
MUTATION: fabF1 mutant is attenuated in Drosophila melanogaster and in mice [PMID:18591226].
MUTATION: wspF mutant is attenuated in Drosophila melanogaster [PMID:18591226].
MUTATION: dsbA mutant is attenuated in Drosophila melanogaster and in mice [PMID:18591226].
MUTATION: plcH mutant is attenuated in burned mouse model [PMID:7604262].
MUTATION: opdO mutant is attenuated in Drosophila melanogaster and in mice [PMID:18591226].
MUTATION: cbpA mutant is attenuated in rat pups [PMID:9364908].
Mutator mutT protein (7,8-dihydro-8-oxoguanine-triphosphatase) (8-oxo-dGTPase)
MUTATION: a bacA mutant was attenuated in a murine model [PMID:11359563]
sugar binding transcriptional regulator RegR
MUTATION: cbpE has reduced colonization of nasopharynx of rats and reduced adherence to human epithelial cells [PMID:10992472].
MUTATION: a purN mutant was attenuated in a murine model [PMID:11359563]
MUTATION: a pepC mutant was attenuated in a murine model [PMID:11359563]
autolysin/N-acetylmuramoyl-L-alanine amidase
MUTATION: a purB mutant was attenuated in a murine model [PMID:11359563]
MUTATION: an aga mutant was attenuated in a murine model [PMID:11359563]
spermidine/putrescine ABC transporter spermidine/putrescine-binding protein
MUTATION: pavA mutant is attenuated in mice [PMID:11580843].
MUTATION: a pbp1A mutant was attenuated in a murine model [PMID:11359563]
MUTATION: An A. hydrophila aroA mutant is highly attenuated in trout [PMID:9573055].
MUTATION: mppA mutant is attenuated in chickens [PMID:15845486].
periplasmic murein peptide-binding protein
MUTATION: sbmA mutant is attenuated in chickens [PMID:15845486].
MUTATION: ychF mutant is attenuated in chickens [PMID:15845486].
GTP-dependent nucleic acid-binding protein EngD
MUTATION: waaL mutant is attenuated in chickens [PMID:15845486].
MUTATION: sitB mutant is attenuated in chickens [PMID:15845486].
MUTATION: malX mutant is attenuated in chickens [PMID:15845486].
bifunctional PTS system maltose and glucose-specific transporter subunits IICB
MUTATION: tia deletion strains were noninvasive and lacked the ability to adhere to human ileocecal cells [PMID:8675335].
MUTATION: kpsS mutant is attenuated in chickens [PMID:15845486].
polysialic acid capsule synthesis protein KpsS
MUTATION: wcaE mutant is attenuated in chickens [PMID:15845486].
MUTATION: yqi mutant is attenuated in chickens [PMID:19907658].
MUTATION: yjjQ mutant is attenuated in chickens [PMID:18375801].
outer membrane heme/hemoglobin receptor ChuA
MUTATION: tktA mutant is attenuated in chickens [PMID:15845486].
MUTATION: PEB1 mutants had a significantly reduced in vivo colonization of broiler chickens [PMID:19349427]
amino acid ABC transporter, ATP-binding protein PEB1
MUTATION: A motB insertion-deletion mutant failed to establish colonization in LF mice [PMID:16926420]
MUTATION: Insertional inactivation of the cheY gene in 81-176 resulted in an approx. threefold increase in adherence and invasion in vitro, but this strain was unable to colonize or cause disease in animals [PMID:9076738]
MUTATION: A cheA insertion-deletion mutant failed to establish colonization in LF mice [PMID:16926420]
MUTATION: pglB impaired in glycosylation showed reduced ability to adhere to INT407 cells and colonize in mice [PMID:11895996].
amino acid ABC transporter, permease protein PEB1
MUTATION: kpsC mutants were defective in colonization and virulence [PMID:16332783]
capsule polysaccharide export protein KpsC
MUTATION: knockout strains showed reduced ability to invade epithelial cells [PMID:18644887].
LPS glycosyltransferase subfamily protein
MUTATION: A flil insertion-deletion mutant failed to establish colonization in LF mice [PMID:16926420]
MUTATION: mutations in ggt showed it to be required for persistent colonization of the avian gut [PMID:17600669]
MUTATION: cadF mutants had reduced binding to immobilized Fn as compared to wt strains [PMID:12576589]
MUTATION: knockout mutant impaired for flagella-mediated motility and invasion of intestinal epithelial cells [PMID:16690622].
MUTATION: kpsM mutant is significantly reduced in invasion of INT407 cells and reduced in virulence in a ferret diarrhoeal disease model [PMID:11359581].
capsular polysaccharide ABC transporter, permease protein
MUTATION: LSS100, a strain that synthesizes markedly greater quantities of GroEL relative to others, significantly accelerates apoptosis of the cocultured HUVECs relative to other strains [PMID:16481529].
MUTATION: mutagenesis of ialB decreased bacterial association and invasion of human erythrocytes by 47 to 53% relative to controls [PMID:11401976].
putative type III secretion effector targeting lipoprotein
virulence regulon transcriptional activator
MUTATION: pstC mutant is attenuated in mice [PMID:10216859].
phosphate transporter permease subunit PstC
MUTATION: dnaJ mutant is attenuated in mice [PMID:10216859].
MUTATION: An aroA mutant is highly attenuated in mice [PMID:2777382].
MUTATION: pspC mutant is attenuated in mice [PMID:10216859].
DNA-binding transcriptional activator PspC
MUTATION: rovA mutant is attenuated when delivered orally in mice [PMID:12761136].
MUTATION: irp1 mutant is attenuated in mice [PMID:10216859].
MUTATION: galE mutant is attenuated in mice [PMID:10216859].
MUTATION: manB mutant is attenuated in mice [PMID:10216859].
MUTATION: manC mutant is attenuated in mice [PMID:10216859].
MUTATION: wcbI mutant is attenuated in mice [PMID:10216859].
MUTATION: wbcH mutant is attenuated in mice [PMID:10216859].
MUTATION: wbcF mutant is attenuated in mice [PMID:10216859].
MUTATION: wbcC mutant is attenuated in mice [PMID:10216859].
MUTATION: ddhB mutant is attenuated in mice [PMID:10216859].
MUTATION: htrB mutant has diminished invasion of HeLa cells and is attenuated in vivo [PMID:20385763].
MUTATION: msbB mutant has diminished invasion of HeLa cells [PMID:20385763].
MUTATION: ddhA mutant is attenuated in mice [PMID:10216859].
glucose-1-phosphate cytidylyltransferase
MUTATION: topA mutant is attenuated in mice [PMID:10216859].
MUTATION: htrA mutant is avirulent in mice [PMID:8675311].
MUTATION: nlpD mutant is attenuated in mice [PMID:10216859].
MUTATION: ompR mutant is unable to invade HeLa cells [PMID:15330261].
MUTATION: A sodA mutant in Yersinia enterocolitica was highly attenuated in mice [PMID:10496939].
Other designations: superoxide dismutase
MUTATION: yibK mutant is attenuated in pigs [PMID:12819083].
MUTATION: dnaK mutant is attenuated in porcine model of infection [PMID:10873489].
MUTATION: ngrA mutant is attenuated in pigs [PMID:12819083].
MUTATION: aroA mutant is attenuated in pigs [PMID:12027598].
MUTATION: fur mutant is attenuated in pigs [PMID:12819083].
MUTATION: moaA mutant is attenuated in pigs [PMID:12819083].
MUTATION: pntB mutant is attenuated in pigs [PMID:12819083].
MUTATION: dksA mutant is attenuated in porcine model of infection [PMID:10873489].
MUTATION: A ΔapxIIA is attenuated in pigs [PMID:12438394]. MUTATION: ureC/apxIIA deletion mutant is attenuated in pigs [PMID:12438394].
MUTATION: napB mutant is attenuated in pigs [PMID:12819083].
nitrate reductase cytochrome c-type subunit
MUTATION: ilvl mutant is attenuated in pigs [PMID:19703979].
MUTATION: mrp mutant is attenuated in pigs [PMID:12819083].
MUTATION: htpG mutant is attenuated in pigs [PMID:12819083].
MUTATION: thrC mutant is attenuated in pigs [PMID:12819083].
MUTATION: recR mutant is attenuated in pigs [PMID:12819083].
MUTATION: frpB mutant is avirulent in pigs [PMID:19343711].
MUTATION: cpxD mutant is attenuated in pigs [PMID:12819083].
MUTATION: cpxC mutant is attenuated in pigs [PMID:12819083].
capsule polysaccharide export inner-membrane protein
MUTATION: pnp mutant is attenuated in porcine model of infection [PMID:10873489].
polynucleotide phosphorylase/polyadenylase
MUTATION: irp mutant is attenuated in competitive index experiment in pig infection model [PMID:19703979].
MUTATION: fkpA mutant is attenuated in porcine model of infection [PMID:10873489].
MUTATION: argG mutant is attenuated in pigs [PMID:12819083].
MUTATION: dmsA mutant is attenuated in pigs [PMID:14638764].
anaerobic dimethyl sulfoxide reductase subunit A
MUTATION: corC mutant is attenuated in pigs [PMID:12819083].
MUTATION: mglA mutant is attenuated in pigs [PMID:12819083].
MUTATION: tbpA mutant is attenuated in pigs [PMID:12007819].
MUTATION: dnaJ mutant is attenuated in pigs [PMID:12819083].
MUTATION: galU mutant is attenuated in pigs [PMID:12819083].
MUTATION: aroQ mutant is attenuated in pigs [PMID:11731178].
MUTATION: tig mutant is attenuated in porcine model of infection [PMID:10873489].
MUTATION: lpdA mutant is attenuated in porcine model of infection [PMID:10873489].
MUTATION: hgbA mutant is attenuated in pigs [PMID:16699590].
MUTATION: exbB mutant is attenuated in porcine model of infection [PMID:10873489].
MUTATION: hemA mutant is attenuated in pigs [PMID:12819083].
MUTATION: apxlC mutant is attenuated in mice [PMID:18062275].
RTX-I toxin-activating lysine-acyltransferase ApxIC
MUTATION: guaA mutant is attenuated in pigs [PMID:12819083].
MUTATION: prc mutant is attenuated in pigs [PMID:12819083].
MUTATION: lon mutant is attenuated in pigs [PMID:12819083].
MUTATION: hemE mutant is attenuated in pigs [PMID:12819083].
MUTATION: dsbA mutant is attenuated in pigs [PMID:12819083].
Thiol:disulfide interchange protein dsbA precursor
MUTATION: hupA mutant is attenuated in porcine model of infection [PMID:10873489].
MUTATION: atpG mutant is attenuated in porcine model of infection [PMID:10873489].
MUTATION: rpmF mutant is attenuated in porcine model of infection [PMID:10873489].
MUTATION: znuA mutant is attenuated in pigs [PMID:12819083].
MUTATION: atpA mutant is attenuated in pigs [PMID:12819083].
MUTATION: cpxB mutant is attenuated in pigs [PMID:12819083].
MUTATION: apxIA mutant is attenuated in mice [PMID:16930871].
MUTATION: visC mutant is attenuated in pigs [PMID:12819083].
MUTATION: hlyX mutant is attenuated in pigs [PMID:16040973].
fumarate/nitrate reduction transcriptional regulator
MUTATION: tbpB mutant is attenuated in pigs [PMID:12007819].
MUTATION: atpH mutant is attenuated in porcine model of infection [PMID:10873489].
MUTATION: luxS mutant is attenuated in mice [PMID:18585450].
MUTATION: arcA mutant is attenuated in pigs [PMID:17881160].
MUTATION: rpoE mutant is attenuated in pigs [PMID:12819083].
MUTATION: prfC mutant is attenuated in pigs [PMID:12819083].
MUTATION: pabB mutant is avirulent in mice [PMID:19121696].
para-aminobenzoate synthase, component I
MUTATION: purM mutant is attenuated in mice [PMID:16714590].
MUTATION: aroC mutant is highly attenuated in mice [PMID:19323044].
MUTATION: BopA mutant is attenuated in mice [PMID:16714590].
MUTATION: pbs2 mutant is attenuated in mice [PMID:15728721].
MUTATION: It serves as an important link between sterol biosynthesis, oxygen sensing, CoCl2 sensitivity. The mutation showed no virulence in a mouse infection model [PMID:19749173].
MUTATION: MPD is required for mannitol biosynthesis and the ability to synthesize mannitol is essential for wild-type stress tolerance and virulence [PMID:11021946].
MUTATION: nmt mutant is attenuated in immunosuppressed rabbits [PMID:7991574].
MUTATION: asaI mutant is attenuated in fish [PMID:20708354].
MUTATION: tapA mutant is attenuated in rainbow trout [PMID:12240967].
MUTATION: asoB mutant was avirulent via immersion bath in rainbow trout [PMID:8917088].
MUTATION: aroA mutant is attenuated in salmon [PMID:8478107].
MUTATION: asaP1 mutant was attenuated in charr and salmon [PMID:18952802].
MUTATION: ascV mutant is attenuated in rainbow trout model [PMID:15942017].
MUTATION: aopH mutant is attenuated in salmon [PMID:16735747].
putative protein-tyrosine phosphatase Aop effector AopH
MUTATION: ascC mutant was less invasive of Atlantic salmon anterior head kidney leucocytes (AHKL) and had less survival than the wild type strain [PMID:19751835].
MUTATION: zwf mutant is attenuated in mice [PMID:11952899].
MUTATION: ydbK mutant is attenuated in mice [PMID:11952899].
MUTATION: phaC mutant is attenuated in mice [PMID:11952899].
MUTATION: pykF mutant is attenuated in mice [PMID:11952899].
MUTATION: fbp mutant is attenuated in mice [PMID:11952899].
MUTATION: frdC mutant is attenuated in mice [PMID:11952899].
MUTATION: rfbB mutant is attenuated in mice [PMID:9515705].
MUTATION: ubiC mutant is attenuated in mice [PMID:11952899].
MUTATION: tcpT mutant is attenuated in mice [PMID:9515705].
MUTATION: toxR mutant is attenuated in mice [PMID:2883655].
MUTATION: gshB mutant is attenuated in mice [PMID:11952899].
MUTATION: nqrE mutant is attenuated in mice [PMID:11952899].
MUTATION: toxT mutant is attenuated in mice [PMID:9515705].
MUTATION: purD mutant is attenuated in mice [PMID:9515705].
MUTATION: rpoS mutants had defective colonization ability of mice intestines compared to the wild type [PMID:11083783].
MUTATION: trpG mutant is attenuated in mice [PMID:11952899].
MUTATION: purF mutant is attenuated in mice [PMID:11952899].
MUTATION: purL mutant is attenuated in mice [PMID:11952899].
MUTATION: rpoE mutant is attenuated in mice [PMID:12228259].
MUTATION: relA mutant is attenuated in mice [PMID:12896985].
MUTATION: lysA mutant is attenuated in mice [PMID:11952899].
MUTATION: tcpA mutant has defect in colonization of infant mice [PMID:8698524].
MUTATION: acfC mutant had a defect in colonization of mice, and had a ten-fold increase in the 50% lethal dose in mice [PMID:2902009].
MUTATION: rfbL mutant is attenuated in mice [PMID:9515705].
MUTATION: nqrF mutant is attenuated in mice [PMID:11952899].
MUTATION: ilvD mutant is attenuated in mice [PMID:11952899].
MUTATION: deoC mutant is attenuated in mice [PMID:11952899].
MUTATION: acfB mutant had a defect in colonization of mice, and had a ten-fold increase in the 50% lethal dose in mice [PMID:2902009].
MUTATION: purK mutant is attenuated in mice [PMID:9515705].
MUTATION: pta mutant is attenuated in mice [PMID:9515705].
MUTATION: acfA mutant had a defect in colonization of mice, and had a ten-fold increase in the 50% lethal dose in mice [PMID:2902009].
MUTATION: galK mutant is attenuated in mice [PMID:11952899].
MUTATION: carA mutant is attenuated in mice [PMID:11952899].
MUTATION: bioB mutant is attenuated in mice [PMID:9515705].
MUTATION: irgA mutant is attenuated in mice [PMID:2152889].
MUTATION: tcpE mutant is attenuated in mice [PMID:9515705].
organelle trafficking lipoprotein defect DotA
organelle trafficking lipoprotein defect DotB
MUTATION: icmG mutant is attenuated in mice [PMID:10393970].
MUTATION: fur mutant is attenuated in growth within U937 cell monolayers [PMID:8975903].
heat shock protein transcriptional repressor HspR
transcriptional regulatory protein whib-like WhiB3
iron-regulated heparin binding hemagglutinin Hbha
two component sensor histidine kinase SenX3
two component sensory transduction protein RegX3
two component transcriptional regulatory protein DevR
two component response transcriptional regulatory protein MprA
daunorubicin-dim ABC transporter permease DrrC
MUTATION: mycP1 is attenuated in chronic infection of mice [PMID:20227664].
two component system response transcriptional positive regulator PhoP
acetolactate synthase 1 catalytic subunit
molybdopterin biosynthesis-like protein MoeZ
long-chain-fatty-acid--[acyl-carrier-protein] ligase
MUTATION: pan CD mutant is attenuated in mice [PMID:12219086].
secreted targeting protein, regulator, Type III system
translocated cysteine protease/Rho GTPase toxin
leucine-rich repeat-containing translocated effector protein
putative secreted pore/translocation protein
translocated protein-tyrosine kinase, inhibitor of phagocytosis
translocated host-GTPase-activating protein
MUTATION: mutant attenuated in a C. elegans-killing model [PMID:15664928].
MUTATION: mutant displayed reduced replication and infection in murine model [PMID:20525824].
immunoglobulin G binding protein A precursor (protein A)
MUTATION: mutant attenuated in a Caenorhabditis elegans-killing model [PMID:15664928].
MUTATION: yscL mutant is attenuated in mice [PMID:11292689].
HrpE/YscL family type III secretion apparatus protein
MUTATION: yopM mutant is attenuated in invasion of mouse host tissues [PMID:20368345].
MUTATION: inserting a group II intron into the botulinum neurotoxin type A gene (bont/A) rendered mutant clones nontoxigenic [PMID:19933346]
MUTATION: a BoNT/A mutant was rendered nontoxigenic [PMID:19933346]
MUTATION: A wbtI mutant is attenuated in mice [PMID:17768257].
DegT/DnrJ/EryC1/StrS family sugar aminotransferase
MUTATION: A sodC mutant in Francisella tularensis subspecies holarctica was attenuated in mice [PMID:19684141].
MUTATION: A guaB mutant is attenuated in mice [PMID:19368784].
MUTATION: NagD mutant attenuated in C. Elegans-killing model [PMID:15664928].
MUTATION: mutant showed less bacterial persistence in kidneys and attenuated virulence in mice [PMID:18692591].
MUTATION: Deletion mutants of eltA and eltB had decreased levels of inducing cAMP secretion in an in vitro culture system, and had less adherence to IPEC-J2 and Caco-2 cells than the wild-type ETEC [PMID:18978047].
dipeptide ABC transporter periplasmic dipeptide-binding protein
positive regulator of conjugative transfer; similar to AAO49515
Other designations: conjugal transfer transcriptional regulator TraJ
surface exclusion and complement resistance protein; similar to AAT85681; identified by match to protein family HMM PF05818
MUTATION: tsh mutant is attenuated in chickens [PMID:18589815].
temperature sensitive hemagglutinin; similar to AAA24698; identified by match to protein family HMM PF02395
salmochelin siderophore system, salmochelin receptor; similar to AAS80269; identified by match to protein family HMM PF00593
salmochelin siderophore system, ferric enterochelin esterase; similar to AAS80267; identified by match to protein family HMM PF
salmochelin siderophore system, ATP-binding cassette; similar to AAP41471; identified by match to protein family HMM PF00005
salmochelin siderophore system, glycosyltransferase; similar to AAS80265; identified by match to protein family HMM PF06722
aerobactin siderophore system, ferric aerobactin receptor protein; similar to ABA54744; identified by match to protein family HMM PF00593
aerobactin siderophore system, L-lysine 6-monooxygenase; similar to CAE55774
aerobactin siderophore system, aerobactin biosynthesis protein; similar to ABA54742; identified by match to protein family HMMPFO4183
aerobactin siderophore system, aerobactin synthetase; similar to ABA54740; identified by match to protein family HMM PF04183
MUTATION: A mutation of the response regulator gene racR reduced the organism's ability to colonize the chicken intestinal tract [PMID:10322038]
MUTATION: the capacity of a kpsE mutant to adhere to the INT-407 cells was reduced 20-fold, and the invasion capability of the kpsE mutant was two-fold lower than that of the wild type [PMID:17266722].
MUTATION: gp63 mutant is attenuated for survival in murine macrophages [PMID:7808483].
MUTATION: Inactivation of LIT1 gene results in attenuated virulence in murine footpad model of infection and reduced viability and replication in bone marrow macrophages [PMID:17257847].
iron/zinc transporter protein-like protein
MUTATION: pilX mutant has reduced adherence to human epithelial cells [PMID:15612917].
MUTATION: pbp3 mutant is attenuated in rats [PMID:11062540].
MUTATION: pnp mutant is attenuated in rats [PMID:11062540].
MUTATION: ntrY mutant is attenuated in rats [PMID:11062540].
nitrogen regulation protein NtrY, putative
MUTATION: siaD mutant is attenuated in rats [PMID:11062540].
MUTATION: hrpA mutants are deficient in the ability to live/grow in HeLa cells [PMID:18680551].
type III secretion low calcium response chaperone LcrH
yersiniabactin synthetase, HMWP2 component
yersiniabactin ABC transporter ATP-binding protein/permease
MUTATION: virD4 mutant is attenuated in rats [PMID:15049812].
dosage-dependent DnaK suppressor protein
MUTATION: yfeB mutant is attenuated in pigs [PMID:12819083].
iron (chelated) transporter, ATP-binding protein
MUTATION: lppB mutant is attenuated in pigs [PMID:12819083].
MUTATION: nqrA mutant is attenuated in pigs [PMID:12819083].
HexD, capsule biosynthetic locus protein
capsule polysaccharide export transport system permease
hemoglobin and hemoglobin-haptoglobin-binding protein 4
MUTATION: ilvI mutant is attenuated in pigs [PMID:19703979].
MUTATION: BoNT/B toxoid without non-toxic components, which are generally associated with the toxin was used attenuated and used as a vaccine candidate [PMID:15225558]
peptide ABC transporter periplasmic substrate-binding protein
type IV secretion-like conjugative transfer system regulator TraJ
aerobactin siderophore biosynthesis protein IucB
aerobactin siderophore biosynthesis protein IucA
aerobactin siderophore biosynthesis protein IucC
MUTATION: pspC mutant is has reduced ability to colonize nasopharynx of mice compared to the wild type [PMID:17261599].
peptidoglycan N-acetylglucosamine deacetylase A
MUTATION: lcrR mutant is attenuated in mice [PMID:11292689].
type III secretion system regulator LcrR
YscU/HrpY family type III secretion protein
MUTATION: yscB mutant is attenuated in mice [PMID:11292689].
YscB family type III secretion system chaperone
MUTATION: mutant attenuated in turkey tracheal colonization [PMID:10931292].
MUTATION: bvgS mutant is avirulent in turkeys [PMID:12704133].
MUTATION: fhaA (fimC) mutant is avirulent in turkeys [PMID:12704133].
MUTATION: fhaB mutant is avirulent in turkeys [PMID:12704133].
P-type conjugative transfer protein VirB9
MUTATION: degP mutant is unable to form plaques on Henle cell monolayers [PMID:17526712].
N(6)-hydroxylysine O-acetyltransferase, aerobactin biosynthetic
MUTATION: skp mutants are capable of infecting Henle cells but are incapable of cell to cell spread [PMID:17526712].
type III secretion outer membrane protein MxiD
type III secretion apparatus protein MxiK
type III secretion apparatus needle protein mxiH
MUTATION: BoNT/E mutants were nontoxigenic as opposed to the toxigenic wild type strain [PMID:4633199]
high-affinity zinc uptake system protein ZnuA precursor
MUTATION: piaA piuB double mutant is attenuated in systemic infection of mice [PMID:12117949].
iron ABC transporter iron-binding protein
MUTATION: cpsC mutant is avirulent in mice [PMID:15122528].
capsular polysaccharide biosynthesis protein Wzh
manganese-dependent superoxide dismutase
MUTATION: lytB has reduced colonization of nasopharynx of rats compared to the wild type [PMID:10992472].
MUTATION: a purL mutant was attenuated in a murine model [PMID:11359563]
phosphoribosylformylglycinamide synthetase
MUTATION: cpsB mutant is avirulent in mice [PMID:15122528].
MUTATION: zmpC mutant is attenuated in mice [PMID:12864860].
MUTATION: ritR mutant is attenuated in lung infection model of mice [PMID:15547286].
ABC transporter amino acid-binding protein/permease
MUTATION: mutX is attenuated in mice [PMID:9826334].
MUTATION: pspC mutant has reduced ability to colonize the nasopharynx of mice compared to t he wild type [PMID:17261599].
manganese ABC transporter substrate-binding lipoprotein
MUTATION: vicK mutant was attenuated in mice [PMID:19088917].
MUTATION: szp mutant is attenuated in mice [PMID:18983882].
MUTATION: lgt mutant is attenuated in mice [PMID:17015455].
MUTATION: A cbiA mutant, in combination with a cobS mutation, is attenuated in chickens [PMID:20153354].
MUTATION: A lon mutant is attenuated in mice [PMID:20487719].
MUTATION: ion mutant is attenuated in chickens [PMID:20487719].
MUTATION: A cobS mutant, in combination with a cbiA mutation, is attenuated in chickens [PMID:20153354].
MUTATION: A cpxR mutant is attenuated in mice [PMID:20487719].
MUTATION: A nuoG mutant is attenuated in chickens [PMID:9682335].
MUTATION: fur mutants are attenuated in mice [PMID:19577637].
MUTATION: rpoS mutants are attenuated in mice [PMID:19577637].
MUTATION: relA mutant is attenuated in mice [PMID:19577637].
MUTATION: htrA mutant is attenuated in mice [PMID:19577637].
MUTATION: ompR mutants are attenuated in mice [PMID:19577637].
MUTATION: galE mutants are attenuated in mice [PMID:19577637].
MUTATION: guaB mutant is attenuated in BALB/c mice [PMID:17261603].
MUTATION: hfq mutant is attenuated in mice [PMID:19577637].
MUTATION: phoP mutants are attenuated in mice [PMID:19577637].
MUTATION: rfaL mutants are attenuated in mice [PMID:19577637].
MUTATION: rfaG mutants are attenuated in mice [PMID:19577637].
MUTATION: misL mutant is attenuated in mice [PMID:19577637].
MUTATION: spoT mutants are attenuated in mice [PMID:19577637].
MUTATION: aroA mutants are attenuated in mice [PMID:19577637].
MUTATION: iacP mutants were noninvasive in chicks [PMID:11731137].
MUTATION: sipD mutants were noninvasive in chicks [PMID:11731137].
MUTATION: sipB mutants were significantly less invasive in chickens than the wild-type [PMID:19322708].
MUTATION: ssrA mutant is attenuated in mice [PMID:19577637].
MUTATION: sseA mutant is attenuated in mice [PMID:19577637].
MUTATION: clpP mutant is attenuated in mice [PMID:19577637].
MUTATION: aroD mutants are attenuated in mice [PMID:19577637].
MUTATION: knockout strain reduced adherence to human gastric epithelial cells [PMID:10454640].
MUTATION: knockout strain showed reduced adhesion and colonization in mice [PMID:17492999].
MUTATION: strains lacking BabA cannot adhere to Leb, expressed on gastric epithelium [PMID:14762173].
MUTATION: knock out deprived wild-type of the pathogenicity for gastritis and gastric ulcer in Mongolian gerbils [PMID:11104802].
MUTATION: mutant strain showed reduction in bacterial adherence to gastric epithelia in vitro [PMID:17054063].
MUTATION: deletion mutant lost ability to bind to sialyl-Lewis antigens [PMID:17121461], and had no neutrophil-activating capacity [PMID:17121461].
MUTATION: knockout did not cause gastric ulcers in mice compared to wild type [PMID:20046046].
dipeptide ABC transporter substrate-binding protein
MUTATION: ska mutant was attenuated in mouse acute poststreptococcal glomerulonephritis model [PMID:10678902].
strepotococcal cysteine protease (streptopain) / streptococcal pyrogenic exotoxin B (SpeB)
MUTATION: sagA mutant is attenuated in mice [PMID:11801184].
streptolysin S associated protein (SagA)
Other designations: streptolysin S associated protein SagA
MUTATION: knockout strains reduced damage and adherence to human gastric epithelial cells [PMID:18811585].
MUTATION: strains slacking BabA cannot adhere to Leb, expressed on gastric epithelium [PMID:14762173].
MUTATION: mutant showed severe reduction in ability to bind to gastric cell line [PMID:10200971].
cag pathogenicity island protein E VirB4-like protein
MUTATION: NSP4 mutants that fail to bind or signal through integrin alpha2 were attenuated in diarrhea induction in neonatal mice [PMID:18587047].
MUTATION: espF mutant of EPEC is deficient in its ability to disrupt electrical resistance across a polarized monolayer of intestinal epithelial cells, suggesting that EspF is an effector molecule required for disrupting intestinal epithelial barrier function [PMID:11238563].
MUTATION: map EPEC mutants have significantly reduced levels of invasion of HeLa cells [PMID:14531893].
MUTATION: ler mutants had less adhesion to HeLa cells, ler is a regulator of many virulence genes in the LEE PAI which are needed for adherence [PMID:18794291].
MUTATION: the inhibitory effect of the espG mutant on Cl– uptake in Caco-2 monolayers was significantly attenuated as compared with wild-type EPEC [PMID:17256057].
MUTATION: ecpA mutant had attenuated adherence to HEp-2 cells compared to the parental EHEC strain [PMID:17563352].
MUTATION: deletion mutant is attenuated in infant rabbits [PMID:15731044].
MUTATION: mutant showed attenuated virulence in mice [PMID:15028680].
MUTATION: mutant strain severely attenuated in cell culture, impaired for adhesion to certain eukaryotic cells [PMID:18599819].
MUTATION: BosR mutant attenuated in mice [PMID:19906179].
Ferric aerobactin receptor precusor IutA
IroC, ATP binding cassette (ABC) transporter homolog
IroD, putative ferric enterochelin esterase
conjugal transfer transcriptional regulator TraJ
dipeptide ABC transporter periplasmic-binding protein
dipeptide transporter ; periplasmic-binding component of ABC superfamily
Fimbrial PapG protein (P pilus class II adhesin) (PapGII)
dipeptide ABC transporter periplasmic-binding
aerobactin siderophore biosynthesis protein
aerobactin siderophore biosynthesis N(6)-hydroxylysine acetylase
MUTATION: attenuated in mice. [PMID:11553558].
aerobactin siderophore biosynthesis protein, N(6)-hydroxylysine acetylase
L-lysine 6-monooxygenase (Lysine N(6)-hydroxylase)
MUTATION: attenuated in mice in humans [PMID:18482721].
MUTATION: mutant showed reduced ability to adhere to human PH cells [PMID:19451251].
complement regulator-acquiring surface protein 1 (CRASP-1)
MUTATION: dbpA deletion mutant was unable to colonize heart tissue of mice [PMID:18195034].
MUTATION: bbk32 knockout was significantly attenuated in murine model [PMID:16468997].
fibronectin-binding protein hypothetical protein
Aerobactin siderophore L-lysine 6-monooxygenase IucD
Aerobactin siderophore ferric receptor protein IutA
Salmochelin siderophore glycosyltransferase IroB
Salmochelin siderophore ATP-binding cassette IroC
Salmochelin siderophore ferric enterochelin esterase IroD
mutator MutX protein (7,8-dihydro-8-oxoguanine-triphosphatase)
MUTATION: htrA mutant is attenuated in mice [PMID:15292127].
MUTATION: pclA mutant was defective in adherence and invasion of host cells in vitro [PMID:18557785].
spermidine/putrescine extracellular binding protein
MUTATION: cbpD has reduced colonization of nasopharynx of rats compared to the wild type [PMID:1099247].
MUTATION: psrP mutants failed to bind to A549 and LA-4 lung cells, yet adhered normally to human nasopharyngeal epithelial cells and to cells from human and rodent capillary endothelial cell lines. psrP mutants were also unable to persist in the lungs of mice [PMID:18507531].
internalin, peptidoglycan bound protein (LPXTG motif)
MUTATION: impaired growth, avirulent in murine model [PMID:11790730].
MUTATION: ptb mutant is attenuated in mice [PMID:11254558].
MUTATION: mutant strain showed a reduced efficiency of phagosomal escape in eucaryotic cells and an attenuated virulence [PMID:12975369].
MUTATION: mutant strain impaired colonization in plant tissue [PMID:19295651], reduced adhesion [PMID:19295651].
MUTATION: dfp mutant is attenuated in mice [PMID:11254558].
MUTATION: attenuated in mice [PMID:16177371].
MUTATION: rpoS mutants are defective in colonization of mouse intestines compared to the wild type [PMID:11083783].
MUTATION: tcpA mutant is defective at colonizing infant mice [PMID:8698524].
MUTATION: glyA-1 mutant is attenuated in mice [PMID:11952899].
MUTATION: ccmF mutant is attenuated in mice [PMID:11952899].
MUTATION: sucA mutant is attenuated in mice [PMID:11952899].
2-oxoglutarate dehydrogenase E1 component
MUTATION: acpB mutant is attenuated in mice [PMID:15616593].
capsule synthesis trans-acting positive regulator AcpB
MUTATION: capE mutant is avirulent in mice [PMID:16267300].
polyglutamate capsule biosynthesis protein CapE
MUTATION: capD mutant is attenuated in mice [PMID:16045616].
anthrax toxin expression trans-acting positive regulator
MUTATION: alo mutant has diminished ability to grow in association of macrophages [PMID:17419764].
MUTATION: asbA mutant is attenuated in macrophages and mice [PMID:14756782].
MUTATION: mntA mutant is attenuated in guinea pigs [PMID:16194238].
manganese ABC transporter, manganese-binding protein
MUTATION: nos mutant is attenuated in mice [PMID:18215992].
nitric-oxide synthase, oxygenase subunit
MUTATION: alo mutant had diminished ability to grow in association with macrophages [PMID:17419764].
MUTATION: pilA mutant is attenuated in mice [PMID:15664977].
MUTATION: mviN mutant displayed an increased LD50 value in the hamster infection model and a loss of the ability to invade human lung epithelial cells [PMID:17110975].
MUTATION: ppsA mutant is attenuated in mice [PMID:17189432].
MUTATION: hisF mutant is attenuated in mice [PMID:16714590].
MUTATION: rpoE mutant is attenuated in mice [PMID:17346071].
MUTATION: Transfection of the virulent ROP18 allele into a nonpathogenic type III strain increased growth and enhanced mortality by 4 to 5 logs [PMID:17170305].
MUTATION: An OMPDC mutant, alone or in combination with an UP mutation, is attenuated in mice [PMID:20605980].
orotidine-monophosphate-decarboxylase, putative
MUTATION: a SAG1 mutant is attenuated in mice in an oral model of infection [PMID:15294991].
MUTATION: A UP mutant, in combination with an OMPDC mutation, is attenuated in mice [PMID:20605980].
MUTATION: M2AP mutant is attenuated for cell invasion and virulence in mice [PMID:16385407].
Neutrophil activating protein NapA (bacterioferritin)
MUTATION: hcpA deletion mutant had attenuated invasion of cultured epithelial cells compared to wild-type EHEC [PMID:18952791].
MUTATION: espK mutant attenuated in calves [PMID:16958848].
MUTATION: nelA deletion mutant attenuated in mice [PMID:14982621].
LEE-encoded type III secretion system factor
enterocyte effacement (LEE)-encoded regulator
MUTATION: hrpA mutant was deficient in the ability to grow/live in HeLa cells [PMID:18680551].
MUTATION: pilX mutant had reduced adherence to human epithelial cells [PMID:15612917].
complement regulator acquiring protein 1; putative lipoprotein
MUTATION: deletion mutant lacks the ability to inhibit lymphokine production and lymphocyte proliferation compared to wild type EPEC [PMID:10722613].
DNA-binding transcriptional antiterminator RfaH
putative translocated intimin receptor Tir
MUTATION: A trpE mutant, in combination with an aroA mutation, is attenuated in mice [PMID:12694904].
MUTATION: An esrB mutant is highly attenuated in fish [PMID:17478097].
two-component response regulator EsrB, LuxR family
MUTATION: An aroA mutant is attenuated in mice [PMID:16714581].
MUTATION: A thymidine kinase-deficient mutant (C7301dlTK) is attenuated in cats [PMID:8645090].
MUTATION: letA mutant is non-motile and is attenuated for infecting murine macrophages [PMID:11967072].
MUTATION: pLM33_p09 (ctpA) mutant is attenuated in in vivo persistence in mice [PMID:9049996].
MUTATION: A 3abc deletion mutant in Feline infectious peritonitis virus (FIPV) was attenuated in kittens [PMID:15047802]
MUTATION: A 7ab deletion mutant in Feline infectious peritonitis virus is attenuated in kittens [PMID:15047802].
MUTATION: The Ras1 signal transduction pathway controls the ability of the pathogenic fungus Cryptococcus neoformans to grow at high temperatures and to mate [PMID:12455960].
MUTATION: Phosphatase Ppg1 is crucial for cell integrity [PMID:16194228].
MUTATION: The regulator of G protein signaling homolog Crg1 is a key regulator of pheromone-responsive mating in Cryptococcus neoformans. A mutation in the CRG1 gene has greatly increased virulence [PMID:15503029].
MUTATION: The cpa1 mutant is inviable at 39℃ and attenuated for virulence [PMID:11415984].
MUTATION: The gta1 mutant exhibited impaired growth on all amino acids tested as sole nitrogen sources, with the exception of arginine and proline. Gat1 is not required for C. neoformans survival during macrophage infection or for virulence in a mouse model of cryptococcosis [PMID:20673806][PMID:20673806].
MUTATION: The avc1? had reduced growth on a selection of carbon sources, capsule inhibition, and poor melanization at 37 degree celsius [PMID:23550133].
MUTATION: Mpr1 (mpr1Δ) failed to breach the endothelium in an in vitro model of the human blood-brain barrier (BBB) [PMID:24895304].
MUTATION: This gene participates in mitochondrial protein synthesis [PMID:15765146].
MUTATION: The Cryptococcus neoformans ILV2 gene, encoding acetolactate synthase. The ilv2 mutants were auxotrophic for isoleucine and valine and the auxotrophy was satisfied by these amino acids only when proline, and not ammonium, was the nitrogen source, indicating nitrogen regulation of amino acid transport [PMID:15133116].
MUTATION: The MET6 gene showed a substantial induction in response to methionine and a dramatic transcriptional induction in response to homocysteine [PMID:15347759].
MUTATION: Ssn8 functions as a global regulator which negatively regulates diverse physiological and developmental processes and is required for virulence in C. neoformans [PMID:21559476].
MUTATION: Mutant strains lacking CMTs or expressing Cmt variants defective in Cu-coordination exhibit severely attenuated virulence and reduced pulmonary colonization [PMID:23498952].
MUTATION: Loss of the C. neoformans Ura4 protein, resulted in an expected uracil/uridine auxotrophy and an unexpected high temperature growth defect [PMID:25011011].
MUTATION: The cig1Δ mutant was less susceptible than the wild-type strain to noniron metalloporphyrins [PMID:23322859].
MUTATION: Crz1 is a calcineurin-dependent transcription factor. Δcna1, and a CRZ1/SP1 mutant (Δcrz1) had attenuated cell wall integrity [PMID:23251520].
MUTATION: The ste6 mutants in either mating-type background showed partially impaired mating functions, and mating was completely abolished in a bilateral mutant cross [PMID:15643070].
MUTATION: SKN1 are involved in beta-1,6-glucan synthesis, maintenance of cell wall integrity and retention of mannoproteins and known cryptococcal virulence factors in the cell wall of C. neoformans [PMID:20384682].
MUTATION: Disruption of the C. neoformans PMT4 gene resulted in abnormal growth morphology and defective cell separation and attenuated virulence [PMID:17142566].
MUTATION: Had no effect on virulence in an animal model of cryptococcosis [PMID:14504286].
MUTATION: met mutants showed attenuated virulence in a mouse model [PMID:17353245].
MUTATION: Ccp1 is a mitochondrial antioxidant that catalyzes the degradation of hydrogen peroxide. The mutant showed attenuated resistance to exogenous oxidative stress in vitro but does not diminish the virulence of C.neofromans in a murine model [PMID:15588993].
MUTATION: The gene encoding a heterotrimeric G-protein beta subunit. This gene is required for mating and haploid fruiting in Cryptococcus neoformans [PMID:10594037].
MUTATION: Deletion of the VTC4 gene encoding a polyphosphate polymerase blocked the ability of C. neoformans to produce polyphosphate. The vtc4 mutant behaved like the wild-type strain in interactions with macrophages and in the mouse infection model [PMID:24711572].
MUTATION: Deletion of Rpb4, growth at host temperature was impaired and virulence was attenuated [PMID:23659661].
MUTATION: Gat201 is a regulator of multiple virulence pathways.GAT201 participates directly or indirectly in the regulation of both capsule induction and melanization [PMID:18854164].
MUTATION: Orthologs of mammalian SREBP and Scap,, monitor oxygen-dependent sterol synthesis as a measure of cellular oxygen supply. Yeast Scp1 responds to 4-methyl sterols and thus shares properties with mammalian HMG-CoA reductase, a sterol-sensing domain protein whose degradation is regulated by the 4-methyl sterol lanosterol [PMID:17595166].
MUTATION: This factor is a homolog of the yeast protein Ada2, a member of the Spt-Ada-Gcn5 Acetyltransferase (SAGA) complex that regulates transcription of stress response genes via histone acetylation. The mutant exhibits significant defects in in response to a variety of stress conditions, sexual development and virulence [PMID:22174677].
MUTATION: Ste7 and Cpk1 kinases were found to act as a co-ordinate signalling module, whereas the Ste12alpha transcription factor functions with a redundant partner or in a branched or parallel signalling pathway [PMID:14614821].
MUTATION: Deletion of PYK1 blocked for entry of 2- and 3-carbon substrates into gluconeogenesis and attenuated for virulence in a murine inhalation model [PMID:21652778].
MUTATION: The mutant displayed sensitivity to copper starvation and defects in polysaccharide capsule production and melanization, leading to increased phagocytosis by murine RAW264.7 macrophages [PMID:20824073].
MUTATION: The deletion of CLP1 leads to a block in sexual development after cell fusion but before filament formation, and cells without CLP1 are unable to grow vegetatively after cell fusion [PMID:17993575].
MUTATION: The glr1Delta mutant is sensitive to nitrosative stress and macrophage killing in addition to being avirulent in mice [PMID:16524907].
MUTATION: Needed for Cryptococcus neoformans melanin biosynthesis [PMID:16102007].
MUTATION: This gene encoding the C. neoformans FKBP12 homolog, Disruption this gene conferred the fungi Rapamycin resistance [PMID:10330150].
MUTATION: Cryptococcus neoformans CDC43 is important for thermotolerance, morphogenesis, and virulence [PMID:24014765].
MUTATION: Δsmt1 mutant loses more than 80% of its virulence compared with the wild type and the reconstituted strain [PMID:22151739].
MUTATION: Pkh2-02-mediated signaling in C. neoformans is crucial for stress tolerance, host-pathogen interactions, and both temperature-dependent and -independent virulence [PMID:23087368].
MUTATION: The loss of VCX1 does not influence cell wall integrity or capsule size but decreases secretion of the major capsular polysaccharide glucuronoxylomannan (GXM) in culture supernatants.Vcx1 also influences C. neoformans phagocytosis by murine macrophages and is required for full virulence in mice [PMID:20889719].
MUTATION: The Δaph1 mutant had reduced virulece in both Galleria mellonella and mice model [PMID:25227465].
MUTATION: CFT2 played no apparent role in iron acquisition;cft2 mutant was attenuated for virulence [PMID:18282105].
MUTATION: ERG11 is the target of FLC and AFR1, the major transporter of azoles in C. neoformans [PMID:20368972][PMID:20368972].
MUTATION: RNA interference of ADA1 expression in Cryptococcus neoformans var. grubii serotype A lead to slow-growing and acapsular [PMID:14622425].
MUTATION: CnΔsec14-1 was hypovirulent in mice and did not disseminate to the CNS by day 14 post infection. Furthermore, macrophage expulsion of live CnΔsec14-1was reduced [PMID:21453402].
MUTATION: The mutantation of UVE1 leads to a UV hypersensitive phenotype [PMID:24039606].
MUTATION: RDI1-overexpressing strains exhibited altered morphology compared to that of the wild type, with apparent defects in maintaining proper cell polarity and cytokinesis. RDI1 deletion resulted in increased vacuole size in tissue culture medium and aberrant cell morphology at neutral pH [PMID:18779335].
MUTATION: The cts1 mutant exhibited defects in cell separation, growth, mating, and haploid fruiting however these were inviable when calcineurin was mutated or inhibited [PMID:14555485].
MUTATION: Eca1 is involved in maintaining ER function, thus contributing to stress tolerance and virulence acting in parallel with Ca2+-calcineurin signaling [PMID:17502401].
MUTATION: This gene encodes one of endochitinases of Cryptococcus neoformans and involved in sexual reproduction [PMID:19734369].
MUTATION: hxt1 mutant strain showed virulence similar to that of the wild-type strain in experiments with Caenorhabditis elegans [PMID:15907385].
MUTATION: AFR1 affects the resistance of Cryptococcus neoformans to microglia-mediated antifungal activity by delaying phagosomal maturation [PMID:19220870].AFR1 deletion lead to the hypersusceptibility to fluconazole of Cryptococcus neoformans in vitro [PMID:19220870].
MUTATION: SPE3-lys9 mutants grew slowly at 30 degrees C, were temperature sensitive in rich medium, and died upon lysine starvation [PMID:15189996].
MUTATION: One of the five components of the homologous RAM-signaling pathway in C. neoformans, deletion of CBK1 gene leading to morphological change of this fungi [PMID:16775005].
MUTATION: KREgenes are required for b-1,6-glucan synthesis,maintenance of capsule architecture and cell wall proteinanchoring in Cryptococcus neoformans [PMID:20384682].
MUTATION: The CPL1 gene is required for capsular formation and virulence [PMID:25261494].
MUTATION: Hxs1 is required for glucose uptake. hxs1Δ mutant exhibited a significant reduction in glucose uptake activity [PMID:23691177].
MUTATION: Mid1, a binding partner of Cch1,function as a store-operated Ca(2+)-selective channel gated by depletion of endoplasmic reticulum (ER) Ca(2+) stores [PMID:23175710].
MUTATION: THR1 were essential for the growth of C. neoformans in rich media, when ammonium was the nitrogen source, or when threonine was supplied as an amino acid instead of a dipeptide [PMID:18757810].
MUTATION: The pex1 and pex6 deletion mutants were unable to localize the fluorescent DsRED-SKL protein to peroxisomal punctate structures, in contrast to wild-type cells. pex1 and pex6 single mutants and a pex1 pex6 double mutant exhibit identical phenotypes, including abolished growth on fatty acids but no growth difference on acetate [PMID:17041184].
MUTATION: Deletion of PCK1 results in defective growth on lactic acid, normal growth on glucose, and attenuated virulence [PMID:15765146].
MUTATION: Cdc24 is a Ras1 effector in C. neoformans to mediate the ability of this fungus to grow at high temperature. Ras1-Cdc24 signalling cascade functions specifically through one of the three Cdc42/Rac1 homologues in C. neoformans [PMID:17233829].
MUTATION: VPS41 plays a key role in regulating starvation response in this pathogenic organism and that defects in cell cycle arrest are associated with attenuated pathogenic fitness in mammalian hosts [PMID:16879414].
MUTATION: Deletion of each PIK1, RUB1, and ENA1 differentially reduced pulmonary growth and dissemination rates of C. neoformans and extended mice survival [PMID:22846723].
MUTATION: itr1a itr3c double mutants showed significant virulence attenuation in murine infection models [PMID:21398509].
MUTATION: ACL1 Gene is responsible for ATP-citrate lyase synthesis and acl1 mutants were unable to cause disease in a murine inhalation model [PMID:23078142].
MUTATION: Deletion of PDK1, SIN1 or YPK1 but not MPK1 affected cell viability in the presence of sphingolipid biosynthesis inhibitors [PMID:22339665].
MUTATION: Deletion of SIN1 affected cell viability in the presence of sphingolipid biosynthesis inhibitors [PMID:22339665].
MUTATION: Endocytic processes were hampered in the sac6Δ mutant, but cell polarity and cytokinesis were not visibly disturbed however had no effect on virulence in mice [PMID:22562467].
MUTATION: BLP1 gene knock promoted the phagocytosis of Cryptococcus by macrophages in vitro [PMID:21402362].
MUTATION: bck1 mutant had defects in cell wall integrity and high temperature endurance [PMID:16194228].
MUTATION: Orthologs of mammalian SREBP and Scap.fission yeast Scp1 responds to 4-methyl sterols and thus shares properties with mammalian HMG-CoA reductase, a sterol-sensing domain protein whose degradation is regulated by the 4-methyl sterol lanosterol [PMID:17595166].
MUTATION: Deletion of UGD1 blocked not only the synthesis of UDP-glucuronic acid but also that of UDP-xylose and modifications in the cell wall [PMID:15590833].
MUTATION: CAT1 encode putative spore-specific catalases, however cat1 mutant is absent of phenotype of virulence changes in mouse infection models [PMID:16963629].
MUTATION: The resulting mutants exhibited moderately elevated levels of melanin and capsule production relative to the wild type [PMID:16339715].
MUTATION: Can2 is the main carbonic anhydrase and suggest a physiological role for bicarbonate during C. neoformans growth [PMID:16400172].
MUTATION: Xylbeta1,2-transferase (Cxt1p) that participates in capsular polysaccharide biosynthesis is also the sole transferase responsible for adding xylose to C. neoformans glycosphingolipids [PMID:17430900][PMID:17430900].
MUTATION: PTP1 and PTP2 were found to be stress-inducible genes, which were controlled by the MAPK Hog1 and the transcription factor Atf1. Ptp2 suppressed the hyperphosphorylation of Hog1 and was involved in mediating vegetative growth, sexual differentiation, stress responses, antifungal drug resistance, and virulence factor regulation through the negative-feedback loop of the HOG pathway. In contrast, Ptp1 was not essential for Hog1 regulation, despite its Hog1-dependent induction [PMID:24728196].
MUTATION: Targeted deletion of ICL1 resulted in a dramatic decline in viability of C. neoformans cells under nitrogen deprivation [PMID:27350614].
MUTATION: Downstream regulation of the Rim101 transcription factor and determined potential cell wall processes involved in the capsule attachment defects and altered mechanisms of virulence in the rim101? mutant [PMID:23550133].
MUTATION: The CnMT1 was identified as one of the metallothioneins (MTs) and played an essential role in C. neoformans copper resistance [PMID:24317230].
MUTATION: Spo11 and Ubc5 promote sporulation during both bisexual and unisexual reproduction [PMID:23966871].
MUTATION: URE2 gene product is involved in the utilization of urea by the organism. The mutant had reduced virulence in mouse infection models [PMID:17159224].
MUTATION: ubp5Δ mutant exhibited severely attenuated virulence and many distinct phenotypes, including decreased capsule formation, hypomelanization, defective sporulation, and elevated sensitivity to several external stressors [PMID:22719877].
MUTATION: Plc1 is a central regulator of cryptococcal virulence, acting through the protein kinase C/MAPK pathway, that it regulates release of Plb1 from the plasma membrane and is a candidate antifungal drug target [PMID:18532984].
MUTATION: Cda1 is one of the four putative chitin/polysaccharide deacetylases in C. neoformans. The chitosan production was abolished only in the cda1Δcda2Δcda3Δ triple-deletion strain however CDA1 single deletion was not sufficient to affect the chiitosan levels [PMID:17400891].
MUTATION: GMT1 is one of the genes encoding GDP-mannose transporters in C. neoformans. Deletion of the GMT1 gene yields cells with small capsules and a defect in capsule induction [PMID:17351078].
MUTATION: The Rac paralogs play a primary role in polarized growth via the organization of reactive oxygen species and play only a minor role in the organization of actin [PMID:23748012].
MUTATION: UGE2 is necessary for C. neoformans cells to utilize galactose as a carbon source at 30 degrees C but is not required for virulence. In contrast, deletion of UGE1 does not affect cell growth on galactose at this temperature [PMID:18820075].
MUTATION: Ypd1 is required for the viability of C. neoformans via the Hog1 mitogen-activated protein kinase (MAPK) pathway but plays multiple cellular roles in both a Hog1-dependent and -independent manner [PMID:21642509].
MUTATION: This gene belongs to the polycomb system that assembles repressive subtelomeric domains of H3K27 methylation (H3K27me) in the yeast Cryptococcus neoformans[PMID:25533783].
MUTATION: The mutant is sensitive to various peroxide stresses while showing wild-type resistance to other oxidant stresses and exhibit wild-type virulence in a mouse model of cryptococcosis [PMID:16079336].
MUTATION: Znf3 participates in transposon silencing during unisexual reproduction and may serve as a link between RNAi silencing and sexual [PMID:23966871].
MUTATION: Kic1 in one of the components of RAM signaling pathway.Disruption of this pathway leads to hyperpolarization and attenuated virulence of Cryptococcus neoformans [PMID:16775005].
MUTATION: One of the genes involved in melanization of Cryptococcus neoformans [PMID:16102007].
MUTATION: Δarg1 mutants had impaired thermotolerance, compromised cell walls, reduced capsule production and melanization, defective cell separation, and the inability to form mating filaments and attenuated homeostasis and virulence in the Galleria mellonella infection model [PMID:23381992].
MUTATION: FRE3 was shown to express an iron reductase activity and to play a role in iron-dependent growth of C. neoformans. Overexpression of FRE3 in the two original environmental strains increased growth in the macrophage cell line J774.16 and increased virulence [PMID:24692633].
MUTATION: The Δapp1 mutant strain showed a decreased virulence in mice deficient for complement C5 (A/Jcr), but it was hypervirulent in mice deficient for T and NK cells (Tgε26) [PMID:14523045].
MUTATION: The Δall1 mutants produced a shorter exo-PS with less branching and structural complexity [PMID:23565821].
MUTATION: Antifungal activity of rapamycin and rapamycin analogs is mediated via conserved complexes with FKBP12 and Tor kinase homologs in divergent yeasts [PMID:11600372].
MUTATION: SXI1alpha establishes alpha cell identity and controls progression through the sexual cycle. Ectopic expression of SXI1alpha in a cells is sufficient to drive a/alpha sexual development [PMID:12464634].
MUTATION: OVA1 encodes a putative phosphatidylethanolamine-binding protein that appears to negatively influence capsule production and melanin accumulation [PMID:17367210].
MUTATION: The pex1 and pex6 deletion mutants were unable to localize the fluorescent DsRED-SKL protein to peroxisomal punctate structures, in contrast to wild-type cells. The pex1 mutant exhibits wild-type virulence in a murine inhalation model and in an insect host, demonstrating that peroxisomes are not required for virulence under these conditions [PMID:17041184].
MUTATION: C. neoformans STE50 gene has both conserved and novel functions during sexual reproduction and monokaryotic fruiting, and these functions are domain-dependent [PMID:21299652].
MUTATION: Ctr1 is a Cu transporter and this gene was significantly induced under Cu limited conditions [PMID:21819456].
MUTATION: Disruption of the CIN1 gene had a pleiotropic effect on growth, normal cytokinesis, intracellular transports and the production of several virulence factors. Additionally, Cin1 interacts with cryptococcal Cdc42 and Wsp1 (a WASP homologue) proteins in vitro, suggesting a conserved role in the regulation of the actin cytoskeleton [PMID:20345666].
MUTATION: Fbp1 mutants showed normal growth and produced normal major virulence factors. Fbp1 is important for fungal sexual reproduction and the mutant showed attenuated virulence in mouse models [PMID:21478432].
A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism.
A material entity which is clinically abnormal and part of an extended organism. Disorders are the physical basis of disease.
The totality of all processes through which a given disease instance is realized.
replace 'OBI:occurrence of disease', need to add logical definition The axioms of OBI occurence of disease: Equivalent classes: realizes some disease Superclasses: 'has part' some 'pathologic process' 'has participant' some (organism and ('has role' some 'host of immune response role')) biological_process realizes some 'host of immune response role'
An object aggregate consisting of an organism and all material entities located within the organism, overlapping the organism, or occupying sites formed in part by the organism.
A process that involves an interaction between a host and a pathogen which can be a virus, bacterium, parasite, fungus, etc.
Potentially we can list 'host-pathogen interaction' as a subclass of GO:interaction with host (http://purl.obolibrary.org/obo/GO_0051701). However, the GO term is a subclass of "interspecies interaction between organisms". Literally, a virus is not considered as an organism, but a virus is a pathogen. Therefore, this GO term (GO_0051701) may not be appropriate as the parent term of 'host-pathogen interaction'. -- Edison and Oliver
host pathogen interaction
host bacterial pathogen interaction
host viral pathogen interaction
host parasitic pathogen interaction
host fungal pathogen interaction
host M. tuberculosis pathogen interaction
host Salmonella spp. pathogen interaction
host N. meningitidis pathogen interaction
host C. diphtheriae pathogen interaction
host A. salmonicida pathogen interaction
host M. gallisepticum pathogen interaction
host A. pleuropneumoniae pathogen interaction
host Rickettsia spp. pathogen interaction
host Y. pseudotuberculosis pathogen interaction
host B. pseudomallei pathogen interaction
host Y. enterocolitica pathogen interaction
host B. burgdorferi pathogen interaction
host L. monocytogenes pathogen interaction
host B. bronchiseptica pathogen interaction
host Leptospira spp. pathogen interaction
host C. perfringens pathogen interaction
host C. trachomatis pathogen interaction
host L. pneumophila pathogen interaction
host Bartonella spp. pathogen interaction
host Enterococcus spp. pathogen interaction
host Human immunodeficiency virus pathogen interaction
host Influenza virus pathogen interaction
host Pseudorabies virus pathogen interaction
host Classical swine fever virus pathogen interaction
host Bovine herpesvirus 1 pathogen interaction
host Infectious hematopoietic necrosis virus pathogen interaction
host Herpes simplex virus type 1 pathogen interaction
host Rift valley fever virus pathogen interaction
host SARS-related coronavirus pathogen interaction
host Bovine respiratory syncytial virus pathogen interaction
host Feline immunodeficiency virus pathogen interaction
host Feline herpesvirus 1 pathogen interaction
host Gallid herpesvirus 1 pathogen interaction
host Feline infectious peritonitis virus pathogen interaction
host Vaccinia virus pathogen interaction
host Simian immunodeficiency virus pathogen interaction
host Ectromelia virus pathogen interaction
A virulence factor role that is inherited in a gene that can encode for a protein, and either the gene or the protein will play the role of a virulence factor.
virulence factor gene role
A role that is inherited in a pathogen molecule that makes the pathogen virulence in terms of colonization, immunoevasion, immunosuppression, entry into or exit out of host cell, and obtaining nutrient from the host.
virulence factor role
A virulence factor role that is inherited in a protein
virulence factor protein role
human host pathogen interaction
human cell host pathogen interaction
human cell line cell host pathogen interaction
mouse host pathogen interaction
mouse cell host pathogen interaction
mouse cell line cell host pathogen interaction
rabbit host pathogen interaction
rabbit cell host pathogen interaction
rabbit cell line cell host pathogen interaction
hamster host pathogen interaction
hamster cell host pathogen interaction
hamster cell line cell host pathogen interaction
chicken host pathogen interaction
chicken cell host pathogen interaction
chicken cell line cell host pathogen interaction
monkey host pathogen interaction
monkey cell host pathogen interaction
monkey cell line cell host pathogen interaction
cattle host pathogen interaction
cattle cell host pathogen interaction
cattle cell line cell host pathogen interaction
goat host pathogen interaction
goat cell host pathogen interaction
goat cell line cell host pathogen interaction
C. elegans host pathogen interaction
C. elegans cell host pathogen interaction
C. elegans cell line cell host pathogen interaction
E. coli eatA mutant interaction with rabbit
E. coli iroB mutant interaction with chicken
E. coli iroC mutant interaction with chicken
E. coli iroD mutant interaction with chicken
E. coli iroN mutant interaction with mouse
E. coli iucA mutant interaction with mouse
E. coli iucB mutant interaction with mouse
E. coli iucC mutant interaction with mouse
E. coli iucD mutant interaction with mouse
E. coli iutA mutant interaction with mouse
E. coli bfpA mutant interaction with human
E. coli bfpF mutant interaction with human
E. coli perA mutant interaction with human
Shigella ipgA mutant interaction with mouse
Shigella ipgA mutant interaction with mouse epithelial cell
Shigella virG mutant interaction with monkey
Shigella virG mutant interaction with monkey epithelial cell
Shigella ipgB mutant interaction with mouse
Shigella ipgB mutant interaction with mouse epithelial cell
Shigella ipaH9.8 mutant interaction with mouse
Shigella sepA mutant interaction with rabbit
Shigella IpaH7.8 mutant interaction with mouse
Shigella IpaH7.8 mutant interaction with mouse macrophage cell
M. tuberculosis sigF mutant interaction with mouse
M. tuberculosis fbpA mutant interaction with mouse
M. tuberculosis panD mutant interaction with mouse
M. tuberculosis sigH mutant interaction with mouse
M. tuberculosis MT3523 mutant interaction with human
M. tuberculosis MT3523 mutant interaction with human macrophage cell
M. tuberculosis MT3523 mutant interaction with mouse
M. tuberculosis MT3523 mutant interaction with mouse macrophage cell
M. tuberculosis hspR mutant interaction with mouse
M. tuberculosis katG mutant interaction with mouse
M. tuberculosis sodC mutant interaction with mouse
M. tuberculosis sodC mutant interaction with mouse macrophage cell
M. tuberculosis mgtC mutant interaction with human
M. tuberculosis mgtC mutant interaction with human macrophage cell
M. tuberculosis mgtC mutant interaction with mouse
M. tuberculosis mgtC mutant interaction with mouse macrophage cell
M. tuberculosis senX3 mutant interaction with mouse
M. tuberculosis regX3 mutant interaction with mouse
M. tuberculosis proC mutant interaction with mouse
M. tuberculosis trpD mutant interaction with mouse
M. tuberculosis lspA mutant interaction with mouse
M. tuberculosis sigC mutant interaction with mouse
M. tuberculosis sigE mutant interaction with human
M. tuberculosis sigE mutant interaction with human macrophage cell
M. tuberculosis sigE mutant interaction with mouse
M. tuberculosis sigE mutant interaction with mouse macrophage cell
M. tuberculosis leuD mutant interaction with mouse
M. tuberculosis cysH mutant interaction with mouse
M. tuberculosis mma4 mutant interaction with mouse
M. tuberculosis sigL mutant interaction with mouse
M. tuberculosis erp mutant interaction with mouse
M. tuberculosis panC mutant interaction with mouse
M. tuberculosis mprA mutant interaction with mouse
M. tuberculosis dppD mutant interaction with mouse
M. tuberculosis PPE31 mutant interaction with mouse
M. tuberculosis pks7 mutant interaction with mouse
M. tuberculosis pks10 mutant interaction with mouse
M. tuberculosis Rv1710 mutant interaction with mouse
M. tuberculosis coaA mutant interaction with mouse
M. tuberculosis argJ mutant interaction with mouse
M. tuberculosis prrA mutant interaction with mouse
M. tuberculosis prrA mutant interaction with mouse macrophage cell
M. tuberculosis ompA mutant interaction with mouse
M. tuberculosis ompA mutant interaction with mouse macrophage cell
M. tuberculosis Rv3651 mutant interaction with mouse
M. tuberculosis hemN mutant interaction with mouse
M. tuberculosis Rv2387 mutant interaction with mouse
M. tuberculosis Rv1747 mutant interaction with mouse
M. tuberculosis Rv3631 mutant interaction with mouse
M. tuberculosis Rv1930c mutant interaction with mouse
M. tuberculosis Rv3616c mutant interaction with mouse
M. tuberculosis pepD mutant interaction with mouse
M. tuberculosis lysS mutant interaction with mouse
M. tuberculosis Rv1931c mutant interaction with mouse
M. tuberculosis Rv0950c mutant interaction with mouse
M. tuberculosis Rv1111c mutant interaction with mouse
M. tuberculosis nirA mutant interaction with mouse
M. tuberculosis Rv1939 mutant interaction with mouse
M. tuberculosis Rv3676 mutant interaction with human
M. tuberculosis Rv3676 mutant interaction with human macrophage cell
M. tuberculosis Rv3676 mutant interaction with mouse
M. tuberculosis Rv3676 mutant interaction with mouse macrophage cell
M. tuberculosis Rv3701c mutant interaction with mouse
M. tuberculosis secA2 mutant interaction with mouse
M. tuberculosis Rv3717 mutant interaction with mouse
M. tuberculosis Rv3615c mutant interaction with mouse
M. tuberculosis Rv3615c mutant interaction with mouse macrophage cell
M. tuberculosis Rv3614c mutant interaction with mouse
M. tuberculosis Rv3614c mutant interaction with mouse macrophage cell
M. tuberculosis Rv3683 mutant interaction with mouse
M. tuberculosis Rv3723 mutant interaction with mouse
M. tuberculosis recN mutant interaction with mouse
M. tuberculosis Rv1524 mutant interaction with mouse
M. tuberculosis Rv1109c mutant interaction with mouse
M. tuberculosis Rv3649 mutant interaction with mouse
M. tuberculosis Rv1128c mutant interaction with mouse
M. tuberculosis glpX mutant interaction with mouse
M. tuberculosis Rv2437 mutant interaction with mouse
M. tuberculosis hrcA mutant interaction with mouse
M. tuberculosis Rv1144 mutant interaction with mouse
M. tuberculosis Rv1974 mutant interaction with mouse
M. tuberculosis mce3A mutant interaction with mouse
M. tuberculosis plcA mutant interaction with mouse
M. tuberculosis plcB mutant interaction with mouse
M. tuberculosis plcC mutant interaction with mouse
M. tuberculosis Rv1192 mutant interaction with mouse
M. tuberculosis furB mutant interaction with mouse
M. tuberculosis cysE mutant interaction with mouse
M. tuberculosis Rv0386 mutant interaction with mouse
M. tuberculosis pks16 mutant interaction with mouse
M. tuberculosis Rv1021 mutant interaction with mouse
M. tuberculosis Rv1184c mutant interaction with mouse
M. tuberculosis fadD21 mutant interaction with mouse
M. tuberculosis lpqT mutant interaction with mouse
M. tuberculosis mmpL10 mutant interaction with mouse
M. tuberculosis kdpD mutant interaction with mouse
M. tuberculosis rfbE mutant interaction with mouse
M. tuberculosis embA mutant interaction with mouse
M. tuberculosis Rv3805c mutant interaction with mouse
M. tuberculosis pirG mutant interaction with mouse
M. tuberculosis mmpL8 mutant interaction with mouse
M. tuberculosis Rv3869 mutant interaction with mouse
M. tuberculosis Rv3865 mutant interaction with mouse
M. tuberculosis sodA mutant interaction with mouse
M. tuberculosis Rv3864 mutant interaction with mouse
M. tuberculosis ethR mutant interaction with mouse
M. tuberculosis PE35 mutant interaction with mouse
M. tuberculosis esxB mutant interaction with mouse
M. tuberculosis Rv3868 mutant interaction with mouse
M. tuberculosis Rv3866 mutant interaction with mouse
M. tuberculosis PPE68 mutant interaction with mouse
M. tuberculosis Rv3871 mutant interaction with mouse
M. tuberculosis Rv3870 mutant interaction with mouse
M. tuberculosis Rv3876 mutant interaction with mouse
M. tuberculosis Rv3877 mutant interaction with mouse
M. tuberculosis Rv3882c mutant interaction with mouse
M. tuberculosis esxA mutant interaction with mouse
M. tuberculosis Rv3887c mutant interaction with mouse
M. tuberculosis mycP1 mutant interaction with mouse
M. tuberculosis Rv3910 mutant interaction with mouse
M. tuberculosis pcaA mutant interaction with mouse
M. tuberculosis Rv1590 mutant interaction with mouse
M. tuberculosis proV mutant interaction with mouse
M. tuberculosis bioB mutant interaction with mouse
M. tuberculosis bioA mutant interaction with mouse
M. tuberculosis bioF1 mutant interaction with mouse
M. tuberculosis Rv1560 mutant interaction with mouse
M. tuberculosis xthA mutant interaction with mouse
M. tuberculosis thiE mutant interaction with mouse
M. tuberculosis pknG mutant interaction with mouse
M. tuberculosis pks5 mutant interaction with mouse
M. tuberculosis Rv1514c mutant interaction with mouse
M. tuberculosis Rv0326 mutant interaction with mouse
M. tuberculosis Rv1465 mutant interaction with mouse
M. tuberculosis Rv1460 mutant interaction with mouse
M. tuberculosis ctpD mutant interaction with mouse
M. tuberculosis Rv1422 mutant interaction with mouse
M. tuberculosis Rv0249c mutant interaction with mouse
M. tuberculosis lprG mutant interaction with mouse
M. tuberculosis Rv1410c mutant interaction with mouse
M. tuberculosis Rv1405c mutant interaction with mouse
M. tuberculosis Rv0218 mutant interaction with mouse
M. tuberculosis Rv0216 mutant interaction with mouse
M. tuberculosis Rv0204c mutant interaction with mouse
M. tuberculosis mmpL11 mutant interaction with mouse
M. tuberculosis Rv0199 mutant interaction with mouse
M. tuberculosis Rv0176 mutant interaction with mouse
M. tuberculosis Rv1371 mutant interaction with mouse
M. tuberculosis Rv0175 mutant interaction with mouse
M. tuberculosis lprK mutant interaction with mouse
M. tuberculosis mce1C mutant interaction with mouse
M. tuberculosis mce1B mutant interaction with mouse
M. tuberculosis yrbE1B mutant interaction with mouse
M. tuberculosis fadD5 mutant interaction with mouse
M. tuberculosis mce1A mutant interaction with mouse
M. tuberculosis fadD33 mutant interaction with mouse
M. tuberculosis murI mutant interaction with mouse
M. tuberculosis Rv1333 mutant interaction with mouse
M. tuberculosis Rv1332 mutant interaction with mouse
M. tuberculosis fadA4 mutant interaction with mouse
M. tuberculosis Rv0100 mutant interaction with mouse
M. tuberculosis fadD10 mutant interaction with mouse
M. tuberculosis Rv0098 mutant interaction with mouse
M. tuberculosis atpB mutant interaction with mouse
M. tuberculosis nrp mutant interaction with mouse
M. tuberculosis Rv1284 mutant interaction with mouse
M. tuberculosis Rv1272c mutant interaction with mouse
M. tuberculosis lpqZ mutant interaction with mouse
M. tuberculosis sugC mutant interaction with mouse
M. tuberculosis sugB mutant interaction with mouse
M. tuberculosis sugA mutant interaction with mouse
M. tuberculosis tatB mutant interaction with mouse
M. tuberculosis lpqY mutant interaction with mouse
M. tuberculosis accD1 mutant interaction with mouse
M. tuberculosis Rv0485 mutant interaction with mouse
M. tuberculosis Rv2885c mutant interaction with mouse
M. tuberculosis Rv3574 mutant interaction with mouse
M. tuberculosis ftsY mutant interaction with mouse
M. tuberculosis gcvT mutant interaction with mouse
M. tuberculosis Rv3551 mutant interaction with mouse
M. tuberculosis aceE mutant interaction with mouse
M. tuberculosis Rv3519 mutant interaction with mouse
M. tuberculosis Rv2472 mutant interaction with mouse
M. tuberculosis fadA6 mutant interaction with mouse
M. tuberculosis ilvB1 mutant interaction with mouse
M. tuberculosis pks15 mutant interaction with mouse
M. tuberculosis ppgK mutant interaction with mouse
M. tuberculosis ung mutant interaction with mouse
M. tuberculosis fadD28 mutant interaction with mouse
M. tuberculosis ceoC mutant interaction with mouse
M. tuberculosis mmpL7 mutant interaction with mouse
M. tuberculosis Rv1204c mutant interaction with mouse
M. tuberculosis hspX mutant interaction with mouse
M. tuberculosis hspX mutant interaction with mouse macrophage cell
M. tuberculosis sigD mutant interaction with human
M. tuberculosis sigD mutant interaction with human macrophage cell
M. tuberculosis sigD mutant interaction with mouse
M. tuberculosis sigD mutant interaction with mouse macrophage cell
M. tuberculosis gcp mutant interaction with mouse
M. tuberculosis whiB3 mutant interaction with mouse
M. tuberculosis fadD26 mutant interaction with mouse
M. tuberculosis fadE22 mutant interaction with mouse
M. tuberculosis Rv0566c mutant interaction with mouse
M. tuberculosis fabG mutant interaction with mouse
M. tuberculosis plsC mutant interaction with mouse
M. tuberculosis mce2A mutant interaction with mouse
M. tuberculosis Rv2707 mutant interaction with mouse
M. tuberculosis cyp125 mutant interaction with mouse
M. tuberculosis serB2 mutant interaction with mouse
M. tuberculosis fadE32 mutant interaction with mouse
M. tuberculosis Rv3588c mutant interaction with mouse
M. tuberculosis fadE30 mutant interaction with mouse
M. tuberculosis Rv2224c mutant interaction with mouse
M. tuberculosis Rv2040c mutant interaction with mouse
M. tuberculosis Rv2693c mutant interaction with mouse
M. tuberculosis Rv3400 mutant interaction with mouse
M. tuberculosis lppX mutant interaction with mouse
M. tuberculosis drrB mutant interaction with mouse
M. tuberculosis Rv1211 mutant interaction with mouse
M. tuberculosis Rv2038c mutant interaction with mouse
M. tuberculosis Rv3472 mutant interaction with mouse
M. tuberculosis Rv2912c mutant interaction with mouse
M. tuberculosis Rv3335c mutant interaction with mouse
M. tuberculosis Rv0636 mutant interaction with mouse
M. tuberculosis Rv3371 mutant interaction with mouse
M. tuberculosis mmaA3 mutant interaction with mouse
M. tuberculosis amiD mutant interaction with mouse
M. tuberculosis mkl mutant interaction with mouse
M. tuberculosis fadE28 mutant interaction with mouse
M. tuberculosis Rv2206 mutant interaction with mouse
M. tuberculosis pks1 mutant interaction with mouse
M. tuberculosis drrA mutant interaction with mouse
M. tuberculosis end mutant interaction with mouse
M. tuberculosis Rv2553c mutant interaction with mouse
M. tuberculosis ltp3 mutant interaction with mouse
M. tuberculosis Rv2734 mutant interaction with mouse
M. tuberculosis yrbE4A mutant interaction with mouse
M. tuberculosis cobL mutant interaction with mouse
M. tuberculosis cobC mutant interaction with mouse
M. tuberculosis mce4A mutant interaction with mouse
M. tuberculosis pks12 mutant interaction with mouse
M. tuberculosis mce4C mutant interaction with mouse
M. tuberculosis Rv2275 mutant interaction with mouse
M. tuberculosis lprN mutant interaction with mouse
M. tuberculosis Rv3534c mutant interaction with mouse
M. tuberculosis Rv3489 mutant interaction with mouse
M. tuberculosis ddl mutant interaction with mouse
M. tuberculosis lipF mutant interaction with mouse
M. tuberculosis cpsA mutant interaction with mouse
M. tuberculosis ltp2 mutant interaction with mouse
M. tuberculosis Rv3541c mutant interaction with mouse
M. tuberculosis Rv2696c mutant interaction with mouse
M. tuberculosis Rv3542c mutant interaction with mouse
M. tuberculosis drrC mutant interaction with mouse
M. tuberculosis Rv2277c mutant interaction with mouse
M. tuberculosis proS mutant interaction with mouse
M. tuberculosis Rv2857c mutant interaction with mouse
M. tuberculosis Rv2813 mutant interaction with mouse
M. tuberculosis Rv2998 mutant interaction with mouse
M. tuberculosis Rv3087 mutant interaction with mouse
M. tuberculosis Rv3258c mutant interaction with mouse
M. tuberculosis ctpC mutant interaction with mouse
M. tuberculosis Rv3277 mutant interaction with mouse
M. tuberculosis mtrA mutant interaction with mouse
M. tuberculosis phoP mutant interaction with mouse
M. tuberculosis Rv3168 mutant interaction with mouse
M. tuberculosis Rv3114 mutant interaction with mouse
M. tuberculosis Rv3178 mutant interaction with mouse
M. tuberculosis Rv3103c mutant interaction with mouse
M. tuberculosis Rv2004c mutant interaction with mouse
M. tuberculosis Rv3229c mutant interaction with mouse
M. tuberculosis Rv3236c mutant interaction with mouse
M. tuberculosis Rv3050c mutant interaction with mouse
M. tuberculosis moeB1 mutant interaction with mouse
M. tuberculosis Rv3210c mutant interaction with mouse
M. tuberculosis Rv2808 mutant interaction with mouse
H. pylori cagA mutant interaction with monkey
H. pylori vacA mutant interaction with mouse
F. tularensis FTL_0837 mutant interaction with mouse
F. tularensis FTL_0846 mutant interaction with mouse
F. tularensis FTL_1528 mutant interaction with mouse
F. tularensis FTL_1096 mutant interaction with mouse
F. tularensis FTL_1097 mutant interaction with mouse
F. tularensis FTL_1867 mutant interaction with mouse
F. tularensis FTL_1672 mutant interaction with mouse
F. tularensis FTL_1678 mutant interaction with mouse
F. tularensis tig mutant interaction with mouse
F. tularensis FTL_0892 mutant interaction with mouse
F. tularensis clpX mutant interaction with mouse
F. tularensis FTL_0894 mutant interaction with mouse
F. tularensis FTL_0899 mutant interaction with mouse
F. tularensis FTL_0903 mutant interaction with mouse
F. tularensis FTL_0483 mutant interaction with mouse
F. tularensis FTL_0485 mutant interaction with mouse
F. tularensis FTL_1134 mutant interaction with mouse
F. tularensis FTL_1030 mutant interaction with mouse
F. tularensis FTL_0768 mutant interaction with mouse
F. tularensis FTL_0584 mutant interaction with mouse
F. tularensis FTL_0421 mutant interaction with mouse
F. tularensis FTL_0428 mutant interaction with mouse
F. tularensis FTL_0430 mutant interaction with mouse
F. tularensis FTL_0439 mutant interaction with mouse
F. tularensis FTL_0950 mutant interaction with mouse
F. tularensis FTL_0960 mutant interaction with mouse
F. tularensis rpmJ mutant interaction with mouse
F. tularensis FTL_0616 mutant interaction with mouse
F. tularensis FTL_0617 mutant interaction with mouse
F. tularensis FTL_0009 mutant interaction with mouse
F. tularensis FTL_0010 mutant interaction with mouse
F. tularensis FTL_0012 mutant interaction with mouse
F. tularensis secE mutant interaction with mouse
F. tularensis FTL_0663 mutant interaction with mouse
F. tularensis FTL_1233 mutant interaction with mouse
F. tularensis FTL_1240 mutant interaction with mouse
F. tularensis FTL_1225 mutant interaction with mouse
F. tularensis FTL_0645 mutant interaction with mouse
F. tularensis FTL_0723 mutant interaction with mouse
F. tularensis FTL_1419 mutant interaction with mouse
F. tularensis FTL_0803 mutant interaction with mouse
F. tularensis FTL_1075 mutant interaction with mouse
F. tularensis FTL_0111 mutant interaction with mouse
F. tularensis FTL_0112 mutant interaction with mouse
F. tularensis FTL_0113 mutant interaction with mouse
F. tularensis FTL_0133 mutant interaction with mouse
F. tularensis FTL_1354 mutant interaction with mouse
F. tularensis sucC mutant interaction with mouse
F. tularensis FTL_1554 mutant interaction with mouse
F. tularensis FTL_1601 mutant interaction with mouse
F. tularensis FTL_1273 mutant interaction with mouse
F. tularensis FTL_1274 mutant interaction with mouse
F. tularensis FTL_1275 mutant interaction with mouse
F. tularensis FTL_1936 mutant interaction with mouse
F. tularensis FTL_1622 mutant interaction with mouse
F. tularensis FTL_1623 mutant interaction with mouse
F. tularensis rpmA mutant interaction with mouse
F. tularensis FTL_1458 mutant interaction with mouse
F. tularensis FTL_R0003 mutant interaction with mouse
F. tularensis FTL_1504 mutant interaction with mouse
F. tularensis FTL_1266 mutant interaction with mouse
F. tularensis FTL_0928 mutant interaction with mouse
F. tularensis rpsA mutant interaction with mouse
F. tularensis glpX mutant interaction with mouse
F. tularensis FTL_0514 mutant interaction with mouse
F. tularensis FTL_0519 mutant interaction with mouse
F. tularensis FTL_0520 mutant interaction with mouse
F. tularensis FTL_0094 mutant interaction with mouse
F. tularensis rpsU mutant interaction with mouse
F. tularensis rplT mutant interaction with mouse
F. tularensis FTL_1414 mutant interaction with mouse
F. tularensis FTL_1415 mutant interaction with mouse
F. tularensis FTL_1416 mutant interaction with mouse
F. tularensis FTL_1832 mutant interaction with mouse
F. tularensis isftu1 mutant interaction with mouse
F. tularensis FTL_1461 mutant interaction with mouse
F. tularensis FTL_1473 mutant interaction with mouse
F. tularensis FTL_1474 mutant interaction with mouse
F. tularensis FTL_1475 mutant interaction with mouse
F. tularensis tRNA-Ile1 mutant interaction with mouse
F. tularensis FTL_0382 mutant interaction with mouse
F. tularensis FTL_0387 mutant interaction with mouse
F. tularensis FTL_1947 mutant interaction with mouse
F. tularensis FTL_1328 mutant interaction with mouse
F. tularensis FTL_0073 mutant interaction with mouse
F. tularensis FTL_0525 mutant interaction with mouse
F. tularensis FTL_0540 mutant interaction with mouse
F. tularensis FTL_0337 mutant interaction with mouse
F. tularensis FTL_1392 mutant interaction with mouse
F. tularensis FTL_1393 mutant interaction with mouse
F. tularensis FTL_0589 mutant interaction with mouse
F. tularensis FTL_0592 mutant interaction with mouse
F. tularensis FTL_0597 mutant interaction with mouse
F. tularensis FTL_0789 mutant interaction with mouse
L. monocytogenes lmo2821 mutant interaction with mouse
L. monocytogenes lmo2067 mutant interaction with mouse
L. monocytogenes gtcA mutant interaction with mouse
L. monocytogenes rnhB mutant interaction with mouse
L. monocytogenes lmo1269 mutant interaction with mouse
L. monocytogenes lmo1271 mutant interaction with mouse
L. monocytogenes tig mutant interaction with mouse
L. monocytogenes iap mutant interaction with mouse
L. monocytogenes inlA mutant interaction with mouse
L. monocytogenes aroA mutant interaction with mouse
L. monocytogenes clpB mutant interaction with mouse
L. monocytogenes lmo1745 mutant interaction with mouse
L. monocytogenes lmo1695 mutant interaction with mouse
L. monocytogenes aroB mutant interaction with mouse
L. monocytogenes lmo1829 mutant interaction with mouse
L. monocytogenes lmo1821 mutant interaction with mouse
L. monocytogenes inlC mutant interaction with mouse
L. monocytogenes lmo1076 mutant interaction with mouse
L. monocytogenes pycA mutant interaction with mouse
L. monocytogenes dltA mutant interaction with mouse
L. monocytogenes lmo0135 mutant interaction with mouse
L. monocytogenes clpE mutant interaction with mouse
L. monocytogenes sod mutant interaction with mouse
L. monocytogenes fri mutant interaction with mouse
L. monocytogenes fri mutant interaction with mouse macrophage cell
L. monocytogenes inlB mutant interaction with mouse
L. monocytogenes prfA mutant interaction with mouse
L. monocytogenes plcA mutant interaction with mouse
L. monocytogenes hly mutant interaction with mouse
L. monocytogenes mpl mutant interaction with mouse
L. monocytogenes plcB mutant interaction with mouse
L. monocytogenes clpC mutant interaction with mouse
L. monocytogenes clpC mutant interaction with mouse macrophage cell
L. monocytogenes ami mutant interaction with mouse
L. monocytogenes inlG mutant interaction with mouse
L. monocytogenes inlH mutant interaction with mouse
L. monocytogenes inlE mutant interaction with mouse
L. monocytogenes clpP mutant interaction with mouse
L. monocytogenes clpP mutant interaction with mouse macrophage cell
L. monocytogenes lmo0292 mutant interaction with mouse
L. monocytogenes lmo2537 mutant interaction with mouse
L. monocytogenes relA mutant interaction with mouse
L. monocytogenes lmo0415 mutant interaction with mouse
F. tularensis FTT0054 mutant interaction with mouse
F. tularensis sodB mutant interaction with mouse
F. tularensis sthA mutant interaction with mouse
F. tularensis sucB mutant interaction with mouse
F. tularensis sucD mutant interaction with mouse
F. tularensis ksgA mutant interaction with mouse
F. tularensis surA mutant interaction with mouse
F. tularensis FTT0105c mutant interaction with mouse
F. tularensis tet mutant interaction with mouse
F. tularensis glgB mutant interaction with mouse
F. tularensis FTT0134 mutant interaction with mouse
F. tularensis FTT1441 mutant interaction with mouse
F. tularensis lon mutant interaction with mouse
F. tularensis lpnB mutant interaction with mouse
F. tularensis FTT1489 mutant interaction with mouse
F. tularensis FTT1400c mutant interaction with mouse
F. tularensis FTT0975 mutant interaction with mouse
F. tularensis metIQ mutant interaction with mouse
F. tularensis glpe mutant interaction with mouse
F. tularensis aroG mutant interaction with mouse
F. tularensis aspC1 mutant interaction with mouse
F. tularensis cdd mutant interaction with mouse
F. tularensis bioD mutant interaction with mouse
F. tularensis bioC mutant interaction with mouse
F. tularensis bipA mutant interaction with mouse
F. tularensis glgC mutant interaction with mouse
F. tularensis bioB mutant interaction with mouse
F. tularensis capB mutant interaction with mouse
F. tularensis bioF mutant interaction with mouse
F. tularensis trpG mutant interaction with mouse
F. tularensis FTT0708 mutant interaction with mouse
F. tularensis FTT0685c mutant interaction with mouse
F. tularensis FTT0667 mutant interaction with mouse
F. tularensis FTT0645c mutant interaction with mouse
F. tularensis carA mutant interaction with mouse
F. tularensis FTT1633c mutant interaction with mouse
F. tularensis FTT1640c mutant interaction with mouse
F. tularensis FTT1314c mutant interaction with mouse
F. tularensis FTT1611 mutant interaction with mouse
F. tularensis FTT1334c mutant interaction with mouse
F. tularensis FTT0615c mutant interaction with mouse
F. tularensis FTT0589 mutant interaction with mouse
F. tularensis FTT0584 mutant interaction with mouse
F. tularensis iglA mutant interaction with mouse
F. tularensis prfC mutant interaction with mouse
F. tularensis FTT1117c mutant interaction with mouse
F. tularensis mtn mutant interaction with mouse
F. tularensis FTT1103 mutant interaction with mouse
F. tularensis FTT1102 mutant interaction with mouse
F. tularensis cadA mutant interaction with mouse
F. tularensis yibK mutant interaction with mouse
F. tularensis pcs mutant interaction with mouse
F. tularensis ruvB mutant interaction with mouse
F. tularensis FTT0295 mutant interaction with mouse
F. tularensis pdpA mutant interaction with mouse
F. tularensis pdpB mutant interaction with mouse
F. tularensis pdxY mutant interaction with mouse
F. tularensis FTT0256c mutant interaction with mouse
F. tularensis FTT0209c mutant interaction with mouse
F. tularensis pgm mutant interaction with mouse
F. tularensis FTT0509c mutant interaction with mouse
F. tularensis sdhC mutant interaction with mouse
F. tularensis FTT0455c mutant interaction with mouse
F. tularensis parB mutant interaction with mouse
F. tularensis FTT0453c mutant interaction with mouse
F. tularensis FTT0443 mutant interaction with mouse
F. tularensis FTT0398c mutant interaction with mouse
F. tularensis FTT0399c mutant interaction with mouse
F. tularensis pcp mutant interaction with mouse
F. tularensis FTT1258 mutant interaction with mouse
F. tularensis htpG mutant interaction with mouse
F. tularensis dedA1 mutant interaction with mouse
F. tularensis deoB mutant interaction with mouse
F. tularensis deoD mutant interaction with mouse
F. tularensis fumA mutant interaction with mouse
F. tularensis cca mutant interaction with mouse
F. tularensis dsbB mutant interaction with mouse
F. tularensis gcvH mutant interaction with mouse
F. tularensis elbB mutant interaction with mouse
F. tularensis iglB mutant interaction with mouse
F. tularensis xerC mutant interaction with mouse
F. tularensis galE mutant interaction with mouse
F. tularensis iglC mutant interaction with mouse
F. tularensis rluC mutant interaction with mouse
F. tularensis rluB mutant interaction with mouse
F. tularensis ribB mutant interaction with mouse
F. tularensis ribA mutant interaction with mouse
F. tularensis relA mutant interaction with mouse
F. tularensis recB mutant interaction with mouse
F. tularensis recA mutant interaction with mouse
F. tularensis rbfA mutant interaction with mouse
F. tularensis qseC mutant interaction with mouse
F. tularensis pyrH mutant interaction with mouse
F. tularensis pyrF mutant interaction with mouse
F. tularensis pyrD mutant interaction with mouse
F. tularensis pyrB mutant interaction with mouse
F. tularensis putA mutant interaction with mouse
F. tularensis purN mutant interaction with mouse
F. tularensis purM mutant interaction with mouse
F. tularensis purL mutant interaction with mouse
F. tularensis purH mutant interaction with mouse
F. tularensis purF mutant interaction with mouse
F. tularensis purE mutant interaction with mouse
F. tularensis FTT1151c mutant interaction with mouse
F. tularensis FTT0918 mutant interaction with mouse
F. tularensis FTT0910 mutant interaction with mouse
F. tularensis FTT0905 mutant interaction with mouse
F. tularensis FTT0903 mutant interaction with mouse
F. tularensis FTT0891 mutant interaction with mouse
F. tularensis FTT0881c mutant interaction with mouse
F. tularensis FTT1129c mutant interaction with mouse
F. tularensis FTT0843 mutant interaction with mouse
F. tularensis FTT1747 mutant interaction with mouse
F. tularensis apt mutant interaction with mouse
F. tularensis phoH mutant interaction with mouse
F. tularensis lpnA mutant interaction with mouse
F. tularensis lpxB mutant interaction with mouse
F. tularensis FTT0800 mutant interaction with mouse
F. tularensis FTT0799 mutant interaction with mouse
F. tularensis FTT0798 mutant interaction with mouse
F. tularensis FTT0793 mutant interaction with mouse
F. tularensis FTT0790 mutant interaction with mouse
F. tularensis FTT0797 mutant interaction with mouse
F. tularensis FTT0807 mutant interaction with mouse
F. tularensis FTT0759 mutant interaction with mouse
F. tularensis FTT0792 mutant interaction with mouse
F. tularensis FTT0748 mutant interaction with mouse
F. tularensis fadD1 mutant interaction with mouse
F. tularensis fadB/acbP mutant interaction with mouse
F. tularensis feoB mutant interaction with mouse
F. tularensis cphB mutant interaction with mouse
F. tularensis cphA mutant interaction with mouse
F. tularensis uvrA mutant interaction with mouse
F. tularensis cyoB mutant interaction with mouse
F. tularensis cyoC mutant interaction with mouse
F. tularensis cyoD mutant interaction with mouse
F. tularensis folD mutant interaction with mouse
F. tularensis wbtA mutant interaction with mouse
F. tularensis FTT1416c mutant interaction with mouse
F. tularensis rpoA2 mutant interaction with mouse
F. tularensis rplY mutant interaction with mouse
F. tularensis rplW mutant interaction with mouse
F. tularensis fopA mutant interaction with mouse
F. tularensis rplQ mutant interaction with mouse
F. tularensis rplD mutant interaction with mouse
F. tularensis FTT1048c mutant interaction with mouse
F. tularensis FTT1047c mutant interaction with mouse
F. tularensis FTT1015 mutant interaction with mouse
F. tularensis secA mutant interaction with mouse
F. tularensis wbtD mutant interaction with mouse
F. tularensis wbtF mutant interaction with mouse
F. tularensis wbtG mutant interaction with mouse
F. tularensis wbtH mutant interaction with mouse
F. tularensis katG mutant interaction with mouse
F. tularensis xasA mutant interaction with mouse
F. tularensis xerD mutant interaction with mouse
F. tularensis FTT0028c mutant interaction with mouse
F. tularensis FTT0029c mutant interaction with mouse
F. tularensis FTT0057 mutant interaction with mouse
F. tularensis FTT0053 mutant interaction with mouse
F. tularensis FTT0056c mutant interaction with mouse
F. tularensis yegQ mutant interaction with mouse
F. tularensis FTT0101 mutant interaction with mouse
F. tularensis yfdH mutant interaction with mouse
F. tularensis FTT1152 mutant interaction with mouse
F. tularensis ppiC mutant interaction with mouse
F. tularensis lolD mutant interaction with mouse
F. tularensis FTT1238c mutant interaction with mouse
F. tularensis FTT1239 mutant interaction with mouse
F. tularensis FTT1236 mutant interaction with mouse
F. tularensis FTT1237 mutant interaction with mouse
F. tularensis FTT1221 mutant interaction with mouse
F. tularensis FTTt19 mutant interaction with mouse
F. tularensis manB mutant interaction with mouse
F. tularensis FTTr07 mutant interaction with mouse
F. tularensis lysA mutant interaction with mouse
F. tularensis ispA mutant interaction with mouse
F. tularensis bioA mutant interaction with mouse
F. tularensis emrA1 mutant interaction with mouse
F. tularensis clpP mutant interaction with mouse
F. tularensis capC mutant interaction with mouse
F. tularensis FTT1676 mutant interaction with mouse
F. tularensis sdaC1 mutant interaction with mouse
F. tularensis yjjK mutant interaction with mouse
F. tularensis hflK mutant interaction with mouse
F. tularensis hflX mutant interaction with mouse
F. tularensis hisS mutant interaction with mouse
F. tularensis FTT0968c mutant interaction with mouse
F. tularensis minD mutant interaction with mouse
F. tularensis FTT0945 mutant interaction with mouse
F. tularensis FTT0944 mutant interaction with mouse
F. tularensis FTT0941c mutant interaction with mouse
F. tularensis FTT0940c mutant interaction with mouse
F. tularensis FTT0928c mutant interaction with mouse
F. tularensis minC mutant interaction with mouse
F. tularensis ampD mutant interaction with mouse
F. tularensis FTT1490 mutant interaction with mouse
F. tularensis gcvP1 mutant interaction with mouse
F. tularensis clpB mutant interaction with mouse
F. tularensis gcvT mutant interaction with mouse
F. tularensis FTT0165c mutant interaction with mouse
F. tularensis aspC2 mutant interaction with mouse
Y. pestis spoT mutant interaction with mouse
Y. pestis purH mutant interaction with mouse
Y. pestis hfq mutant interaction with mouse
Y. pestis hfq mutant interaction with mouse macrophage cell
Y. pestis greA mutant interaction with mouse
Y. pestis relA mutant interaction with mouse
Y. pestis pcm mutant interaction with mouse
Y. pestis nlpD mutant interaction with mouse
Y. pestis purK mutant interaction with mouse
Y. pestis y1136 mutant interaction with mouse
Y. pestis pgm mutant interaction with mouse
Y. pestis y1436 mutant interaction with mouse
Y. pestis y1537 mutant interaction with mouse
Y. pestis y1718 mutant interaction with mouse
Y. pestis phoP mutant interaction with mouse
Y. pestis phoP mutant interaction with mouse macrophage cell
Y. pestis yfeB mutant interaction with mouse
Y. pestis yfeA mutant interaction with mouse
Y. pestis msbB mutant interaction with mouse
Y. pestis y2285 mutant interaction with mouse
Y. pestis y2316 mutant interaction with mouse
Y. pestis ybtP mutant interaction with mouse
Y. pestis y2785 mutant interaction with mouse
Y. pestis y2786 mutant interaction with mouse
Y. pestis psaA mutant interaction with mouse
Y. pestis psaE mutant interaction with mouse
Y. pestis y3010 mutant interaction with mouse
Y. pestis smpB mutant interaction with mouse
Y. pestis dnaE mutant interaction with mouse
Y. pestis y3395 mutant interaction with mouse
Y. pestis thrL mutant interaction with mouse
Y. pestis yapE mutant interaction with mouse
Y. pestis y3857 mutant interaction with mouse
Y. pestis dam mutant interaction with mouse
Y. pestis crp mutant interaction with mouse
Y. pestis caf1M mutant interaction with mouse
B. anthracis atxA mutant interaction with mouse
B. anthracis pagA mutant interaction with mouse
B. anthracis lef mutant interaction with mouse
C. jejuni Cj0019c mutant interaction with chicken
C. jejuni Cj0020c mutant interaction with chicken
C. jejuni fliA mutant interaction with chicken
C. jejuni Cj0248 mutant interaction with chicken
C. jejuni motB mutant interaction with chicken
C. jejuni motA mutant interaction with chicken
C. jejuni Cj0415 mutant interaction with chicken
C. jejuni Cj0454c mutant interaction with chicken
C. jejuni Cj0456c mutant interaction with chicken
C. jejuni Cj0618 mutant interaction with chicken
C. jejuni Cj0629 mutant interaction with chicken
C. jejuni rpoN mutant interaction with chicken
C. jejuni pta mutant interaction with chicken
C. jejuni Cj0903c mutant interaction with chicken
C. jejuni aas mutant interaction with chicken
C. jejuni livJ mutant interaction with chicken
C. jejuni cheY mutant interaction with chicken
C. jejuni pglF mutant interaction with chicken
C. jejuni pglH mutant interaction with chicken
C. jejuni fliR mutant interaction with chicken
C. jejuni dccR mutant interaction with mouse
C. jejuni dnaJ mutant interaction with chicken
C. jejuni Cj1279c mutant interaction with chicken
C. jejuni Cj1279c mutant interaction with chicken epithelial cell
C. jejuni Cj1321 mutant interaction with chicken
C. jejuni Cj1324 mutant interaction with chicken
C. jejuni Cj1349c mutant interaction with chicken
C. jejuni Cj1349c mutant interaction with chicken epithelial cell
C. jejuni Cj1461 mutant interaction with human
C. jejuni Cj1461 mutant interaction with human epithelial cell
C. jejuni flgK mutant interaction with chicken
C. jejuni sdaA mutant interaction with chicken
C. jejuni peb1A mutant interaction with mouse
C. jejuni peb1A mutant interaction with mouse epithelial cell
C. jejuni CJE0997 mutant interaction with chicken
C. jejuni CJE0998 mutant interaction with chicken
C. jejuni pebC mutant interaction with chicken
C. jejuni pglH mutant interaction with human
C. perfringens plc mutant interaction with mouse
C. perfringens virS mutant interaction with mouse
B. anthracis clpX mutant interaction with mouse
B. anthracis sodC mutant interaction with mouse
B. anthracis codY mutant interaction with mouse
B. anthracis sigB mutant interaction with mouse
Shigella sodB mutant interaction with rabbit
Shigella sitA mutant interaction with mouse
Shigella aroD mutant interaction with monkey
Shigella sigA mutant interaction with rabbit
Shigella iucD mutant interaction with rabbit
Shigella iucD mutant interaction with chicken
Shigella iucC mutant interaction with rabbit
Shigella iucC mutant interaction with chicken
Shigella iucA mutant interaction with rabbit
Shigella iucA mutant interaction with chicken
Shigella iutA mutant interaction with chicken
Shigella iucB mutant interaction with rabbit
Shigella iucB mutant interaction with chicken
Shigella ospG mutant interaction with rabbit
Brucella spp. virB10 mutant interaction with mouse
Brucella spp. virB10 mutant interaction with mouse macrophage cell
Brucella spp. virB9 mutant interaction with human
Brucella spp. virB9 mutant interaction with human macrophage cell
Brucella spp. virB9 mutant interaction with human HeLa cell
Brucella spp. virB5 mutant interaction with human
Brucella spp. virB5 mutant interaction with human macrophage cell
Brucella spp. virB4 mutant interaction with mouse
Brucella spp. virB4 mutant interaction with mouse macrophage cell
Brucella spp. virB2 mutant interaction with mouse
Brucella spp. virB2 mutant interaction with mouse macrophage cell
Brucella spp. virB1 mutant interaction with mouse
Brucella spp. virB1 mutant interaction with mouse macrophage cell
Brucella spp. gnd mutant interaction with mouse
Brucella spp. narG mutant interaction with human
Brucella spp. narG mutant interaction with human macrophage cell
Brucella spp. cydB mutant interaction with mouse
Brucella spp. pcs mutant interaction with mouse
Brucella spp. pcs mutant interaction with mouse macrophage cell
Brucella spp. ugpB mutant interaction with human
Brucella spp. ugpB mutant interaction with human epithelial cell
Brucella spp. ugpB mutant interaction with human HeLa cell
Brucella spp. ugpA mutant interaction with mouse
Brucella spp. gcvT mutant interaction with human
Brucella spp. gcvT mutant interaction with human macrophage cell
Brucella spp. eryB mutant interaction with human
Brucella spp. eryB mutant interaction with human macrophage cell
Brucella spp. eryC mutant interaction with mouse
Brucella spp. eryC mutant interaction with mouse macrophage cell
Brucella spp. cobW mutant interaction with human
Brucella spp. cobW mutant interaction with human macrophage cell
Brucella spp. znuA mutant interaction with mouse
Brucella spp. znuA mutant interaction with mouse macrophage cell
Brucella spp. pheA mutant interaction with mouse
Brucella spp. pheA mutant interaction with mouse macrophage cell
Brucella spp. bacA mutant interaction with mouse
Brucella spp. bacA mutant interaction with mouse macrophage cell
Brucella spp. glnA mutant interaction with human
Brucella spp. glnA mutant interaction with human macrophage cell
Brucella spp. ntrC mutant interaction with mouse
Brucella spp. ntrC mutant interaction with mouse macrophage cell
Brucella spp. serB mutant interaction with human
Brucella spp. serB mutant interaction with human macrophage cell
Brucella spp. pncA mutant interaction with mouse
Brucella spp. pncA mutant interaction with mouse macrophage cell
Brucella spp. lysA mutant interaction with human
Brucella spp. lysA mutant interaction with human macrophage cell
Brucella spp. bvrR mutant interaction with mouse
Brucella spp. bvrR mutant interaction with mouse epithelial cell
Brucella spp. bvrR mutant interaction with mouse macrophage cell
Brucella spp. bvrS mutant interaction with mouse
Brucella spp. bvrS mutant interaction with mouse epithelial cell
Brucella spp. bvrS mutant interaction with mouse macrophage cell
Brucella spp. pmtA mutant interaction with mouse
Brucella spp. pmtA mutant interaction with mouse macrophage cell
Y. pestis pla mutant interaction with mouse
Y. pestis yopE mutant interaction with mouse
Y. pestis yopQ mutant interaction with mouse
Y. pestis yopM mutant interaction with mouse
Y. pestis yopB mutant interaction with mouse
Y. pestis yopB mutant interaction with mouse macrophage cell
Y. pestis sycD mutant interaction with mouse
Y. pestis lcrV mutant interaction with mouse
Y. pestis virF mutant interaction with mouse
Y. pestis ypkA mutant interaction with mouse
Y. pestis caf1A mutant interaction with mouse
Y. pestis arcA mutant interaction with mouse
Y. pestis YPO1003 mutant interaction with mouse
Y. pestis ssrA mutant interaction with mouse
Y. pestis YPO1179 mutant interaction with mouse
Y. pestis YPO1387 mutant interaction with mouse
Y. pestis YPO1388 mutant interaction with mouse
Y. pestis ail mutant interaction with mouse
Y. pestis YPO1994 mutant interaction with mouse
Y. pestis YPO2027 mutant interaction with mouse
Y. pestis slyA mutant interaction with mouse
Y. pestis lpp mutant interaction with mouse
Y. pestis YPO2471 mutant interaction with mouse
Y. pestis YPO2793 mutant interaction with mouse
Y. pestis guaA mutant interaction with mouse
Y. pestis guaB mutant interaction with mouse
Y. pestis YPO2947 mutant interaction with mouse
Y. pestis YPO3045 mutant interaction with mouse
Y. pestis YPO3398 mutant interaction with mouse
Y. pestis YPO3973 mutant interaction with mouse
Salmonella spp. ssaV mutant interaction with human
Salmonella spp. ssaM mutant interaction with mouse
Salmonella spp. sseD mutant interaction with mouse
Salmonella spp. sseC mutant interaction with mouse
Salmonella spp. spiC mutant interaction with mouse
Salmonella spp. spiC mutant interaction with mouse macrophage cell
Salmonella spp. fliC mutant interaction with chicken
Salmonella spp. aroC mutant interaction with human
Salmonella spp. invH mutant interaction with cattle
Brucella spp. ftcR mutant interaction with cattle
Brucella spp. ftcR mutant interaction with cattle macrophage cell
Brucella spp. ftcR mutant interaction with mouse
Brucella spp. ftcR mutant interaction with mouse macrophage cell
B. anthracis BAS4929 mutant interaction with mouse
B. anthracis GBAA4766 mutant interaction with mouse
B. anthracis GBAA0552 mutant interaction with mouse
B. anthracis phnX mutant interaction with mouse
L. monocytogenes degU mutant interaction with mouse
L. monocytogenes inlF mutant interaction with mouse
L. monocytogenes recQ mutant interaction with mouse
L. monocytogenes LMOf2365_0094 mutant interaction with mouse
L. monocytogenes LMOf2365_1971 mutant interaction with mouse
L. monocytogenes gtcA mutant interaction with mouse epithelial cell
L. monocytogenes agrA mutant interaction with mouse
L. monocytogenes ctsR mutant interaction with mouse
L. monocytogenes prsA-2 mutant interaction with mouse
L. pneumophila lpg0742 mutant interaction with mouse
L. pneumophila lpg0742 mutant interaction with mouse macrophage cell
L. pneumophila cpxR mutant interaction with mouse
L. pneumophila cpxR mutant interaction with mouse macrophage cell
L. pneumophila mip mutant interaction with human
L. pneumophila lpg1905 mutant interaction with human
L. pneumophila lpg1905 mutant interaction with human macrophage cell
L. pneumophila enhC mutant interaction with mouse
L. pneumophila enhC mutant interaction with mouse macrophage cell
L. pneumophila dotA mutant interaction with mouse
L. pneumophila dotA mutant interaction with mouse macrophage cell
L. pneumophila feoB mutant interaction with human
L. pneumophila feoB mutant interaction with human macrophage cell
L. pneumophila djlA mutant interaction with mouse
L. pneumophila djlA mutant interaction with mouse macrophage cell
L. pneumophila lpg2515 mutant interaction with mouse
L. pneumophila rtxA-2 mutant interaction with mouse
L. pneumophila sdhA mutant interaction with mouse
L. pneumophila sdhA mutant interaction with mouse macrophage cell
L. pneumophila rtxA-1 mutant interaction with mouse
Shigella icsA mutant interaction with monkey
Shigella icsA mutant interaction with monkey epithelial cell
Shigella ipaH mutant interaction with mouse
Salmonella spp. sptP mutant interaction with mouse
Salmonella spp. sptP mutant interaction with mouse epithelial cell
Salmonella spp. tdcA mutant interaction with mouse
Salmonella spp. tdcA mutant interaction with mouse epithelial cell
C. jejuni motB mutant interaction with mouse
C. jejuni cheA mutant interaction with mouse
C. jejuni pglB mutant interaction with mouse
C. jejuni CJJ81176_0927 mutant interaction with chicken
C. jejuni fliI mutant interaction with mouse
C. jejuni CJJ81176_0926 mutant interaction with chicken
C. jejuni JJD26997_0895 mutant interaction with chicken
C. jejuni pebA mutant interaction with chicken
C. jejuni JJD26997_0894 mutant interaction with chicken
L. pneumophila icmG mutant interaction with mouse
C. jejuni racR mutant interaction with chicken
C. perfringens pCPF5603_44 mutant interaction with rabbit
Vaccinia virus C12L mutant interaction with mouse
Vaccinia virus E3L mutant interaction with mouse
Vaccinia virus N1L mutant interaction with mouse
Vaccinia virus A46R mutant interaction with mouse
Measles virus P mutant interaction with monkey
Rift valley fever virus RVFVsSgp1 mutant interaction with mouse
Human immunodeficiency virus nef mutant interaction with mouse
C. perfringens cpe mutant interaction with rabbit
Y. pestis yscH mutant interaction with mouse
Y. pestis yopK mutant interaction with mouse
Y. pestis lcrH mutant interaction with mouse
Y. pestis lcrF mutant interaction with mouse
B. pseudomallei aroC mutant interaction with mouse
B. pseudomallei pabB mutant interaction with mouse
B. mallei virG mutant interaction with hamster
B. pseudomallei BURPS668_A2153 mutant interaction with mouse
B. pseudomallei purM mutant interaction with mouse
B. pseudomallei sctU mutant interaction with mouse
B. pseudomallei bopA mutant interaction with mouse
B. pseudomallei leuB mutant interaction with mouse
B. pseudomallei BPSS1509 mutant interaction with mouse
B. pseudomallei sctU mutant interaction with hamster
B. pseudomallei BPSS2074 mutant interaction with hamster
B. pseudomallei bipD mutant interaction with mouse
B. pseudomallei BPSS1539 mutant interaction with mouse
B. pseudomallei bopE mutant interaction with mouse
B. pseudomallei bsaZ mutant interaction with mouse
B. pseudomallei bsaZ mutant interaction with mouse macrophage cell
B. pseudomallei BPSS0067 mutant interaction with mouse
B. pseudomallei BPSS2053 mutant interaction with human
B. pseudomallei BPSS2053 mutant interaction with human epithelial cell
B. pseudomallei pmlI mutant interaction with mouse
B. pseudomallei BPSL1039 mutant interaction with mouse
B. pseudomallei BPSL1263 mutant interaction with human
B. pseudomallei BPSL1263 mutant interaction with human epithelial cell
B. pseudomallei BPSL1263 mutant interaction with human macrophage cell
B. pseudomallei lipB mutant interaction with mouse
B. pseudomallei hisF mutant interaction with mouse
B. pseudomallei wcbN mutant interaction with mouse
B. pseudomallei BPSL2825 mutant interaction with mouse
B. pseudomallei BPSL0634 mutant interaction with mouse
B. pseudomallei BPSL1528 mutant interaction with mouse
B. pseudomallei aroB mutant interaction with mouse
B. pseudomallei trpG mutant interaction with mouse
B. pseudomallei purN mutant interaction with mouse
B. pseudomallei wcbB mutant interaction with mouse
B. pseudomallei wcbC mutant interaction with mouse
B. pseudomallei nth mutant interaction with mouse
B. pseudomallei BPSL0872 mutant interaction with human
B. pseudomallei BPSL0872 mutant interaction with human epithelial cell
B. pseudomallei BPSL0872 mutant interaction with hamster
B. pseudomallei BPSL0872 mutant interaction with hamster epithelial cell
B. pseudomallei BPSL0395 mutant interaction with mouse
B. pseudomallei wzm mutant interaction with mouse
B. pseudomallei ilvI mutant interaction with mouse
B. pseudomallei fliC mutant interaction with mouse
B. pseudomallei wcbD mutant interaction with mouse
B. pseudomallei BPSL3147 mutant interaction with mouse
B. pseudomallei serC mutant interaction with mouse
B. pseudomallei recA mutant interaction with mouse
B. pseudomallei BPSL1876 mutant interaction with mouse
B. pseudomallei BPSL1705 mutant interaction with mouse
B. pseudomallei BPSL1705 mutant interaction with mouse macrophage cell
B. mallei BMAA0739 mutant interaction with hamster
B. mallei BMAA0743 mutant interaction with hamster
B. mallei BMAA0742 mutant interaction with hamster
B. mallei BMAA0649 mutant interaction with human
B. mallei BMAA0649 mutant interaction with human epithelial cell
B. mallei BMAA0740 mutant interaction with hamster
E. coli bfpT mutant interaction with human
E. coli rfaH mutant interaction with mouse
E. coli dppA mutant interaction with mouse
E. coli fliC mutant interaction with cattle
E. coli fimH mutant interaction with human
E. coli fimH mutant interaction with mouse
E. coli tonB mutant interaction with mouse
E. coli mppA mutant interaction with chicken
E. coli sbmA mutant interaction with chicken
E. coli ychF mutant interaction with chicken
E. coli waaL mutant interaction with chicken
E. coli ibeA mutant interaction with human
E. coli sitB mutant interaction with chicken
E. coli malX mutant interaction with chicken
E. coli tia mutant interaction with human
E. coli papG mutant interaction with human
E. coli kpsS mutant interaction with chicken
E. coli wcaE mutant interaction with chicken
E. coli APECO1_3367 mutant interaction with chicken
E. coli yjjQ mutant interaction with chicken
E. coli tktA mutant interaction with chicken
E. coli ECP_4655 mutant interaction with human
E. coli ECP_4655 mutant interaction with mouse
E. coli cnf1 mutant interaction with mouse
E. coli ycjM mutant interaction with chicken
E. coli wecE mutant interaction with mouse
E. coli fimF mutant interaction with mouse
E. coli fimD mutant interaction with mouse
E. coli fimC mutant interaction with mouse
E. coli fimI mutant interaction with mouse
E. coli fimB mutant interaction with mouse
E. coli manB mutant interaction with mouse
E. coli waaW mutant interaction with chicken
E. coli kpsC mutant interaction with mouse
E. coli pyrD mutant interaction with mouse
E. coli phoU mutant interaction with mouse
E. coli map mutant interaction with cattle
E. coli Z3341 mutant interaction with cattle
E. coli Z0275 mutant interaction with cattle
E. coli sanA mutant interaction with cattle
E. coli mglA mutant interaction with cattle
E. coli Z0390 mutant interaction with cattle
E. coli Z3496 mutant interaction with cattle
E. coli Z0469 mutant interaction with cattle
E. coli rdgC mutant interaction with cattle
E. coli Z0609 mutant interaction with cattle
E. coli evgS mutant interaction with cattle
E. coli yfhH mutant interaction with cattle
E. coli trxC mutant interaction with cattle
E. coli Z0990 mutant interaction with cattle
E. coli Z3950 mutant interaction with cattle
E. coli recD mutant interaction with cattle
E. coli kduI mutant interaction with cattle
E. coli Z4200 mutant interaction with cattle
E. coli Z3635 mutant interaction with cattle
E. coli Z4282 mutant interaction with cattle
E. coli speA mutant interaction with cattle
E. coli Z4318 mutant interaction with cattle
E. coli pitB mutant interaction with cattle
E. coli Z1126 mutant interaction with cattle
E. coli Z1129 mutant interaction with cattle
E. coli tdcE mutant interaction with cattle
E. coli Z1182 mutant interaction with cattle
E. coli Z1202 mutant interaction with cattle
E. coli trxB mutant interaction with cattle
E. coli Z1328 mutant interaction with cattle
E. coli yqeJ mutant interaction with cattle
E. coli ymcC mutant interaction with cattle
E. coli pgaA mutant interaction with cattle
E. coli agaB mutant interaction with cattle
E. coli mdoC mutant interaction with cattle
E. coli ypjA mutant interaction with cattle
E. coli serA mutant interaction with cattle
E. coli Z1829 mutant interaction with cattle
E. coli Z5946 mutant interaction with cattle
E. coli fimE mutant interaction with cattle
E. coli yjhS mutant interaction with cattle
E. coli Z5886 mutant interaction with cattle
E. coli nrdD mutant interaction with cattle
E. coli Z1930 mutant interaction with cattle
E. coli yjeJ mutant interaction with cattle
E. coli yjcF mutant interaction with cattle
E. coli arp mutant interaction with cattle
E. coli Z5444 mutant interaction with cattle
E. coli ilvG mutant interaction with cattle
E. coli narG mutant interaction with cattle
E. coli Z2056 mutant interaction with cattle
E. coli Z2142 mutant interaction with cattle
E. coli Z2144 mutant interaction with cattle
E. coli Z2149 mutant interaction with cattle
E. coli Z2176 mutant interaction with cattle
E. coli ydeK mutant interaction with cattle
E. coli Z2203 mutant interaction with cattle
E. coli Z2205 mutant interaction with cattle
E. coli Z2207 mutant interaction with cattle
E. coli yddA mutant interaction with cattle
E. coli Z5214 mutant interaction with cattle
E. coli Z5212 mutant interaction with cattle
E. coli Z5131 mutant interaction with cattle
E. coli escC mutant interaction with cattle
E. coli Z5121 mutant interaction with cattle
E. coli escV mutant interaction with cattle
E. coli escN mutant interaction with rabbit
E. coli sepQ mutant interaction with cattle
E. coli Z5114 mutant interaction with cattle
E. coli eae mutant interaction with human
E. coli espB mutant interaction with human
E. coli yibD mutant interaction with cattle
E. coli rhsA mutant interaction with cattle
E. coli hrpA mutant interaction with cattle
E. coli Z2318 mutant interaction with cattle
E. coli dctA mutant interaction with cattle
E. coli Z2368 mutant interaction with cattle
E. coli yhiJ mutant interaction with cattle
E. coli Z3620 mutant interaction with cattle
E. coli ycjV mutant interaction with cattle
E. coli acnA mutant interaction with cattle
E. coli trpB mutant interaction with cattle
E. coli Z6010 mutant interaction with cattle
E. coli trkA mutant interaction with cattle
E. coli Z2702 mutant interaction with cattle
E. coli Z2749 mutant interaction with cattle
E. coli Z2751 mutant interaction with cattle
E. coli celF mutant interaction with cattle
E. coli cspC mutant interaction with cattle
E. coli Z2984 mutant interaction with cattle
E. coli sdiA mutant interaction with cattle
E. coli Z3023 mutant interaction with cattle
E. coli Z3026 mutant interaction with cattle
E. coli Z3062 mutant interaction with cattle
E. coli manB mutant interaction with cattle
E. coli manC mutant interaction with cattle
E. coli fcI mutant interaction with cattle
E. coli wbdP mutant interaction with cattle
E. coli per mutant interaction with cattle
E. coli espP mutant interaction with cattle
E. coli tsh mutant interaction with chicken
E. coli EHEC-hlyA mutant interaction with cattle
Salmonella spp. invE mutant interaction with human
Salmonella spp. waaP mutant interaction with mouse
V. cholerae pykF mutant interaction with mouse
V. cholerae fbp mutant interaction with mouse
V. cholerae cyaA mutant interaction with mouse
V. cholerae fur mutant interaction with mouse
V. cholerae mukB mutant interaction with mouse
V. cholerae frdC mutant interaction with mouse
V. cholerae rfbB mutant interaction with mouse
V. cholerae ubiC mutant interaction with mouse
V. cholerae tolB mutant interaction with mouse
V. cholerae acpS mutant interaction with mouse
V. cholerae tcpT mutant interaction with mouse
V. cholerae toxR mutant interaction with mouse
V. cholerae carB mutant interaction with mouse
V. cholerae gshB mutant interaction with mouse
V. cholerae nqrE mutant interaction with mouse
V. cholerae fabG mutant interaction with mouse
V. cholerae tcpN/toxT mutant interaction with mouse
V. cholerae purD mutant interaction with mouse
V. cholerae rpoS mutant interaction with mouse
V. cholerae trpG mutant interaction with mouse
V. cholerae purF mutant interaction with mouse
V. cholerae purL mutant interaction with mouse
V. cholerae rpoE mutant interaction with mouse
V. cholerae relA mutant interaction with mouse
V. cholerae lysA mutant interaction with mouse
V. cholerae aceF mutant interaction with mouse
V. cholerae tcpA mutant interaction with mouse
V. cholerae acfC mutant interaction with mouse
V. cholerae rfbL mutant interaction with mouse
V. cholerae nqrF mutant interaction with mouse
V. cholerae galM mutant interaction with mouse
V. cholerae recO mutant interaction with mouse
V. cholerae ilvD mutant interaction with mouse
V. cholerae deoC mutant interaction with mouse
V. cholerae acfB mutant interaction with mouse
V. cholerae purK mutant interaction with mouse
V. cholerae pta mutant interaction with mouse
V. cholerae acfA mutant interaction with mouse
V. cholerae galK mutant interaction with mouse
V. cholerae carA mutant interaction with mouse
V. cholerae sspA mutant interaction with mouse
V. cholerae bioB mutant interaction with mouse
V. cholerae irgA mutant interaction with mouse
V. cholerae tcpE mutant interaction with mouse
V. cholerae zwf mutant interaction with mouse
V. cholerae ydbK mutant interaction with mouse
V. cholerae phaC mutant interaction with mouse
V. cholerae VCA0688 mutant interaction with mouse
V. cholerae VCA0910 mutant interaction with mouse
V. cholerae VCA0006 mutant interaction with mouse
V. cholerae VCA0903 mutant interaction with mouse
V. cholerae VCA0896 mutant interaction with mouse
V. cholerae VCA0600 mutant interaction with mouse
V. cholerae VCA0578 mutant interaction with mouse
V. cholerae VCA0530 mutant interaction with mouse
V. cholerae VCA0583 mutant interaction with mouse
V. cholerae VCA0930 mutant interaction with mouse
V. cholerae VC0028 mutant interaction with mouse
V. cholerae VC2426 mutant interaction with mouse
V. cholerae VC2433 mutant interaction with mouse
V. cholerae tolC mutant interaction with mouse
V. cholerae VC2437 mutant interaction with mouse
V. cholerae VC2453 mutant interaction with mouse
V. cholerae VC2455 mutant interaction with mouse
V. cholerae VC2390 mutant interaction with mouse
V. cholerae VC2295 mutant interaction with mouse
V. cholerae VC2320 mutant interaction with mouse
V. cholerae VC2290 mutant interaction with mouse
V. cholerae VC2291 mutant interaction with mouse
V. cholerae VC2206 mutant interaction with mouse
V. cholerae VC2030 mutant interaction with mouse
V. cholerae VC2042 mutant interaction with mouse
V. cholerae VC2052 mutant interaction with mouse
V. cholerae VC2067 mutant interaction with mouse
V. cholerae VC1887 mutant interaction with mouse
V. cholerae VC1771 mutant interaction with mouse
V. cholerae VC1715 mutant interaction with mouse
V. cholerae VC1716 mutant interaction with mouse
V. cholerae VC1639 mutant interaction with mouse
V. cholerae VC1675 mutant interaction with mouse
V. cholerae VC1595 mutant interaction with mouse
V. cholerae VC0257 mutant interaction with mouse
V. cholerae VC0965 mutant interaction with mouse
V. cholerae VC1004 mutant interaction with mouse
V. cholerae VC1012 mutant interaction with mouse
V. cholerae VC0251 mutant interaction with mouse
V. cholerae VC0249 mutant interaction with mouse
V. cholerae VC0250 mutant interaction with mouse
V. cholerae VC1021 mutant interaction with mouse
V. cholerae VC1075 mutant interaction with mouse
V. cholerae VC1098 mutant interaction with mouse
V. cholerae VC0051 mutant interaction with mouse
V. cholerae VC0032 mutant interaction with mouse
V. cholerae VC0036 mutant interaction with mouse
V. cholerae VC0826 mutant interaction with mouse
V. cholerae VC0828 mutant interaction with mouse
V. cholerae VC0831 mutant interaction with mouse
V. cholerae VC0835 mutant interaction with mouse
V. cholerae VC0836 mutant interaction with mouse
V. cholerae VC0837 mutant interaction with mouse
V. cholerae VC0869 mutant interaction with mouse
V. cholerae VC0247 mutant interaction with mouse
V. cholerae VC0244 mutant interaction with mouse
V. cholerae VC1162 mutant interaction with mouse
V. cholerae VC1173 mutant interaction with mouse
V. cholerae VC0192 mutant interaction with mouse
V. cholerae VC0212 mutant interaction with mouse
V. cholerae VC0242 mutant interaction with mouse
V. cholerae VC0243 mutant interaction with mouse
V. cholerae VC0239 mutant interaction with mouse
V. cholerae VC1380 mutant interaction with mouse
V. cholerae VC0238 mutant interaction with mouse
V. cholerae VC0260 mutant interaction with mouse
V. cholerae hfq mutant interaction with mouse
V. cholerae VC0459 mutant interaction with mouse
V. cholerae VC0468 mutant interaction with mouse
V. cholerae VC2506 mutant interaction with mouse
V. cholerae VC0259 mutant interaction with mouse
V. cholerae VC0485 mutant interaction with mouse
V. cholerae VC0125 mutant interaction with mouse
V. cholerae VC0596 mutant interaction with mouse
V. cholerae glmM mutant interaction with mouse
V. cholerae VC0647 mutant interaction with mouse
V. cholerae VC2544 mutant interaction with mouse
V. cholerae VC2647 mutant interaction with mouse
V. cholerae VC2660 mutant interaction with mouse
V. cholerae VC0724 mutant interaction with mouse
V. cholerae VC0727 mutant interaction with mouse
V. cholerae VC0523 mutant interaction with mouse
V. cholerae VC0095 mutant interaction with mouse
V. cholerae VC0132 mutant interaction with mouse
Salmonella spp. slyA mutant interaction with mouse
Salmonella spp. sodC mutant interaction with mouse
Salmonella spp. sopE mutant interaction with mouse
Salmonella spp. sopA mutant interaction with cattle
Salmonella spp. sopB mutant interaction with cattle
Salmonella spp. PSLT072 mutant interaction with mouse
Salmonella spp. spvR mutant interaction with mouse
Salmonella spp. spvB mutant interaction with mouse
Salmonella spp. spvA mutant interaction with mouse
Salmonella spp. spvC mutant interaction with mouse
Salmonella spp. spvD mutant interaction with mouse
Salmonella spp. pefC mutant interaction with mouse
Salmonella spp. STM0016 mutant interaction with mouse
Salmonella spp. STM0030 mutant interaction with mouse
Salmonella spp. dgt mutant interaction with mouse
Salmonella spp. yafS mutant interaction with mouse
Salmonella spp. STM0298 mutant interaction with mouse
Salmonella spp. dinP mutant interaction with mouse
Salmonella spp. cyoB mutant interaction with mouse
Salmonella spp. clpP mutant interaction with mouse
Salmonella spp. gip mutant interaction with mouse
Salmonella spp. STM0520 mutant interaction with mouse
Salmonella spp. allD mutant interaction with mouse
Salmonella spp. fimA mutant interaction with mouse
Salmonella spp. fimW mutant interaction with mouse
Salmonella spp. nfnB mutant interaction with mouse
Salmonella spp. cspE mutant interaction with mouse
Salmonella spp. STM0723 mutant interaction with mouse
Salmonella spp. slrP mutant interaction with mouse
Salmonella spp. STM0972 mutant interaction with mouse
Salmonella spp. focA mutant interaction with mouse
Salmonella spp. STM1002 mutant interaction with mouse
Salmonella spp. sseI mutant interaction with mouse
Salmonella spp. ycbG mutant interaction with mouse
Salmonella spp. pipD mutant interaction with mouse
Salmonella spp. copS mutant interaction with mouse
Salmonella spp. csgF mutant interaction with mouse
Salmonella spp. csgD mutant interaction with mouse
Salmonella spp. csgC mutant interaction with mouse
Salmonella spp. solA mutant interaction with mouse
Salmonella spp. sifA mutant interaction with mouse
Salmonella spp. sifA mutant interaction with mouse epithelial cell
Salmonella spp. pagC mutant interaction with mouse
Salmonella spp. yeaJ mutant interaction with mouse
Salmonella spp. nlpC mutant interaction with mouse
Salmonella spp. ydiK mutant interaction with mouse
Salmonella spp. ssaC mutant interaction with mouse
Salmonella spp. ssaC mutant interaction with mouse macrophage cell
Salmonella spp. ssaE mutant interaction with mouse
Salmonella spp. sseB mutant interaction with mouse
Salmonella spp. sseE mutant interaction with mouse
Salmonella spp. sseE mutant interaction with mouse macrophage cell
Salmonella spp. sseF mutant interaction with mouse
Salmonella spp. sseF mutant interaction with mouse macrophage cell
Salmonella spp. sseG mutant interaction with mouse
Salmonella spp. sseG mutant interaction with mouse macrophage cell
Salmonella spp. ssaN mutant interaction with mouse
Salmonella spp. ssaU mutant interaction with mouse
Salmonella spp. ydgF mutant interaction with mouse
Salmonella spp. STM1549 mutant interaction with mouse
Salmonella spp. yddX mutant interaction with mouse
Salmonella spp. STM1583 mutant interaction with mouse
Salmonella spp. sseJ mutant interaction with mouse
Salmonella spp. sseJ mutant interaction with mouse epithelial cell
Salmonella spp. STM1669 mutant interaction with mouse
Salmonella spp. yciH mutant interaction with mouse
Salmonella spp. fadD mutant interaction with mouse
Salmonella spp. cspC mutant interaction with mouse
Salmonella spp. znuA mutant interaction with mouse
Salmonella spp. znuC mutant interaction with mouse
Salmonella spp. znuB mutant interaction with mouse
Salmonella spp. STM1934 mutant interaction with mouse
Salmonella spp. uvrY mutant interaction with mouse
Salmonella spp. uvrY mutant interaction with mouse epithelial cell
Salmonella spp. uvrY mutant interaction with mouse macrophage cell
Salmonella spp. fliQ mutant interaction with mouse
Salmonella spp. udg mutant interaction with mouse
Salmonella spp. rfbP mutant interaction with mouse
Salmonella spp. rfbM mutant interaction with mouse
Salmonella spp. rfbC mutant interaction with mouse
Salmonella spp. rfbA mutant interaction with mouse
Salmonella spp. rfbD mutant interaction with mouse
Salmonella spp. rfbB mutant interaction with mouse
Salmonella spp. galF mutant interaction with mouse
Salmonella spp. wcaM mutant interaction with mouse
Salmonella spp. yegQ mutant interaction with mouse
Salmonella spp. STM2137 mutant interaction with mouse
Salmonella spp. stcD mutant interaction with mouse
Salmonella spp. stcC mutant interaction with mouse
Salmonella spp. bglX mutant interaction with mouse
Salmonella spp. yeiA mutant interaction with mouse
Salmonella spp. STM2197 mutant interaction with mouse
Salmonella spp. STM2373 mutant interaction with mouse
Salmonella spp. shdA mutant interaction with mouse
Salmonella spp. ratB mutant interaction with mouse
Salmonella spp. yfhL mutant interaction with mouse
Salmonella spp. STM2585 mutant interaction with mouse
Salmonella spp. STM2680 mutant interaction with mouse
Salmonella spp. STM2689 mutant interaction with mouse
Salmonella spp. mig-14 mutant interaction with mouse
Salmonella spp. yqaE mutant interaction with mouse
Salmonella spp. hilA mutant interaction with mouse
Salmonella spp. invC mutant interaction with chicken
Salmonella spp. invA mutant interaction with chicken
Salmonella spp. sopD mutant interaction with cattle
Salmonella spp. STM3036 mutant interaction with mouse
Salmonella spp. STM3128 mutant interaction with mouse
Salmonella spp. STM3192 mutant interaction with mouse
Salmonella spp. sspA mutant interaction with cattle
Salmonella spp. crp mutant interaction with mouse
Salmonella spp. envZ mutant interaction with mouse
Salmonella spp. yiaO mutant interaction with mouse
Salmonella spp. STM3690 mutant interaction with mouse
Salmonella spp. yibD mutant interaction with mouse
Salmonella spp. rfaZ mutant interaction with mouse
Salmonella spp. misL mutant interaction with mouse
Salmonella spp. marT mutant interaction with mouse
Salmonella spp. ibpA mutant interaction with mouse
Salmonella spp. torD mutant interaction with mouse
Salmonella spp. STM3907 mutant interaction with mouse
Salmonella spp. ppiC mutant interaction with mouse
Salmonella spp. trxA mutant interaction with mouse
Salmonella spp. yigG mutant interaction with mouse
Salmonella spp. STM3980 mutant interaction with mouse
Salmonella spp. yneB mutant interaction with mouse
Salmonella spp. yneC mutant interaction with mouse
Salmonella spp. STM4155 mutant interaction with mouse
Salmonella spp. STM4158 mutant interaction with mouse
Salmonella spp. yjaG mutant interaction with mouse
Salmonella spp. purD mutant interaction with mouse
Salmonella spp. metA mutant interaction with mouse
Salmonella spp. STM4206 mutant interaction with mouse
Salmonella spp. STM4260 mutant interaction with mouse
Salmonella spp. STM4261 mutant interaction with mouse
Salmonella spp. yjdB mutant interaction with mouse
Salmonella spp. phoN mutant interaction with mouse
Salmonella spp. yjeJ mutant interaction with mouse
Salmonella spp. idnK mutant interaction with mouse
Salmonella spp. sthA mutant interaction with mouse
H. influenzae dam mutant interaction with human
H. influenzae dam mutant interaction with human epithelial cell
H. influenzae pgmB mutant interaction with human
H. influenzae pgmB mutant interaction with human epithelial cell
H. influenzae dsbA mutant interaction with mouse
H. influenzae hbpA mutant interaction with mouse
H. influenzae licD mutant interaction with mouse
H. influenzae ptsI mutant interaction with mouse
H. influenzae arcA mutant interaction with mouse
H. influenzae ompA mutant interaction with human
Hantavirus HTNVsMgp1 mutant interaction with mouse
N. meningitidis pilX mutant interaction with human
N. meningitidis pilX mutant interaction with human epithelial cell
N. meningitidis pilQ mutant interaction with human
N. meningitidis tonB mutant interaction with human
N. meningitidis tonB mutant interaction with human epithelial cell
N. meningitidis pilF mutant interaction with human
N. meningitidis NMA0798 mutant interaction with mouse
N. meningitidis NMB0103 mutant interaction with human
N. meningitidis lpxA mutant interaction with mouse
N. meningitidis NMB0313 mutant interaction with human
N. meningitidis NMB0541 mutant interaction with human
N. meningitidis pgm mutant interaction with mouse
N. meningitidis rfaD mutant interaction with mouse
N. meningitidis NMB1012 mutant interaction with human
N. meningitidis NMB1829 mutant interaction with human
N. meningitidis NMB1726 mutant interaction with human
N. meningitidis NMB1638 mutant interaction with human
N. meningitidis NMB1638 mutant interaction with human epithelial cell
N. meningitidis NMB1966 mutant interaction with human
N. meningitidis NMB1966 mutant interaction with human epithelial cell
N. meningitidis NMB1966 mutant interaction with mouse
N. meningitidis NMB1966 mutant interaction with mouse epithelial cell
Rabies virus RABVgp1 mutant interaction with mouse
Rabies virus RABVgp2 mutant interaction with mouse
Rabies virus RABVgp3 mutant interaction with mouse
Rabies virus RABVgp4 mutant interaction with mouse
Rotavirus VP4 mutant interaction with mouse
S. pneumoniae iga mutant interaction with mouse
S. pneumoniae regR mutant interaction with mouse
S. pneumoniae spxB mutant interaction with rabbit
S. pneumoniae nox mutant interaction with mouse
S. pneumoniae ccpA mutant interaction with mouse
S. pneumoniae luxS mutant interaction with mouse
S. pneumoniae ply mutant interaction with mouse
S. pneumoniae zmpB mutant interaction with mouse
S. pneumoniae pspC mutant interaction with mouse
S. pneumoniae cbpG mutant interaction with human
S. pneumoniae cbpG mutant interaction with human epithelial cell
S. pneumoniae nanA mutant interaction with mouse
S. pneumoniae sodA mutant interaction with mouse
S. pneumoniae pspA mutant interaction with mouse
S. pneumoniae pgdA mutant interaction with mouse
S. pneumoniae lytA mutant interaction with mouse
S. pneumoniae ciaR mutant interaction with mouse
S. pneumoniae glnA mutant interaction with human
S. pneumoniae glnA mutant interaction with human epithelial cell
S. pneumoniae codY mutant interaction with mouse
S. pneumoniae mutX mutant interaction with mouse
S. pneumoniae clpP mutant interaction with mouse
S. pneumoniae bacA mutant interaction with mouse
S. pneumoniae cbpE mutant interaction with human
S. pneumoniae cbpE mutant interaction with human epithelial cell
S. pneumoniae purN mutant interaction with mouse
S. pneumoniae pepC mutant interaction with mouse
S. pneumoniae psaC mutant interaction with mouse
S. pneumoniae purB mutant interaction with mouse
S. pneumoniae aga mutant interaction with mouse
S. pneumoniae potD mutant interaction with mouse
S. pneumoniae pavA mutant interaction with mouse
S. pneumoniae psaB mutant interaction with mouse
S. pneumoniae pbp1A mutant interaction with mouse
S. pneumoniae glnP mutant interaction with mouse
S. pneumoniae psaA mutant interaction with mouse
S. pneumoniae radA mutant interaction with mouse
S. pneumoniae SP_1976 mutant interaction with mouse
S. pneumoniae SP_2239 mutant interaction with mouse
S. pneumoniae SP_0049 mutant interaction with mouse
S. pneumoniae purH mutant interaction with mouse
S. pneumoniae SP_0057 mutant interaction with mouse
S. pneumoniae SP_0063 mutant interaction with mouse
S. pneumoniae SP_2231 mutant interaction with mouse
S. pneumoniae SP_0071 mutant interaction with mouse
S. pneumoniae SP_0078 mutant interaction with mouse
S. pneumoniae SP_2210 mutant interaction with mouse
S. pneumoniae SP_0092 mutant interaction with mouse
S. pneumoniae SP_0095 mutant interaction with mouse
S. pneumoniae SP_0100 mutant interaction with mouse
S. pneumoniae SP_0102 mutant interaction with mouse
S. pneumoniae SP_0110 mutant interaction with mouse
S. pneumoniae SP_0117 mutant interaction with mouse
S. pneumoniae SP_0121 mutant interaction with mouse
S. pneumoniae SP_0128 mutant interaction with mouse
S. pneumoniae SP_0136 mutant interaction with mouse
S. pneumoniae SP_0141 mutant interaction with mouse
S. pneumoniae SP_0145 mutant interaction with mouse
S. pneumoniae SP_0146 mutant interaction with mouse
S. pneumoniae SP_0150 mutant interaction with mouse
S. pneumoniae SP_0156 mutant interaction with mouse
S. pneumoniae SP_0157 mutant interaction with mouse
S. pneumoniae SP_0160 mutant interaction with mouse
S. pneumoniae SP_1964 mutant interaction with mouse
S. pneumoniae SP_0177 mutant interaction with mouse
S. pneumoniae SP_0198 mutant interaction with mouse
S. pneumoniae SP_0199 mutant interaction with mouse
S. pneumoniae SP_0240 mutant interaction with mouse
S. pneumoniae SP_0242 mutant interaction with mouse
S. pneumoniae SP_0246 mutant interaction with mouse
S. pneumoniae SP_0247 mutant interaction with mouse
S. pneumoniae SP_0251 mutant interaction with mouse
S. pneumoniae gldA mutant interaction with mouse
S. pneumoniae leuS mutant interaction with mouse
S. pneumoniae SP_0265 mutant interaction with mouse
S. pneumoniae SP_0267 mutant interaction with mouse
S. pneumoniae SP_0268 mutant interaction with mouse
S. pneumoniae polC mutant interaction with mouse
S. pneumoniae SP_0298 mutant interaction with mouse
S. pneumoniae SP_0306 mutant interaction with mouse
S. pneumoniae SP_0312 mutant interaction with mouse
S. pneumoniae SP_0314 mutant interaction with mouse
S. pneumoniae SP_0320 mutant interaction with mouse
S. pneumoniae SP_0332 mutant interaction with mouse
S. pneumoniae SP_0338 mutant interaction with mouse
S. pneumoniae SP_2175 mutant interaction with mouse
S. pneumoniae SP_2164 mutant interaction with mouse
S. pneumoniae SP_2162 mutant interaction with mouse
S. pneumoniae SP_2145 mutant interaction with mouse
S. pneumoniae SP_2143 mutant interaction with mouse
S. pneumoniae SP_2128 mutant interaction with mouse
S. pneumoniae SP_2108 mutant interaction with mouse
S. pneumoniae SP_2101 mutant interaction with mouse
S. pneumoniae SP_2098 mutant interaction with mouse
S. pneumoniae SP_2095 mutant interaction with mouse
S. pneumoniae SP_2076 mutant interaction with mouse
S. pneumoniae SP_1952 mutant interaction with mouse
S. pneumoniae SP_0377 mutant interaction with mouse
S. pneumoniae SP_0385 mutant interaction with mouse
S. pneumoniae SP_0396 mutant interaction with mouse
S. pneumoniae SP_0445 mutant interaction with mouse
S. pneumoniae SP_0454 mutant interaction with mouse
S. pneumoniae SP_0461 mutant interaction with mouse
S. pneumoniae SP_0468 mutant interaction with mouse
S. pneumoniae SP_0474 mutant interaction with mouse
S. pneumoniae SP_0478 mutant interaction with mouse
S. pneumoniae SP_0479 mutant interaction with mouse
S. pneumoniae SP_0492 mutant interaction with mouse
S. pneumoniae SP_0494 mutant interaction with mouse
S. pneumoniae SP_0498 mutant interaction with mouse
S. pneumoniae SP_0510 mutant interaction with mouse
S. pneumoniae blpA mutant interaction with mouse
S. pneumoniae SP_0571 mutant interaction with mouse
S. pneumoniae SP_0586 mutant interaction with mouse
S. pneumoniae SP_0595 mutant interaction with mouse
S. pneumoniae SP_0600 mutant interaction with mouse
S. pneumoniae SP_0614 mutant interaction with mouse
S. pneumoniae SP_0622 mutant interaction with mouse
S. pneumoniae SP_0633 mutant interaction with mouse
S. pneumoniae SP_0641 mutant interaction with mouse
S. pneumoniae SP_0645 mutant interaction with mouse
S. pneumoniae SP_0648 mutant interaction with mouse
S. pneumoniae SP_0655 mutant interaction with mouse
S. pneumoniae SP_0661 mutant interaction with mouse
S. pneumoniae SP_0663 mutant interaction with mouse
S. pneumoniae SP_0664 mutant interaction with mouse
S. pneumoniae SP_0665 mutant interaction with mouse
S. pneumoniae SP_0686 mutant interaction with mouse
S. pneumoniae SP_0690 mutant interaction with mouse
S. pneumoniae SP_0719 mutant interaction with mouse
S. pneumoniae SP_0720 mutant interaction with mouse
S. pneumoniae SP_0726 mutant interaction with mouse
S. pneumoniae SP_0728 mutant interaction with mouse
S. pneumoniae SP_0729 mutant interaction with mouse
S. pneumoniae SP_0766 mutant interaction with mouse
S. pneumoniae SP_0767 mutant interaction with mouse
S. pneumoniae SP_0774 mutant interaction with mouse
S. pneumoniae SP_0785 mutant interaction with mouse
S. pneumoniae SP_0789 mutant interaction with mouse
S. pneumoniae SP_0797 mutant interaction with mouse
S. pneumoniae SP_0807 mutant interaction with mouse
S. pneumoniae SP_0829 mutant interaction with mouse
S. pneumoniae SP_0842 mutant interaction with mouse
S. pneumoniae SP_0856 mutant interaction with mouse
S. pneumoniae SP_0886 mutant interaction with mouse
S. pneumoniae SP_0887 mutant interaction with mouse
S. pneumoniae SP_0892 mutant interaction with mouse
S. pneumoniae SP_0916 mutant interaction with mouse
S. pneumoniae SP_0927 mutant interaction with mouse
S. pneumoniae SP_0939 mutant interaction with mouse
S. pneumoniae SP_0943 mutant interaction with mouse
S. pneumoniae SP_1889 mutant interaction with mouse
S. pneumoniae SP_1898 mutant interaction with mouse
S. pneumoniae SP_1896 mutant interaction with mouse
S. pneumoniae SP_1890 mutant interaction with mouse
S. pneumoniae SP_1891 mutant interaction with mouse
S. pneumoniae SP_1879 mutant interaction with mouse
S. pneumoniae SP_1869 mutant interaction with mouse
S. pneumoniae SP_1861 mutant interaction with mouse
S. pneumoniae SP_1859 mutant interaction with mouse
S. pneumoniae SP_1856 mutant interaction with mouse
S. pneumoniae SP_1855 mutant interaction with mouse
S. pneumoniae SP_1854 mutant interaction with mouse
S. pneumoniae SP_1847 mutant interaction with mouse
S. pneumoniae SP_1830 mutant interaction with mouse
S. pneumoniae SP_1817 mutant interaction with mouse
S. pneumoniae SP_1800 mutant interaction with mouse
S. pneumoniae SP_1816 mutant interaction with mouse
S. pneumoniae trpD mutant interaction with mouse
S. pneumoniae SP_1793 mutant interaction with mouse
S. pneumoniae SP_1770 mutant interaction with mouse
S. pneumoniae SP_1780 mutant interaction with mouse
S. pneumoniae SP_1771 mutant interaction with mouse
S. pneumoniae SP_1779 mutant interaction with mouse
S. pneumoniae SP_1772 mutant interaction with mouse
S. pneumoniae SP_1760 mutant interaction with mouse
S. pneumoniae SP_1717 mutant interaction with mouse
S. pneumoniae SP_1715 mutant interaction with mouse
S. pneumoniae SP_1706 mutant interaction with mouse
S. pneumoniae SP_1652 mutant interaction with mouse
S. pneumoniae SP_1654 mutant interaction with mouse
S. pneumoniae SP_1646 mutant interaction with mouse
S. pneumoniae SP_1645 mutant interaction with mouse
S. pneumoniae SP_1636 mutant interaction with mouse
S. pneumoniae SP_1633 mutant interaction with mouse
S. pneumoniae SP_1591 mutant interaction with mouse
S. pneumoniae SP_1580 mutant interaction with mouse
S. pneumoniae SP_1544 mutant interaction with mouse
S. pneumoniae SP_1538 mutant interaction with mouse
S. pneumoniae SP_1529 mutant interaction with mouse
S. pneumoniae SP_1518 mutant interaction with mouse
S. pneumoniae SP_1483 mutant interaction with mouse
S. pneumoniae SP_1433 mutant interaction with mouse
S. pneumoniae SP_1434 mutant interaction with mouse
S. pneumoniae SP_1431 mutant interaction with mouse
S. pneumoniae SP_1400 mutant interaction with mouse
S. pneumoniae SP_1399 mutant interaction with mouse
S. pneumoniae SP_1398 mutant interaction with mouse
S. pneumoniae SP_1396 mutant interaction with mouse
S. pneumoniae SP_1378 mutant interaction with mouse
S. pneumoniae SP_1382 mutant interaction with mouse
S. pneumoniae aroD mutant interaction with mouse
S. pneumoniae SP_0978 mutant interaction with mouse
S. pneumoniae SP_0979 mutant interaction with mouse
S. pneumoniae SP_1001 mutant interaction with mouse
S. pneumoniae SP_1003 mutant interaction with mouse
S. pneumoniae SP_1018 mutant interaction with mouse
S. pneumoniae SP_1023 mutant interaction with mouse
S. pneumoniae SP_1029 mutant interaction with mouse
S. pneumoniae SP_1032 mutant interaction with mouse
S. pneumoniae SP_1040 mutant interaction with mouse
S. pneumoniae SP_1043 mutant interaction with mouse
S. pneumoniae SP_1045 mutant interaction with mouse
S. pneumoniae SP_1089 mutant interaction with mouse
S. pneumoniae SP_1111 mutant interaction with mouse
S. pneumoniae SP_1112 mutant interaction with mouse
S. pneumoniae SP_1115 mutant interaction with mouse
S. pneumoniae SP_1118 mutant interaction with mouse
S. pneumoniae SP_1121 mutant interaction with mouse
S. pneumoniae SP_1127 mutant interaction with mouse
S. pneumoniae SP_1143 mutant interaction with mouse
S. pneumoniae SP_1153 mutant interaction with mouse
S. pneumoniae SP_1154 mutant interaction with mouse
S. pneumoniae rnhB mutant interaction with mouse
S. pneumoniae SP_1174 mutant interaction with mouse
S. pneumoniae SP_1175 mutant interaction with mouse
S. pneumoniae SP_1193 mutant interaction with mouse
S. pneumoniae SP_1202 mutant interaction with mouse
S. pneumoniae SP_1278 mutant interaction with mouse
S. pneumoniae SP_1281 mutant interaction with mouse
S. pneumoniae gidB mutant interaction with mouse
S. pneumoniae SP_1286 mutant interaction with mouse
S. pneumoniae SP_1292 mutant interaction with mouse
S. pneumoniae SP_1321 mutant interaction with mouse
S. pneumoniae SP_1328 mutant interaction with mouse
S. pneumoniae SP_1343 mutant interaction with mouse
S. pneumoniae SP_1344 mutant interaction with mouse
S. pneumoniae SP_1941 mutant interaction with mouse
S. pneumoniae SP_1970 mutant interaction with mouse
S. pneumoniae SP_1998 mutant interaction with mouse
S. pneumoniae SP_2201 mutant interaction with mouse
S. pneumoniae SP_2236 mutant interaction with mouse
S. pneumoniae SP_1923 mutant interaction with mouse
S. pneumoniae SP_1956 mutant interaction with mouse
S. pneumoniae SP_2190 mutant interaction with mouse
S. pneumoniae SP_2176 mutant interaction with mouse
S. pneumoniae SP_2182 mutant interaction with mouse
S. pneumoniae SP_2167 mutant interaction with mouse
S. pneumoniae SP_2159 mutant interaction with mouse
S. pneumoniae SP_2146 mutant interaction with mouse
S. pneumoniae SP_2142 mutant interaction with mouse
S. pneumoniae SP_2136 mutant interaction with mouse
S. pneumoniae SP_2131 mutant interaction with mouse
S. pneumoniae SP_2105 mutant interaction with mouse
S. pneumoniae SP_2086 mutant interaction with mouse
S. pneumoniae SP_2060 mutant interaction with mouse
S. pneumoniae SP_2052 mutant interaction with mouse
S. pneumoniae SP_1939 mutant interaction with mouse
S. pneumoniae SP_2002 mutant interaction with mouse
S. pneumoniae SP_2017 mutant interaction with mouse
S. pneumoniae SP_2022 mutant interaction with mouse
S. pneumoniae SP_2039 mutant interaction with mouse
C. diphtheriae DIP2010 mutant interaction with human
C. diphtheriae DIP2010 mutant interaction with human epithelial cell
C. diphtheriae DIP2011 mutant interaction with human
C. diphtheriae DIP2011 mutant interaction with human epithelial cell
H. pylori homB mutant interaction with human
H. pylori homB mutant interaction with human epithelial cell
H. pylori hopZ mutant interaction with human
H. pylori hopZ mutant interaction with human epithelial cell
H. pylori horB mutant interaction with mouse
Salmonella spp. fur mutant interaction with mouse
Salmonella spp. rpoS mutant interaction with mouse
Salmonella spp. relA mutant interaction with mouse
Salmonella spp. htrA mutant interaction with mouse
Salmonella spp. ompR mutant interaction with mouse
Salmonella spp. galE mutant interaction with mouse
Salmonella spp. hfq mutant interaction with mouse
Salmonella spp. phoP mutant interaction with mouse
Salmonella spp. rfaL mutant interaction with mouse
Salmonella spp. rfaG mutant interaction with mouse
Salmonella spp. spoT mutant interaction with mouse
Salmonella spp. aroA mutant interaction with mouse
Salmonella spp. iacP mutant interaction with chicken
Salmonella spp. sipD mutant interaction with chicken
Salmonella spp. sipB mutant interaction with chicken
Salmonella spp. ssrA mutant interaction with mouse
Salmonella spp. sseA mutant interaction with mouse
Salmonella spp. aroD mutant interaction with mouse
Rotavirus RVA_s10gp1 mutant interaction with mouse
S. pneumoniae piaA mutant interaction with mouse
S. pneumoniae cpsC mutant interaction with mouse
S. pneumoniae purL mutant interaction with mouse
S. pneumoniae cpsB mutant interaction with mouse
S. pneumoniae zmpC mutant interaction with mouse
S. pneumoniae ritR mutant interaction with mouse
E. coli eaeA mutant interaction with human
E. coli espH mutant interaction with rabbit
L. monocytogenes LMHCC_0048 mutant interaction with mouse
L. monocytogenes LMHCC_0614 mutant interaction with mouse
L. monocytogenes srtB mutant interaction with mouse
L. monocytogenes LMHCC_2768 mutant interaction with mouse
L. monocytogenes LMHCC_2601 mutant interaction with mouse
S. pneumoniae htrA mutant interaction with mouse
S. pneumoniae psrP mutant interaction with human
S. pneumoniae psrP mutant interaction with human epithelial cell
S. pneumoniae psrP mutant interaction with mouse
S. pneumoniae psrP mutant interaction with mouse epithelial cell
B. anthracis nos mutant interaction with mouse
B. anthracis asbA mutant interaction with mouse
B. anthracis asbA mutant interaction with mouse macrophage cell
B. anthracis sodA2 mutant interaction with mouse
B. anthracis sodA1 mutant interaction with mouse
B. anthracis acpB mutant interaction with mouse
B. anthracis capD mutant interaction with mouse
B. anthracis capE mutant interaction with mouse
B. pseudomallei GBP346_A0742 mutant interaction with mouse
B. pseudomallei mviN mutant interaction with human
B. pseudomallei mviN mutant interaction with human epithelial cell
B. pseudomallei mviN mutant interaction with hamster
B. pseudomallei mviN mutant interaction with hamster epithelial cell
B. pseudomallei ppsA mutant interaction with mouse
B. pseudomallei rpoE mutant interaction with mouse
E. coli espK mutant interaction with cattle
E. coli nleA mutant interaction with mouse
L. monocytogenes Lm4b_01887 mutant interaction with mouse
L. monocytogenes Lm4b_00320 mutant interaction with mouse
L. monocytogenes srtA mutant interaction with mouse
V. cholerae glyA-1 mutant interaction with mouse
V. cholerae ccmF mutant interaction with mouse
V. cholerae sucA mutant interaction with mouse
C. pneumoniae groEL_3 mutant interaction with mouse
Y. enterocolitica yopP mutant interaction with mouse
Y. enterocolitica lcrV mutant interaction with mouse
Y. enterocolitica yscR mutant interaction with mouse
Y. enterocolitica yscU mutant interaction with mouse
Y. enterocolitica virG mutant interaction with mouse
Y. enterocolitica virF mutant interaction with mouse
Y. enterocolitica yscC mutant interaction with mouse
Y. enterocolitica yscL mutant interaction with mouse
Y. enterocolitica sycH mutant interaction with mouse
Y. enterocolitica yadA mutant interaction with mouse
B. pertussis bhuR mutant interaction with mouse
B. pertussis prn mutant interaction with human
B. pertussis prn mutant interaction with human HeLa cell
B. pertussis cyaA mutant interaction with mouse
B. pertussis brkB mutant interaction with mouse
B. pertussis brkA mutant interaction with mouse
B. pertussis tonB mutant interaction with mouse
B. pertussis exbB mutant interaction with mouse
B. pertussis ptxA mutant interaction with mouse
B. pertussis ptxB mutant interaction with mouse
B. pertussis BP0123 mutant interaction with mouse
B. pertussis fim3 mutant interaction with mouse
B. pertussis BP3072 mutant interaction with human
B. pertussis BP3072 mutant interaction with human macrophage cell
B. pertussis dnt mutant interaction with mouse
B. pertussis bvgR mutant interaction with mouse
B. pertussis fhaB mutant interaction with hamster
B. pertussis fimD mutant interaction with mouse
B. pertussis fauA mutant interaction with mouse
M. gallisepticum MGA_0674 mutant interaction with chicken
M. gallisepticum MGA_1107 mutant interaction with chicken
Y. pseudotuberculosis pYV0047 mutant interaction with mouse
Y. pseudotuberculosis pYV0074 mutant interaction with mouse
Y. pseudotuberculosis pYV0084 mutant interaction with mouse
Y. pseudotuberculosis pYV0094 mutant interaction with mouse
Y. pseudotuberculosis cls mutant interaction with mouse
Y. pseudotuberculosis ddhC mutant interaction with mouse
Y. pseudotuberculosis gmd mutant interaction with mouse
Y. pseudotuberculosis ksgA mutant interaction with mouse
Y. pseudotuberculosis wzx mutant interaction with mouse
Y. pseudotuberculosis wzxE mutant interaction with mouse
Y. pseudotuberculosis hfq mutant interaction with mouse
Y. enterocolitica pstC mutant interaction with mouse
Y. enterocolitica dnaJ mutant interaction with mouse
Y. enterocolitica pspC mutant interaction with mouse
Y. enterocolitica horYe mutant interaction with mouse
Y. enterocolitica irp1 mutant interaction with mouse
Y. enterocolitica galE mutant interaction with mouse
Y. enterocolitica manB mutant interaction with mouse
Y. enterocolitica manC mutant interaction with mouse
Y. enterocolitica rfpB mutant interaction with mouse
Y. enterocolitica wbcH mutant interaction with mouse
Y. enterocolitica wbcF mutant interaction with mouse
Y. enterocolitica wbcC mutant interaction with mouse
Y. enterocolitica ddhB mutant interaction with mouse
Y. enterocolitica ddhA mutant interaction with mouse
Y. enterocolitica supX mutant interaction with mouse
Y. enterocolitica degP mutant interaction with mouse
Y. enterocolitica nlpD mutant interaction with mouse
A. pleuropneumoniae apxIC mutant interaction with mouse
A. pleuropneumoniae apxIA mutant interaction with mouse
A. pleuropneumoniae luxS mutant interaction with mouse
Y. pseudotuberculosis YpsIP31758_3820 mutant interaction with mouse
Y. pseudotuberculosis YpsIP31758_3046 mutant interaction with mouse
Y. pseudotuberculosis yopM mutant interaction with mouse
Y. pseudotuberculosis YPK_3908 mutant interaction with mouse
Y. pseudotuberculosis YPTS_0345 mutant interaction with mouse
Y. pseudotuberculosis YPTS_4218 mutant interaction with mouse
Y. pseudotuberculosis YPTS_4278 mutant interaction with mouse
Y. pseudotuberculosis YPTS_4292 mutant interaction with mouse
Y. pseudotuberculosis YPTS_4207 mutant interaction with mouse
Y. pseudotuberculosis YPTS_4221 mutant interaction with mouse
S. equi vicK mutant interaction with mouse
S. equi szp mutant interaction with mouse
S. equi lgt mutant interaction with mouse
L. pneumophila lpa_03874 mutant interaction with mouse
L. pneumophila lpa_03874 mutant interaction with mouse macrophage cell
L. monocytogenes pLM33_p09 mutant interaction with mouse
B. burgdorferi ruvB mutant interaction with mouse
B. burgdorferi ruvA mutant interaction with mouse
B. burgdorferi BB0098 mutant interaction with mouse
B. burgdorferi BB0153 mutant interaction with mouse
B. burgdorferi BB0198 mutant interaction with mouse
B. burgdorferi BB0210 mutant interaction with mouse
B. burgdorferi BB0219 mutant interaction with mouse
B. burgdorferi BB0268 mutant interaction with mouse
B. burgdorferi BB0323 mutant interaction with mouse
B. burgdorferi BB0363 mutant interaction with mouse
B. burgdorferi BB0797 mutant interaction with mouse
P. aeruginosa algR mutant interaction with mouse
P. aeruginosa hfq mutant interaction with mouse
P. aeruginosa algC mutant interaction with mouse
P. aeruginosa wzz mutant interaction with mouse
P. aeruginosa galU mutant interaction with mouse
P. aeruginosa phzM mutant interaction with mouse
P. aeruginosa fur mutant interaction with mouse
P. aeruginosa lasR mutant interaction with mouse
P. aeruginosa phzS mutant interaction with mouse
P. aeruginosa fliC mutant interaction with mouse
P. aeruginosa pvdS mutant interaction with rabbit
S. pyogenes SPy_0019 mutant interaction with mouse
S. pyogenes nga mutant interaction with mouse
S. pyogenes sagA mutant interaction with mouse
S. pyogenes lsp mutant interaction with mouse
S. pyogenes dltA mutant interaction with human
S. pyogenes dltA mutant interaction with human epithelial cell
S. pyogenes scpA mutant interaction with mouse
S. pyogenes sic mutant interaction with human
S. pyogenes mga mutant interaction with human
S. pyogenes mga mutant interaction with mouse
S. pyogenes speB mutant interaction with mouse
S. pyogenes gidA mutant interaction with mouse
S. pyogenes SPy_1633 mutant interaction with mouse
S. pyogenes SPy_1718 mutant interaction with mouse
S. pyogenes fba mutant interaction with mouse
S. aureus oppF mutant interaction with mouse
S. aureus oppD mutant interaction with mouse
S. aureus purL mutant interaction with mouse
S. aureus SA1062 mutant interaction with mouse
S. aureus SA1063 mutant interaction with mouse
S. aureus recA mutant interaction with mouse
S. aureus thrB mutant interaction with mouse
S. aureus citB mutant interaction with mouse
S. aureus msrA mutant interaction with mouse
S. aureus trpD mutant interaction with mouse
S. aureus trpB mutant interaction with mouse
S. aureus trpA mutant interaction with mouse
S. aureus femA mutant interaction with mouse
S. aureus femB mutant interaction with mouse
S. aureus opp-2C mutant interaction with mouse
S. aureus asd mutant interaction with mouse
S. aureus lysA mutant interaction with mouse
S. aureus braB mutant interaction with mouse
S. aureus odhB mutant interaction with mouse
S. aureus dinG mutant interaction with mouse
S. aureus SA1453 mutant interaction with mouse
S. aureus clpX mutant interaction with mouse
S. aureus fbp mutant interaction with mouse
S. aureus mprF mutant interaction with mouse
S. pyogenes slo mutant interaction with mouse
S. agalactiae ciaR mutant interaction with human
S. agalactiae ciaR mutant interaction with human macrophage cell
S. agalactiae ciaR mutant interaction with mouse
S. agalactiae ciaR mutant interaction with mouse macrophage cell
S. agalactiae lmb mutant interaction with human
S. agalactiae csrS mutant interaction with mouse
S. agalactiae csrR mutant interaction with mouse
S. agalactiae gbs1020 mutant interaction with human
S. agalactiae gbs1020 mutant interaction with human macrophage cell
S. agalactiae gbs1020 mutant interaction with mouse
S. agalactiae gbs1020 mutant interaction with mouse macrophage cell
S. agalactiae cpsD mutant interaction with human
S. agalactiae scpB mutant interaction with human
S. agalactiae gbs1402 mutant interaction with mouse
S. pyogenes M5005_Spy_1305 mutant interaction with mouse
S. pyogenes grab mutant interaction with mouse
S. pyogenes ccpA mutant interaction with mouse
S. pyogenes oppA mutant interaction with mouse
S. pyogenes perR mutant interaction with mouse
S. agalactiae SAK_0517 mutant interaction with mouse
S. agalactiae cpsY mutant interaction with human
S. agalactiae lgt mutant interaction with human
S. aureus SAOUHSC_01373 mutant interaction with mouse
P. aeruginosa mvfR mutant interaction with mouse
P. aeruginosa flhB mutant interaction with mouse
P. aeruginosa PA14_38610 mutant interaction with mouse
P. aeruginosa PA14_37650 mutant interaction with mouse
P. aeruginosa PA14_33610 mutant interaction with mouse
P. aeruginosa gacA mutant interaction with mouse
P. aeruginosa PA14_41070 mutant interaction with mouse
P. aeruginosa prpR mutant interaction with mouse
P. aeruginosa toxA mutant interaction with mouse
P. aeruginosa pilF mutant interaction with mouse
P. aeruginosa PA14_35740 mutant interaction with mouse
P. aeruginosa katA mutant interaction with mouse
P. aeruginosa PA14_03120 mutant interaction with mouse
P. aeruginosa PA14_03530 mutant interaction with mouse
P. aeruginosa PA14_04850 mutant interaction with mouse
P. aeruginosa fabF1 mutant interaction with mouse
P. aeruginosa dsbA mutant interaction with mouse
P. aeruginosa plcH mutant interaction with mouse
P. aeruginosa PA14_37260 mutant interaction with mouse
S. aureus tilS mutant interaction with C. elegans
S. aureus fbp mutant interaction with C. elegans
S. aureus ccpA mutant interaction with mouse
S. aureus pyrAA mutant interaction with C. elegans
S. aureus SAHV_0924 mutant interaction with C. elegans
S. aureus mgrA mutant interaction with mouse
S. pyogenes ska mutant interaction with mouse
B. burgdorferi bosR mutant interaction with mouse
B. burgdorferi cspA mutant interaction with human
B. burgdorferi dbpA mutant interaction with mouse
B. burgdorferi bbk32 mutant interaction with mouse
C. trachomatis CT135 mutant interaction with mouse
C. trachomatis incA mutant interaction with mouse
P. multocida dcaA mutant interaction with mouse
P. multocida dcaA mutant interaction with chicken
P. multocida PM0855 mutant interaction with mouse
P. multocida PM0855 mutant interaction with chicken
P. multocida PM1294 mutant interaction with mouse
P. multocida PM1294 mutant interaction with chicken
P. multocida purN mutant interaction with mouse
P. multocida purN mutant interaction with chicken
P. multocida PM1069 mutant interaction with chicken
P. multocida deoC mutant interaction with chicken
P. multocida pyrF mutant interaction with chicken
P. multocida ponC mutant interaction with chicken
P. multocida PM0081 mutant interaction with chicken
P. multocida dam mutant interaction with mouse
P. multocida purF mutant interaction with mouse
P. multocida guaA mutant interaction with mouse
P. multocida atpG mutant interaction with mouse
P. multocida PM1466 mutant interaction with mouse
P. multocida dsbB mutant interaction with mouse
Pseudorabies virus UL41 mutant interaction with mouse
Herpes simplex virus type 1 ICP0 mutant interaction with mouse
Herpes simplex virus type 1 gD mutant interaction with mouse
Herpes simplex virus type 1 ICP34.5 mutant interaction with mouse
Herpes simplex virus type 1 UL41 mutant interaction with mouse
Bartonella spp. ialB mutant interaction with human
Enterococcus spp. EF3314 mutant interaction with C. elegans
Enterococcus spp. EF3314 mutant interaction with C. elegans macrophage cell
Enterococcus spp. srtC mutant interaction with mouse
Enterococcus spp. scrB-1 mutant interaction with C. elegans
Enterococcus spp. scrB-1 mutant interaction with mouse
Enterococcus spp. purL mutant interaction with mouse
Enterococcus spp. glf mutant interaction with mouse
Enterococcus spp. bopD mutant interaction with mouse
Enterococcus spp. srtA mutant interaction with mouse
Enterococcus spp. prgB mutant interaction with rabbit
Enterococcus spp. EF0382 mutant interaction with C. elegans
Enterococcus spp. EF1302 mutant interaction with C. elegans
Enterococcus spp. psr mutant interaction with C. elegans
Enterococcus spp. scrR-1 mutant interaction with C. elegans
Enterococcus spp. agrBfs mutant interaction with C. elegans
Enterococcus spp. agrBfs mutant interaction with mouse
Enterococcus spp. brnQ mutant interaction with C. elegans
Enterococcus spp. EF1513 mutant interaction with C. elegans
Enterococcus spp. EF2598 mutant interaction with C. elegans
Enterococcus spp. recQ-1 mutant interaction with C. elegans
Enterococcus spp. recQ-1 mutant interaction with mouse
Enterococcus spp. phrB mutant interaction with C. elegans
Enterococcus spp. phrB mutant interaction with mouse
Enterococcus spp. EF2591 mutant interaction with C. elegans
Enterococcus spp. EF0737 mutant interaction with C. elegans
Enterococcus spp. EF1623 mutant interaction with C. elegans
Enterococcus spp. thyA mutant interaction with C. elegans
Enterococcus spp. map mutant interaction with C. elegans
Enterococcus spp. EF0376 mutant interaction with C. elegans
Enterococcus spp. EF0861 mutant interaction with C. elegans
Enterococcus spp. EF1542 mutant interaction with C. elegans
Enterococcus spp. EF1590 mutant interaction with C. elegans
Enterococcus spp. EF1590 mutant interaction with mouse
Enterococcus spp. EF1792 mutant interaction with C. elegans
Enterococcus spp. EF2675 mutant interaction with C. elegans
Enterococcus spp. EF2957 mutant interaction with C. elegans
Leptospira spp. hemO mutant interaction with hamster
Influenza virus NS1 mutant interaction with mouse
L. monocytogenes Dfp mutant interaction with mouse
L. monocytogenes Ptb mutant interaction with mouse
Brucella spp. BMEI0066 mutant interaction with mouse
Brucella spp. BMEI0066 mutant interaction with mouse macrophage cell
B. bronchiseptica aroA mutant interaction with mouse
Bovine herpesvirus 1 US8 mutant interaction with cattle
M. gallisepticum lpd mutant interaction with chicken
L. monocytogenes mogR mutant interaction with mouse
F. tularensis guaA mutant interaction with mouse
F. tularensis guaB mutant interaction with mouse
F. tularensis wbtI mutant interaction with mouse
M. tuberculosis lysA mutant interaction with mouse
M. tuberculosis mce-2 mutant interaction with mouse
M. tuberculosis mce-3 mutant interaction with mouse
Salmonella spp. cbiA mutant interaction with chicken
Salmonella spp. cobS mutant interaction with chicken
Salmonella spp. guaB mutant interaction with mouse
Salmonella spp. lon mutant interaction with mouse
Salmonella spp. cpxR mutant interaction with mouse
Salmonella spp. nuoG mutant interaction with chicken
Salmonella spp. ruvB mutant interaction with mouse
Salmonella spp. tolA mutant interaction with mouse
S. aureus aroA mutant interaction with mouse
Y. enterocolitica aroA mutant interaction with mouse
B. bronchiseptica bscN mutant interaction with mouse
B. bronchiseptica cyaA mutant interaction with mouse
B. bronchiseptica trpE mutant interaction with mouse
Bovine herpesvirus 1 UL23 mutant interaction with cattle
Bovine respiratory syncytial virus glycoprotein G mutant interaction with cattle
Brucella spp. manA mutant interaction with mouse
Brucella spp. pgk mutant interaction with mouse
F. tularensis sodC mutant interaction with mouse
F. tularensis purC/purD mutant interaction with mouse
F. tularensis FTL0552 mutant interaction with mouse
Gallid herpesvirus 1 UL0 mutant interaction with chicken
Gallid herpesvirus 1 UL23 mutant interaction with chicken
Gallid herpesvirus 1 sORF1 mutant interaction with chicken
Herpes simplex virus type 1 US8 mutant interaction with mouse
Herpes simplex virus type 1 UL29 mutant interaction with mouse
Herpes simplex virus type 1 UL23 mutant interaction with mouse
Influenza virus M2 mutant interaction with mouse
M. avium relA mutant interaction with goat
M. avium relA mutant interaction with cattle
Salmonella spp. atpA mutant interaction with mouse
Salmonella spp. cpxA mutant interaction with mouse
Salmonella spp. lon mutant interaction with chicken
Salmonella spp. yjeA mutant interaction with mouse
Salmonella spp. surA mutant interaction with mouse
SARS-related coronavirus E mutant interaction with hamster
Simian immunodeficiency virus nef mutant interaction with monkey
Y. enterocolitica sodA mutant interaction with mouse
Y. pseudotuberculosis phoP mutant interaction with mouse
Myxoma virus MYXV_gp168 mutant interaction with rabbit
Vaccinia virus VGF mutant interaction with rabbit
Vaccinia virus VGF mutant interaction with mouse
Ectromelia virus C13R mutant interaction with mouse
A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure.
A morphology quality inhering in a bearer by virtue of the bearer's relative position, shape, arrangements and connectivity of an organism's various parts; the pattern underlying its form.
An organismal quality inhering in a bearer by virtue of the bearer's behavior aggregate of the responses or reactions or movements in a given situation.
A quality which inheres in a continuant.
A quality that inheres in an entire organism or part of an organism.
A behavioral quality inhering ina bearer by virtue of the bearer's unequal distribution of fine motor skill between its left and right hands or feet.
Handedness where the organism preferentially uses the left hand or foot for tasks requiring the use of a single hand or foot or a dominant hand or foot.
Handedness where the organism preferentially uses the right hand or foot for tasks requiring the use of a single hand or foot or a dominant hand or foot.
Handedness where the organism exhibits no overall dominance in the use of right or left hand or foot in the performance of tasks that require one hand or foot or a dominant hand or foot.
protein
A biological macromolecule that is composed of amino acids linked in a linear sequence (a polypeptide chain) and is genetically encoded. 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.
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 process that is the means during which the pathogen is transmitted directly or indirectly from its natural reservoir, a susceptible host or source to a new host.
An occurrent [span:Occurrent] that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity.
Lower, narrow portion of the uterus where it joins with the top end of the vagina.
The narrow caudal end of the uterus that opens into the vagina. [TFD][VHOG]
The evolution of mammals is associated with radical changes in their reproductive biology, particularly the structure and function of the female reproductive organs. These changes include the evolution of the uterus, cervix, vagina, placenta and specialized cell types associated with each of those structures.[well established][VHOG]
cervix
uterine cervix
子宫颈(cervix)
子宫颈(uterine cervix)
DOI:10.1098/rspb.2004.2848 Lynch VJ, Roth JJ, Takahashi K, Dunn CW, Nonaka DF, Stopper GF, Wagner GP, Adaptive evolution of HoxA-11 and HoxA-13 at the origin of the uterus in mammals. Proceedings of the Royal Society of London, Series B (2004)
The olfactory organ of vertebrates, consisting of nares, olfactory epithelia and the structures and skeletal framework of the nasal cavity.
Organ that is the specialized structure of the face that contains olfactory neurons. The peripheral olfactory organ is paired[ZFA:0000047].
a protuberance in vertebrates that houses the nostrils, or nares, which admit and expel air for respiration in conjunction with the mouth. Behind the nose are the olfactory mucosa and the sinuses. Behind the nasal cavity, air next passes through the pharynx, shared with the digestive system, and then into the rest of the respiratory system. In humans, the nose is located centrally on the face; on most other mammals, it is on the upper tip of the snout[WP]. GO: The nose is the specialized structure of the face that serves as the organ of the sense of smell and as part of the respiratory system. Includes the nasi externus (external nose) and cavitas nasi (nasal cavity)[Wikipedia:Nose].
the organ that is specialized for smell and is part of the respiratory system
the structure of the nose varies across vertebrates. In tetrapods the nose is part of the respiratory system.[PMID:25312359]
A layer of dense irregular connective tissue that lines organs and supports the mucosa, as well as joins the mucosa to the bulk of underlying smooth muscle. [WP,unvetted].
A major division of the nervous system that contains nerves which connect the central nervous system (CNS) with sensory organs, other organs, muscles, blood vessels and glands.
Nervous structures including ganglia outside of the central nervous system. Kimmel et al, 1995.[TAO]
Part of nervous system in which nerves extend throughout the body outside of the brain and spinal cord.[AAO]
The peripheral nervous system (PNS) is the part of the nervous system connected to the CNS which contains cranial nerves III - XII, spinal, peripheral and autonomic nerves. (CUMBO)
(...) specific vertebrate traits within the chordate phylum such as skeletal tissues, PNS, and spectacular head and brain development, are linked to the NC (neural crest) and its derivatives.[well established][VHOG]
DOI:10.1007/978-0-387-46954-6_6 Dupin E, Creuzet S, Le Douarin NM, The contribution of the neural crest to the vertebrate body. Advances in experimental medicine and biology (2006)
Part of peripheral nervous system that includes the somatic parts of the cranial and spinal nerves and their ganglia and the peripheral sensory receptors.
somatic nervous system, somatic division
somatic part of peripheral nervous system
The sympathetic nervous system is one of the two divisions of the vertebrate autonomic nervous system (the other being the parasympathetic nervous system). The sympathetic preganglionic neurons have their cell bodies in the thoracic and lumbar regions of the spinal cord and connect to the paravertebral chain of sympathetic ganglia. Innervate heart and blood vessels, sweat glands, viscera and the adrenal medulla. Most sympathetic neurons, but not all, use noradrenaline as a post-ganglionic neurotransmitter [GO].
Part of the autonomic nervous system which has opposing physiological effects of the parasympathetic nervous system. Examples include increasing the heart rate or constricting the blood vessels.[AAO]
The part of the autonomic nervous system which chiefly contains adrenergic fibres and tends to control and reduce secretions, decrease the contractility and hence the tone of smooth muscles and provoke the contraction of blood vessels. Essentially, it consists of preganglionic fibres from the thoracic and upper lumbar parts of the spinal cord. These fibres, by means of delicate rami communicantes, cross over to ganglia sited in a pair of ganglionated cords on each side of the vertebral column or to more peripheral ganglia. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
The autonomic nervous system is composed of three divisions: the sympathetic division, the parasympathetic division, and the enteric division. (...) In ray-finned teleost fishes, a sympathetic chain is present, and dual innervation of additional organs can be observed. A similar pattern can be found in amphibians (...). The evolution of the autonomic nervous system has been quite conservative, especially in the tetrapod lineage.[well established][VHOG]
has developmental contribution from NC in verteberates (https://github.com/obophenotype/uberon/wiki/The-neural-crest)
pars sympathica divisionis autonomici systematis nervosi
sympathetic part of autonomic division of nervous system
ISBN:978-0471210054 Butler AB and Hodos W, Comparative vertebrate neuroanatomy: Evolution and Adaptation (2005) p.461-463
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
DOI:10.1111/j.1469-7580.2008.01043.x Vickaryous MK, Sire JY, The integumentary skeleton of tetrapods: origin, evolution, and development. J Anat (2009)
A non-material anatomical entity of two dimensions. Anatomical boundaries are contiguous structures.
Except in the case of abstracted fiat boundaries such as the midline plane of an organism, all 2D anatomical entities have a 3 dimensional projection. For example, the surface of the shell of a muscle has a distinct shape that projects into the third dimension. Note that boundaries are 2D structures. They have no thickness - and so can not be sites of gene expression or gene product localisation. For this, use boundary region terms.
An organ of sight that includes the camera-type eyeball and supporting structures such as the lacrimal apparatus, the conjunctiva, the eyelid.
A cavitated compound organ that transduces light waves into neural signals.[TAO]
The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG]
FMA distinguishes Eye (subdivision of face) which has its parts an Eyeball (organ), as well as other structures, and the orbit of skull. MA includes eyelid, conjunctiva and lacrimal apparatus as part of MA:eye - consistent with FMA - so we can infer that MA:eye is more like FMA:eye than FMA:eyeball. For other AOs this distinction is less meaningful - e.g. ZFA has no eyelid; XAO has no eyelid, but it has conjuctiva, which is considered part of the xao:eye. GO considers eyelid development part of eye development. See also notes on optic nerve - XAO, AAO and BTO consider this part of the eye. MA considers the eye muscles part of the eye, whereas FMA has a class 'orbital content' for this
camera-type eye plus associated structures
DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007)
An organ that is capable of transducing sensory stimulus to the nervous system.
Any hollow cylindrical anatomical structure containing a lumen through which substances are transported.
not every anatomical conduit is a tube - for example, a bone foramen is an opening in the bone, and there is no distinct separate tube structure. Tubes may transport large mixed objects (for example, a bolus of food in the digestive tube) or they may transport the secretions of a single gland (for example, gland ducts)
Major subdivision of an organism that protrudes from the body[DOS, CARO].
An appendage is an external body part, or natural prolongation, that protrudes from an organism's body, such as a vertebrate's limbs[BILA][BILA:0000018].
Organ or organ part that is attached to the body of an organism. For example a limb[GO, modified][GO:0048736].
this is currently a subtype of organism subdivision - which would exclude feathers
The head is the anterior-most division of the body [GO].
Organism subdivision that is the part of the body consisting of the cranial and pharyngeal regions.[AAO]
Organism subdivision which is the part of the body which consists of the cranial and pharygeal regions.[TAO]
Vertebrate evolution has been characterized by a fresh and vast array of cranial structures that collectively form the head.[well established][VHOG]
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.82
multi-tissue structure that is comprised of a secretory epithelial layer (mesothelium) and a connective tissue layer.
A multi-tissue structure that is comprised of a secretory epithelial layer and a connective tissue layer.[TAO]
a smooth membrane consisting of a thin layer of cells which excrete serous fluid. Serous membranes line and enclose several body cavities, known as serous cavities, where they secrete a lubricating fluid which reduces friction from muscle movement. Serosa is not to be confused with adventitia, a connective tissue layer which binds together structures rather than reducing friction between them. Each serous membrane is composed of a secretory epithelial layer and a connective tissue layer underneath. The epithelial layer, known as mesothelium, consists of a single layer of avascular flat nucleated cells (cuboidal epithelium) which produce the lubricating serous fluid. This fluid has a consistency similar to thin mucus. These cells are bound tightly to the underlying connective tissue. The connective tissue layer provides the blood vessels and nerves for the overlying secretory cells, and also serves as the binding layer which allows the whole serous membrane to adhere to organs and other structures.[WP]
in FMA, SM = mesothelium + connective tissue. It excludes the cavity. Serous sac = SM + cavity. Note that the SM is a subtype of wall in FMA.
Dense regular connective tissue that connects muscle to bone[VSAO].
Dense regular connective tissue that connects muscle to bone.[VSAO]
Phylogenetically, tendinous tissue first appears in the invertebrate chordate Branchiostoma as myosepta. This two-dimensional array of collagen fibers is highly organized, with fibers running along two primary axes. In hagfish the first linear tendons appear and the myosepta have developed specialized regions with unidirectional fiber orientation - a linear tendon within the flat sheet of myoseptum.[well established][VHOG]
in FMA, tendon is an organ component that with parts dense-irregular-connective-tissue of tendon and dense-irregular-connective-tissue of tendon sheath; we follow VSAO in making it a subtype of the former. In VSAO tendons connect muscle to bone; in WP the def states integument (e.g. auricular muscles) - but JB confirms this is not actually tendon but aponeurosis
DOI:10.1016/S1095-6433(02)00241-6 Summers AP, Koob TJ, The evolution of tendon - morphology and material properties. Comparative Biochemistry and Physiology-Part A: Molecular and Integrative Physiology (2002)
A biological tissue mass, most commonly a mass of nerve cell bodies.
TODO - check vert vs invert. Other species: Any of a number of aggregations of neurons, glial cells and their processes, surrounded by a glial cell and connective tissue sheath (plural: ganglia). // Subdivision of neural tree (organ) which primarily consists of cell bodies of neurons located outside the neuraxis (brain and spinal cord); together with a nucleus and its associated nerve, it constitutes a neural tree (organ). Examples: spinal ganglion, trigeminal ganglion, superior cervical ganglion, celiac ganglion, inferior hypogastric (pelvic) ganglion. // a cluster of nerve cells and associated glial cells (nuclear location) // Portion of tissue that contains cell bodies of neurons and is located outside the central nervous system.
A ganglion is a cluster of neurons. It is part of a nervous system. It may include glial cells. The neurons are arranged in a specific constellation: neuronal somata are concentrated at the surface, thus forming a cell cortex, and neurites are concentrated in the centre of the ganglion to form the neuropil. A ganglion is a distinct unit but several ganglia may be anterio-posteriorly joined by connectives or transversally by commissures
Portion of tissue that contains cell bodies of neurons and is located outside the central nervous system.[AAO]
Structures containing a collection of nerve cell bodies. (Source: BioGlossary, www.Biology-Text.com)[TAO]
Subdivision of nervous system which primarily consists of cell bodies of neurons located outside the neuraxis (brain and spinal cord. Examples: spinal ganglion, trigeminal ganglion, superior cervical ganglion, celiac ganglion, inferior hypogastric (pelvic) ganglion (adapted from Foundational Model of Anatomy)[NIFSTD:nlx_anat_100302].
Cranial sensory placodes are focused areas of the head ectoderm of vertebrates that contribute to the development of the cranial sense organs and their associated ganglia. Placodes have long been considered a key character of vertebrates, and their evolution is proposed to have been essential for the evolution of an active predatory lifestyle by early vertebrates.[well established][VHOG]
DOI:10.1016/j.ydbio.2005.02.021 Mazet F, Hutt JA, Milloz J, Millard J, Graham A, Shimeld SM, Molecular evidence from Ciona intestinalis for the evolutionary origin of vertebrate sensory placodes. Developmental Biology (2005)
An eye with one concave chamber. Note that 'simple' does not imply a reduced level of complexity or acuity.
A tubular structure that contains, conveys body fluid, such as blood or lymph.
Muscular duct that propels urine from the kidneys to the urinary bladder, or related organs.
Anatomical structure consisting of long narrow duct which carries urine from the kidney to the urinary bladder.[AAO]
The duct of amniotes that carries urine from a metanephric kidney to the urinary bladder. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-29, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]
The first embryonic hint of a metanephros is the formation of the metanephric duct that appears as a ureteric diverticulum arising at the base of preexisting mesonephric duct. The ureteric diverticulum grows dorsally into the posterior region of the nephric ridge. Here it enlarges and stimulates the growth of metanephric tubules that come to make up the metanephric kidney. The metanephros becomes the adult kidney of amniotes, and the metanephric duct is usually called the ureter.[well established][VHOG]
in humans, consists of adventitial, muscular and mucoa layers
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.543
the fibromuscular tubular canal through which urine is discharged from the bladder to the exterior via the external urinary meatus; in males, the urethra is joined by the ejaculatory ducts and serves as a passageway for semen during ejaculation, as well as a canal for urine during voiding; in females, the urethra is shorter and emerges above the vaginal opening
In human males, the urethra travels through the penis, and carries semen as well as urine. In females, the urethra is shorter and emerges above the vaginal opening.
pelvic part of UG sinus gives rise to prostatic and membranous parts of urethra
A tubular structure that transports secreted or excreted substances.
A tube shaped portion of tissue lined with epithelial cells that collects secretions and routes them to their destination[ZFA:0005171].
Most ducts, but not all, are exocrine gland ducts. Some ontologies classify structures such as the oviduct here.
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]
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.566
Organ component adjacent to an organ cavity and which consists of a maximal aggregate of organ component layers.
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 part of an organ that constitutes a distinct modular sub-unit. In some cases, the organ may also contain other sub-units of identical or similar types, in other cases this may be a distinct entity.
FMA distinguishes segment from zone by whether the fiat boundaries are fixed/anchored (segments) or floating (zone). It's not completely clear how to apply this distinction
Organ region with one or more anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyeball.
Organ region with one or more fixed or anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyebal.
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
Anatomical structure that is part of the respiratory system. In mammals consists of upper and lower tracts
The stage of development at which the animal is fully formed, including immaturity and maturity. Includes both sexually immature stage, and adult stage.
A life cycle stage that starts with fertilization and ends with the fully formed embryo.
embryo stage
胚胎期
MA:0000434 has subclasses upper and lower, so it corresponds to a segment of the tract, rather than the tract as a whole
proximo-distal subdivision of respiratory tract
Any part or collection of parts of the central or peripheral nervous system. Parts may span both CNS and PNS.
Anatomical cluster consisting of the skeletal elements and articular elements that are part of an individual subdivision of the organism.
The surface (external) layer of ectoderm which begins to proliferate shortly after separation from the neuroectoderm.
merge with non-neural. In vertebrates, the ectoderm has three parts: external ectoderm (also known as surface ectoderm), the neurectoderm (neural crest, and neural tube)
(or external ectoderm) forms the following structures: Skin Epithelium of the mouth and nasal cavity saliavary glands, and glands of mouth and nasal cavity Enamel - as a side note dentin and dental pulp are formed from ectomesenchyme which is derived from ectoderm Epithelium of pineal and pituitary glands Lens and cornea of the eye Apical ectodermal ridge inducing development of the limb buds of the embryo. Sensory receptors in epidermis
An anatomical structure that develops from the endoderm and the mesoderm.
Grouping term for query purposes. Notes that the developmental relationships are being refined such that most structures should develop in whole from at most one layer, but may have contributions from multiple
mixed endoderm/mesoderm-derived structure
An anatomical structure that develops from the ectoderm, mesoderm and endoderm.
mixed ectoderm/mesoderm/endoderm-derived structure
The second stage of the kidney. It serves as the main excretory organ of aquatic vertebrates and as a temporary embryonic kidney in higher vertebrates. It is composed of the mesonephric duct (also called the Wolffian duct), mesonephric tubules, and associated capillary tufts. A single tubule and its associated capillary tuft is called a mesonephric excretory unit; these units are similar in structure and function to nephrons of the adult kidney. The mesonephros is derived from intermediate mesoderm in the vertebrate embryo.
A kidney formed of nephric tubules arising in the middle region of the nephric ridge; a transient embryonic stage that replaces the pronephros, but is itself replaced by the adult metanephros [in mammals; in fishes and amphibians it is the adult kidney]. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Kardong_KV, Vertebrates:_Comparative_Anatomy, p.745][VHOG]
Organ that is the definitive adult kidney. It replaces the earlier pronephros, which degenerates as the mesonephros becomes functional in feeding stage tadpoles.[AAO]
As the pronephros regresses, the archinephric duct induces the sequential differentiation of tubules in the more caudal parts of the nephric ridge. (...) Tubules that differentiate in the middle part of the nephric ridge form a kidney called the mesonephros. This kidney functions in the embryos and larvae of all vertebrates. (...) In all vertebrate embryos, the kidney begins with the differentiation of a few renal tubules from the anterior end of the nephric ridge overlying the pericardial cavity. (...) This early-developing embryonic kidney is called the pronephros.[well established][VHOG]
In mammals, the mesonephros is the second of the three embryonic kidneys to be established and exists only transiently. In fish and amphibians, the mesonephros will form the mature kidney
By contrast to the pronephros, the histological features of the mammalian mesonephros, with its primitive glomeruli, suggest that it probably functions as a primitive kidney, and is involved in the production of much of the amniotic fluid. Within the two mesonephroi, one located on either side of the dorsal mesentery of the hindgut, a substantial number (in the region of about 40 or more) of cranio-caudally segmented mesonephric tubules are formed. It has, however, been suggested that only the most rostrally located 4-6 pairs of mesonephric tubules drain into the mesonephric portion of the nephric duct. This is now seen to extend along the length of the mesonephroi, being located towards their lateral sides. The mesonephros is also retained over a considerably longer period than the pronephros, but gradually undergoes regression in a cranio-caudal direction. While the rostral part displays clear evidence of regression its more caudal part appears to display evidence of functional activity. Within the medial part of the mesonephros, vesicles are formed, although no glomeruli are formed there in this species. It is, however, difficult to believe that the relatively enormous mesonephroi do not have an excretory role in the mouse, only serving as a base for gonadal differentiation. In the human embryo, the medial part of the mesonephric tubules enlarges, become invaginated by capillaries, and form glomeruli. These then take on an excretory role. In the mouse, the mesonephric ducts appear to be patent throughout their length[GUDMAP, modified]
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.639
In mammals, the metanephros is the excretory organ of the fetus, which develops into the mature kidney and is formed from the rear portion of the nephrogenic cord. The metanephros is an endocrine and metabolic organ that filters the blood and excretes the end products of body metabolism in the form of urine[GO]
A kidney formed of nephric tubules arising in the posterior region of the nephric ridge and drained by a ureter; replaces the embryonic pronephros and mesonephros [in mammals]. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Kardong_KV, Vertebrates:_Comparative_Anatomy, p.745][VHOG]
The ureteric diverticulum grows dorsally into the posterior region of the nephric ridge. Here it enlarges and stimulates the growth of metanephric tubules that come to make up the metanephric kidney. The metanephros becomes the adult kidney of amniotes.[well established][VHOG]
During the fifth week of gestation, the mesonephric duct develops an outpouching, the ureteric bud, near its attachment to the cloaca. This bud, also called the metanephrogenic diverticulum, grows posteriorly and towards the head of the embryo. The elongated stalk of the ureteric bud, the metanephric duct, later forms the ureter. As the cranial end of the bud extends into the intermediate mesoderm, it undergoes a series of branchings to form the collecting duct system of the kidney. It also forms the major and minor calyces and the renal pelvis
A mesonephric tubule is an epithelial tube that is part of the mesonephros[GO]. Genital ridge that is next to the mesonephros[WP].
Any of the renal tubules composing the mesonephros. In mammals they function as excretory structures during the early embryonic development but are later incorporated into the reproductive system. [TFD][VHOG]
As the pronephros regresses, the archinephric duct induces the sequential differentiation of tubules in the more caudal parts of the nephric ridge. (...) Tubules that differentiate in the middle part of the nephric ridge form a kidney called the mesonephros. This kidney functions in the embryos and larvae of all vertebrates.[well established][VHOG]
An epithelial swelling on the Wolffian duct that elongates to invade the adjacent metanephric mesenchyme[MP]
Outgrowth of the mesonephric duct that penetrates the metanephric mesoderm and forms the ureter, renal pelvis, major and minor calyces and collecting ducts. [Embryology, See_Dudek_RW_and_Fix_JD, Third_Edition_(2004)_Philadelphia:_Lippincott_William_and_Wilkins, p.137][VHOG]
Outgrowth of the mesonephric duct that penetrates the metanephric mesoderm and forms the ureter, renal pelvis, major and minor calyces and collecting ducts[VHOG:0000541].
stage succeeding embryo, including mature structure
In birds, the postnatal stage begins when the beak penetrates the shell (i.e., external pipping) (Brown et al. 1997)
Nonparenchymatous organ that primarily consists of dense connective tissue organized into a sheet which interconnects two or more organs, separates two or more body spaces from one another, or surrounds an organ or body part. Examples: interosseous membrane of forearm, obturator membrane, tympanic membrane, fibrous pericardium, fascia lata, dura mater. [FMA]
portion of neural crest that develops from the dorsal neural tube. It overlaps the vagal neural crest and migrates to populate the pharyngeal arches 3, 4 and 6 (producing structures in the head) and to the heart, forming connective tissue that separates the great vessels of the heart. [Wikipedia]
A subpopulation of the cephalic neural crest that emerges from the otic level to the anterior limit of somite 4. It migrates to the heart and is essential for the septation of the outflow track[doi:10.1242/dev.091751].
The lung vasculature is composed of the tubule structures that carry blood or lymph in the lungs[GO].
An entire span of an organism's life, commencing with the zygote stage and ending in the death of the organism.
A spatiotemporal region encompassing some part of the life cycle of an organism.
this class represents a proper part of the life cycle of an organism. The class 'life cycle' should not be placed here
the WBls class 'all stages' belongs here as it is the superclass of other WBls stages
we map the ZFS unknown stage here as it is logically equivalent to saying *some* life cycle stage
A stage at which the organism is a single cell produced by means of sexual reproduction.
As in all metazoans, eumetazoan development begins with a fertilized egg, or zygote.[well established][VHOG]
ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.107
The first few specialized divisions of an activated animal egg; Stage consisting of division of cells in the early embryo. The zygotes of many species undergo rapid cell cycles with no significant growth, producing a cluster of cells the same size as the original zygote. The different cells derived from cleavage are called blastomeres and form a compact mass called the morula. Cleavage ends with the formation of the blastula.
An early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence.
consider adding a preceding stage 'morula stage' as part of cleavage
A stage defined by complex and coordinated series of cellular movements that occurs at the end of cleavage during embryonic development of most animals. The details of gastrulation vary from species to species, but usually result in the formation of the three primary germ layers, ectoderm, mesoderm and endoderm.
Staged defined by the formation of a tube from the flat layer of ectodermal cells known as the neural plate. This will give rise to the central nervous system.
A stage at which the ectoderm, endoderm, and mesoderm develop into the internal organs of the organism.
The stage of being a sexually immature adult animal[XAO:1000010].
In mammals this would include infant (nourishment from lactation) and juvenile (prepubertal no longer dependent on mother)
The stage of being a sexually mature adult animal.
the connective tissue located between the respiratory (airway and alveolar) epithelium, the capillary endothelium and pleural mesothelium; it contains basement membrane composed of collagen, elastin, proteoglycans, and fibronectin
it functions in the mechanical behavior of the lung, and forms a barrier to regulate the flow of plasma constituents from the capillaries to the airway and alveolar spaces
A pseudostratified epithelium, containing basal cells, stem cells of the airway, submucosal glands and cartilage rings, is limited to the trachea and large lobar airways in the mouse (Morrisey and Hogan, 2010). This more complex epithelium extends to terminal bronchioles in the human[doi:10.1242/dev.115469]
A tube in the respiratory system. Examples: bronchus, bronchiole, trachea.
in GO lung development is part of respiratory tube development. This can lead to inconsistencies with other ontologies, e.g. VT. The GO structure may be better represented by a tree of tubes (see the FMA class)
Structure derived from foregut that becomes a lung[GO].
A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses.
A spatially aggregated collection of nerve cell bodies in the CNS, consisting of one or more subpopulations that share cell type, chemical phenotype, and connections, and including nearby cells that share the same cell type, chemical phenotype, and connections. (CUMBO)
Anatomical structure consisting of a discrete aggregate of neuronal soma[GO][GO_REF:0000021].
Proposed CUMBO def from MM: A subcortical part of the nervous system consisting of a relatively compact group of cells that is distinguishable histologically that share a commonality of cytoarchitecture, chemoarchitecturel and connectivity. (comments: I put in 'subcortical' because I don't think we consider either the cerebellar cortex or cerebral cortex to be nuclei. Some people distinguish between a nucleus and a laminar structure (see Wikipedia definition). However, there are structures identified as nuclei that are laminar, e.g., lateral geniculate nucleus, although they are not laminated in all species. Also, I put in 'relatively compact' and 'distiguishable by histology' because we have groups of cells, e.g., cholinergic cell groups, doparminergic cell groups that are related on the 3 criteria but which we don't tend to consider nuclei because they don't occupy an easily defined territory. But all is open to debate.
Nucleus that receives projections from or contains neurons that send projections through one of the cranial nerves
the group of motor neurons residing in the pons that innervate the muscles of facial expression
FMA has 3 subclasses - left, right and motor nucleus of facial nerve, but no defs. It's not clear how facial nucleus is distinct from facial motor nucleus.
A thin sheet or layer of pliable tissue, serving as a covering or envelope of a part, as the lining of a cavity, as a partition or septum, or to connect two structures.
The terminal part of the large intestine, continuous proximally with the rectum and distally terminates with the anus.
requires alignment with EHDAA2 and complete developmental relationships
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.
Anatomical conduit that connects two adjacent body spaces (or a body space with the space surrounding the organism)[FMA,modified].
in FMA, this is an anatomical conduit *space*, rather than anatomical conduit
Common chamber into which the intestines and excretory system opens. Arises during development in all vertebrates, but in many it becomes subdivided, lost or incorporated into other structures
adding df link to embryonic cloaca leads to a cycle in uberon-simple, as cloaca is a suberclass of embryonic cloaca
A common passage for fecal, urinary, and reproductive discharge in most lower vertebrates as well as the terminal end of the hindgut before division into rectum, bladder, and genital primordia in mammalian embryos. [TFD][VHOG]
Anatomical structure which is the common receptacle for the alimentary canal, Wolffian ducts, oviducts, and the bladder.[AAO]
A cloaca is apparently a primitive vertebrate feature because it occurs in most primitive gnathostomes and persists in the embryos of almost all vertebrates.[well established][VHOG]
Human beings only have an embryonic cloaca, which is split up into separate tracts during the development of the urinary and reproductive organs
hindgut endoderm and proctodeal ectoderm.
most adult placentals have no trace of a cloaca. However, the tenrecs and golden moles, small placental mammals native to Africa, retain a cloaca as adults.
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.572
endoderm-lined chamber that develops as pouch-like dilation of the caudal end of the hindgut and receives the allantois ventrally and two mesonephric ducts laterally; caudally it ends blindly at the cloacal membrane formed by the union of proctodeal (anal pit) ectoderm and cloacal endoderm, with no intervening mesoderm[MP].
this class represents the embryonic form of the cloaca, as found in both mammals and non-mammals.
the ventral part of the cloaca remaining after septation of the rectum, which further develops into part of the bladder, part of the prostatic part of the male urethra and the urethra and vestibule in females
The ventral part of the cloaca after its separation from the rectum, giving rise to the lower part of the bladder in both sexes, to the prostatic portion of the male urethra, and to the urethra and vestibule in the female. [TFD][VHOG]
In mammals the lowly monotremes still have a cloaca. Higher types have done away with this structure and have a separate anal outlet for the rectum. The monotreme cloaca shows the initiation of this subdivision. The cloaca has such includes only the distal part, roughly comparable to the proctodeum. The more proximal part is divided into (1) a large dorsal passage into which the intestine opens, the coprodeum, and (2) a ventral portion, the urodeum with which the bladder connects. (...) the development of the placental mammals recapitulates in many respects the phylogenetic story. In the sexually indifferent stage of placental mammal there is a cloaca. While the indifferent stage still persists, a septum develops, and extends out to the closing membrane. This divides the cloaca into two chambers: a coprodeum continuous with the gut above, and a urodeum or urogenital sinus below.[well established][VHOG]
the term 'urogenital sinus' may refer to the primitive urogenital sinus present as a transient developmental structure in most mammals or it may refer to a condition in which an unseptated cloaca persists in animals longer than normal
ISBN:978-0721676678 Romer AS, Vertebrate body (1970)p.388-89 and Figure 300
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
the mouth contains structures such as jaw skeleton that may not strictly be considered tract parts
DOI:10.1038/nature07309 Hejnol A, Martindale MQ, Acoel development indicates the independent evolution of the bilaterian mouth and anus. Nature (2008)
The orifice that connects the mouth to the exterior of the body.
(...) mouth development is very similar in protostomes and 'basal' deuterostomes, whereas the chordate mouth seems to develop at a new position. Recent data for echinoderms and hemichordates further suggest that this change in mouth position may result from change in the influence of a conserved ectodermal patterning system on mouth development. It has been suggested that the mouths of vertebrates and urochordates may constitute a 'new' mouth.[well established][VHOG]
DOI:10.1016/j.semcdb.2007.06.002 Christiaen L, Jaszczyszyn Y, Kerfant M, Kanob S, Thermes V, Joly JS, Evolutionary modification of mouth position in deuterostomes. Seminars in Cell and Developmental Biology (2007)
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]
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.32
A section dividing a colon along a proximal-distal axis.
The pair of anatomical structures comprised of a left lung and right lung.
pair of lungs
肺对
Organ that functions in gaseous exchange between an organism and its environment. In plants, microorganisms, and many small animals, air or water makes direct contact with the organism's cells or tissue fluids, and the processes of diffusion supply the organism with dioxygen (O2) and remove carbon dioxide (CO2). In larger animals the efficiency of gaseous exchange is improved by specialized respiratory organs, such as lungs and gills, which are ventilated by breathing mechanisms.
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
A fluid that is composed of blood plasma and erythrocytes.
This class excludes blood analogues, such as the insect analog of blood. See UBERON:0000179 haemolymphatic fluid.
A complex mixture of cells suspended in a liquid matrix that delivers nutrients to cells and removes wastes. (Source: BioGlossary, www.Biology-Text.com)[TAO]
Highly specialized circulating tissue consisting of several types of cells suspended in a fluid medium known as plasma.[AAO]
relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO]
Recent findings strongly suggest that the molecular pathways involved in the development and function of blood cells are highly conserved among vertebrates and various invertebrates phyla. (...) There is now good reason to believe that, in vertebrates and invertebrates alike, blood cell lineages diverge from a common type of progenitor cell, the hemocytoblast.[well established][VHOG]
DOI:10.1146/annurev.cellbio.22.010605.093317 Hartenstein V, Blood cells and blood cell development in the animal kingdom. Annual review of cell and developmental biology (2006)
Circulating fluid that is part of the hemolymphoid system. Blood, lymph, interstitial fluid or its analogs.
A layer of membrane around a tendon. It has 2 layers: synovial sheath + fibrous tendon sheath
TODO - add layer relations. 'tendon sheath' GAT in FMA.
Organism at the blastula stage - an early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence.
TODO - check relationship with epiblast. Note in FMA this is not a subclass of embryo, but in uberon embryo is the whole organism from zygote onwards and thus includes the blastula
A substance produced by the cervix and endocervical glands[BTO]. Thick acidic mucus that blocks the cervical os after mestruation[WP]. This 'infertile' mucus blocks spermatozoa from entering the uterus.
Mucosa that is part of a colon. The mucosa of the colon is lined by a simple columnar epithelium with a thin brush border and numerous goblet cells.
The branched tubular glands found in the mucosa of the fundus and body of the stomach which contain parietal cells that secrete hydrochloric acid and zymogenic cells that produce pepsin.
The wall of the digestive tract. This encompasses all parts of the digestive tract with the exception of the lumen (cavity).
We model the digestive tract as consisting of two parts: the wall and the lumen.
A gland that is part of the intestinal mucosa. Examples include the intestinal crypts, duodenal gland[cjm].
Note that some sources treat 'intestinal gland' as synonymous with crypts
A lining of mostly endodermal origin, covered in epithelium, which is involved in absorption and secretion. They line various body cavities that are exposed to the external environment and internal organs. It is at several places continuous with skin: at the nostrils, the lips, the ears, the genital area, and the anus. The sticky, thick fluid secreted by the mucous membranes and gland is termed mucus. The term mucous membrane refers to where they are found in the body and not every mucous membrane secretes mucus[WP]
FMA has mucosa vs region of mucosa; these are subtypes of Mucosa: Mucosa of gallbladder, tongue, .... The following are subtypes of Region of mucosa: Mucosa of zone of stomach, trachea, bronchus, dorsum of tongue.... Depends on whether the covered area is an organ or organ component. Uberon does not regard organ vs organ component as crucial distinction and thus collapses these into a single class deliberately
A mucosa that is part of a pharynx [Automatically generated definition].
The sensory nerve subdivision of the trigeminal nerve that transmits sensory information from the palate, upper teeth and gingiva, the skin between the palpebral fissure and the mouth, and from the nasal cavity and maxillary sinuses.
Medial ramus (sensory) of the trigeminal nerve.[AAO]
relationship loss: part_of trunk maxillary-mandibularis (AAO:0010669)[AAO]
maxillary division of fifth cranial nerve
maxillary division of trigeminal nerve (Vb; V2)
A mucosa that is part of a respiratory airway.
The subdivision of the musculoskeletal system that consists of all the muscles of the body[VSAO, modified].
consider whether this should be restricted to skeletal musculature. See https://github.com/obophenotype/uberon/issues/77
Anatomical system that consists of the muscles of the body.[VSAO]
we place the MA term musculature here, rather than under uberon:musculature, as this seems more appropriate given the structure of MA
The core of the crystalline lens, surrounded by the cortex.
An epithelium that is part of a colon [Automatically generated definition].
Intestinal epithelium which lines the lumen of the posterior intestine.[TAO]
The nasal vestibule is the most anterior part of the nasal cavity. It's enclosed by the cartilages of nose and lined by the same epithelium of the skin. The other part of the nasal cavity, which is lined by the respiratory epithelium, is called nasal cavity proper. [WP,unvetted].
A gland in which the principal secretory cells are serous secreting cells.
glands that secrete watery albuminous material that often contains enzymes[MP:0008052].
A mucosa that is part of a bronchus [Automatically generated definition].
A gland in which the principal secretory cells are mucus secreting cells.
In frogs and salamanders, this is the smaller of the two types of gland, the other being the granular (poison) gland. In these species the mucous gland is a cluster of cells that release secretion into a common duct[Kardong]
An anatomical wall that is part of an artery [Automatically generated definition].
A portion of organism substance that is produced by exocrine glands.
BTO has two distunct classes, with exocrine glandular secretion a subtype of secretion - however, all examples in BTO directly under secretion appear to be exocrine gland secretions
The region of the opening of the uterine cervix into the uterine cavity.
An anatomical wall that is part of a uterus [Automatically generated definition].
Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body.
this relationship may be too strong and may be weakened in future
Non-material anatomical entity of three dimensions, that is generated by morphogenetic or other physiologic processes; is surrounded by one or more anatomical structures; contains one or more organism substances or anatomical structures.
Multicellular, connected anatomical structure that has multiple organs as parts and whose parts work together to achieve some shared function.
Anatomical structure that is an individual member of a species and consists of more than one cell.
TODO - split body and mc organism? body continues after death stage
The organs and associated structures associated with bearing offspring in a female animal.
By far, sexual reproduction is the more common pattern among living vertebrate forms and its widespread occurrence suggests that it is the plesiomorphic, or primitive, reproductive mode among the vertebrates.[well established][VHOG]
ISBN:978-0792383369 Lombardi J, Comparative vertebrate reproduction (1998) p.43
Anatomical structure which is a subdivision of a whole organism, consisting of components of multiple anatomical systems, largely surrounded by a contiguous region of integument.
Reflects CARO2. todo - check the inclusion of FMA 'cardinal body part here', and check child terms for consistency
Anatomical structure that consists of cell parts and cell substances and together does not constitute a cell or a tissue.
Anatomical group that has its parts adjacent to one another.
Will be obsoleted in CARO v2 [https://github.com/obophenotype/caro/issues/3]
A multicellular anatomical structure that is associated with an embryo and derived from the zygote from which it develops, but which does not contribute to the embryo proper or to structures that are part of the same organism after embryogenesis.
see also conceptus extraembryonic component in EHDAA2.
Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation.
changed label and definition to reflect CARO2
Anatomical structure that has as its parts two or more portions of tissue of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona-fide boundaries from other distinct structural units of different types.
Portion of tissue, that consists of one or more layers of epithelial cells connected to each other by cell junctions and which is underlain by a basal lamina. Examples: simple squamous epithelium, glandular cuboidal epithelium, transitional epithelium, myoepithelium[CARO].
The two basic types of metazoan tissue are epithelial and connective. The simplest metazoans, and developmental stages of many primitive invertebrates, consist solely of these two layers. Thus, epithelial and connective tissues may be the primary (original) tissues of metazoans, and both are important in the functional organization of animals.[well established][VHOG]
ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.59
Unilaminar epithelium that consists of a single layer of cuboidal cells.
needs to be synchronized with CL - there is no distinct cuboidal cell in CL
Unilaminar epithelium, which consists of a single layer of columnar cells. Examples: ciliated columnar epithelium, gastric epithelium, microvillus columnar epithelium.[FMA]
Epithelium which consists of more than one layer of epithelial cells that may or may not be in contact with a basement membrane. Examples: keratinized stratified squamous epithelium, ciliated stratified columnar epithelium.[FMA]
Epithelium that consists of more than one layer of epithelial cells.[CARO]
Unilaminar epithelium which consists of a single layer of squamous cells. Examples: pulmonary alveolar epithelium, endothelium.[FMA]
Unilaminar epithelium that consists of a single layer of squamous cells.[CARO]
Epithelium that consists of epithelial cells not arranged in one ore more layers.
Compound organ that contains one or more macroscopic anatomical spaces.
this class was introduced for consistency with CARO, however, it has yet to be used in this or other ontologies. It may be retired in the future
Epithelium which consists of a single layer of epithelial cells. Examples: endothelium, mesothelium, glandular squamous epithelium.[FMA]
consider adding disjointness axiom between unilaminar and multilaminar - but note that this will render EHDAA2:0003244 (chorionic trophoblast) unsatisfiable
Epithelium that consists of a single layer of epithelial cells.[CARO]
Mucus is a bodily fluid consisting of a slippery secretion of the lining of the mucous membranes in the body. It is a viscous colloid containing antiseptic enzymes (such as lysozyme) and immunoglobulins. Mucus is produced by goblet cells in the mucous membranes that cover the surfaces of the membranes. It is made up of mucins and inorganic salts suspended in water.
Subdivision of trunk that lies between the head and the abdomen.
note that we use the slightly verbose term 'thoracic segment of trunk' to avoid confusuon with insect thorax. todo - taxonomic constraints. Also, in FMA 'thorax' is a synonym for chest
The subdivision of the vertebrate body between the thorax and pelvis. The ventral part of the abdomen contains the abdominal cavity and visceral organs. The dorsal part includes the abdominal section of the vertebral column.
Vertebrate specific. In arthropods 'abdomen' is the most distal section of the body which lies behind the thorax or cephalothorax. If need be we can introduce some grouping class
Anatomical entity that comprises the organism in the early stages of growth and differentiation that are characterized by cleavage, the laying down of fundamental tissues, and the formation of primitive organs and organ systems. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant.
Obsoleted in ZFA. Note that embryo is not classified as an embryonic structure - an embryonic structure is only the parts of an embryo
A layer of cells produced during the process of gastrulation during the early development of the animal embryo, which is distinct from other such layers of cells, as an early step of cell differentiation. The three types of germ layers are the endoderm, ectoderm, and mesoderm.
The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]
Classically the germ layers are ectoderm, mesoderm and endoderm. Alternatively: primary = ectoderm, endoderm; secondary=mesoderm; tertiary=dorsal mesoderm, NC[https://github.com/obophenotype/uberon/wiki/The-neural-crest]
ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722
Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue.
Primary germ layer that is the outer of the embryonic germ layers and gives rise to epidermis and neural tissue.[AAO]
Primary germ layer that lies remote from the surface of the embryo and gives rise to internal tissues such as gut.
The middle germ layer of the embryo, between the endoderm and ectoderm.
Primary germ layer that is the middle of the embryonic germ layers.[AAO]
sponges do not seem to have a mesoderm and accordingly Amphimedon lacks transcription factors involved in mesoderm development (Fkh, Gsc, Twist, Snail)[http://www.nature.com/nature/journal/v466/n7307/full/nature09201.html]. Mesoderm may not be homologous across verteberates
Anterior part of the embryonic digestive tract that develops into a mouth. The stomodeum includes as parts an invagination of the ectoderm and the stomodeal cavity.
consider indicating location. e.g. anterior. Note some AOs place this as part of oral opening, but it's not clear when this structure comes into existence
Anterior part of the embryonic alimentary canal formed as an invagination of the ectoderm; the future mouth.[TAO]
the primordial mouth region of the developing head, initially a midline ectodermal depression between the forebrain bulge (cranially) and the heart bulge (caudally) and between the maxillary and mandibular components of the first pharyngeal arch; the stomodeum is separated from the anterior end of the foregut by the buccopharyngeal membrane; the mouth is developed partly from the stomodeum, and partly from the floor of the anterior portion of the foregut; the lips, teeth, and gums are formed from the walls of the stomodeum, but the tongue is developed in the floor of the pharynx
This class groups together disparate structures as all being the anterior part of the early metazoan digestive tract and precursor of the mouth. However, the developmental processes vary, so this class may be split in future. E.g. in mammals it is a rostral depression surrounded by prominences. Outgrowth of the prominences produces a stomodeal cavity.
Inward fold on the surface of the embryonic ectoderm that develops into an ectodermal terminal part of the digestive tract.
removed WBbt:0006795 'proctodeum' - junction between the alimentary and genital tracts in the male.
An inward fold on the surface of the embryonic ectoderm that develops into part of the anal passage.[TAO]
Inward fold on the surface of the embryonic ectoderm that develops into part of the anal passage.[AAO]
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
stomach
DOI:10.1046/j.1525-142x.2000.00076.x Smith DM, Grasty RC, Theodosiou NA, Tabin CJ, Nascone-Yoder NM, Evolutionary relationships between the amphibian, avian, and mammalian stomachs. Evolution and development (2000)
The main trunk of the systemic arterial system that carries blood from the heart to all the organs and other structures of the body, bringing oxygenated blood to all parts of the body in the systemic circulation
This class is currently a mixed bag, encompassing (1) the entirety of the mammalian aorta together with (2) the developmental and phylogenetic homologs of its segments: the ventral aorta and dorsal aortae.
The main artery of the circulatory system which carries oxygenated blood from the heart to all the arteries of the body except those of the lungs.[AAO]
When vertebrates first appeared, they must have possessed a ventral and dorsal aorta with aortic arches between them.[well established][VHOG]
All amniotes have a broadly similar arrangement to that of humans, albeit with a number of individual variations. In fish, however, there are two separate vessels referred to as aortas. The ventral aorta carries de-oxygenated blood from the heart to the gills; part of this vessel forms the ascending aorta in tetrapods (the remainder forms the pulmonary artery). A second, dorsal aorta carries oxygenated blood from the gills to the rest of the body, and is homologous with the descending aorta of tetrapods. The two aortas are connected by a number of vessels, one passing through each of the gills. Amphibians also retain the fifth connecting vessel, so that the aorta has two parallel arches
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620
A myogenic muscular circulatory organ found in the vertebrate cardiovascular system composed of chambers of cardiac muscle. It is the primary circulatory organ.
Blood pumping organ composed of four chambers: sinus venosus, atrium, cardiac ventricle and bulbus arteriosus.[TAO]
Part of the circulatory system responsible for pumping blood; composed of three chambers--two atria and one ventricle.[AAO]
relationship type change: differentiates_from lateral plate mesoderm (AAO:0010574) CHANGED TO: develops_from lateral plate mesoderm (UBERON:0003081)[AAO]
As noted, the hearts of birds and mammals have four chambers that arises from the two chambers (atrium and ventricle) of the fish heart.[well established][VHOG]
Taxon notes:" the ascidian tube-like heart lacks chambers....The ascidian heart is formed after metamorphosis as a simple tube-like structure with a single-layered myoepithelium that is continuous with a single-layered pericar- dial wall. It lacks chambers and endocardium.... The innovation of the chambered heart was a key event in vertebrate evolution, because the chambered heart generates one-way blood flow with high pressure, a critical requirement for the efficient blood supply of large-body vertebrates... all extant vertebrates have hearts with two or more chambers (Moorman and Christoffels 2003)" https://doi.org/10.1101/gad.1485706
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.481
Anatomical system that consists of the glands and parts of glands that produce endocrine secretions and help to integrate and control bodily metabolic activity.
Anatomical system containing glands which regulates bodily functions though the secretion of hormones.[AAO]
Multicellular organisms have complex endocrine systems, allowing responses to environmental stimuli, regulation of development, reproduction, and homeostasis. Nuclear receptors (NRs), a metazoan-specific family of ligand-activated transcription factors, play central roles in endocrine responses, as intermediates between signaling molecules and target genes. The NR family includes ligand-bound and orphan receptors, that is, receptors with no known ligand or for which there is no ligand Pocket. Understanding NR evolution has been further improved by comparison of several completed genomes, particularly those of deuterostomes and ecdysozoans. In contrast, evolution of NR ligands is still much debated. One hypothesis proposes that several independent gains and losses of ligand-binding ability in NRs occurred in protostomes and deuterostomes. A second hypothesis, pertaining to the NR3 subfamily (vertebrate steroid hormone receptors and estrogen related receptor), proposes that before the divergence of protostomes and deuterostomes, there was an ancestral steroid receptor (AncSR) that was ligand-activated and that orphan receptors secondarily lost the ability to bind a ligand. (...) Our analysis reveals that steroidogenesis has been independently elaborated in the 3 main bilaterian lineages (...).[well established][VHOG]
DOI:10.1073/pnas.0812138106 Markov GV, Tavares R, Dauphin-Villemant C, Demeneix BA, Baker ME, Laudet V, Independent elaboration of steroid hormone signaling pathways in metazoans. PNAS (2009)
The brain is the center of the nervous system in all vertebrate, and most invertebrate, animals. Some primitive animals such as jellyfish and starfish have a decentralized nervous system without a brain, while sponges lack any nervous system at all. In vertebrates, the brain is located in the head, protected by the skull and close to the primary sensory apparatus of vision, hearing, balance, taste, and smell[WP].
requires review for applicability to invertebrate structures, e.g. synganglion
Cavitated compound organ which is comprised of gray and white matter and surrounds the cerebral ventricular system.[TAO]
Part of the central nervous system situated within the cranium and composed of both nerve cell bodies and nerve fibers.[AAO]
The part of the central nervous system contained within the cranium, comprising the forebrain, midbrain, hindbrain, and metencephalon. It is derived from the anterior part of the embryonic neural tube (or the encephalon). Does not include retina. (CUMBO)
(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2).[well established][VHOG]
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.165
the transparent anterior portion of the fibrous coat of the eye that serves as the chief refractory structure
Compared to terrestial animals, the cornea of zebrafish is relatively flat. It consists of nonpigmented, stratified squamous nonkeratinizing epithelial cells, attached to a thick basement membrane that is considered to be analogous to the Bowman's membrane in mammals. In fish, and aquatic vertebrates in general, the cornea plays no role in focusing light, since it has virtually the same refractive index as water
Transparent part of camera-type eye that helps to refract light to be focused on the retina.
This class excludes compound eye corneal lenses.
The lens is avascular and nourished by diffusion from the aqueous and vitreous
The retina is the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates.
The portion of the eye developing from the optic primordium and including the neural retina and the retinal pigment layer. Kimmel et al, 1995.[TAO]
Currently this class encompasses only verteberate AOs but could in theory also include cephalopod - we may want to make a more specific class for vertebrate retina. note that this class excludes ommatidial retinas, as the retina must be part of an eyeball. Use the parent class photoreceptor array / light-sensitive tissue for arthropods
This class encompasses a variety of light-detecting structures from different phyla with no implication of homology, from the compound insect eye to the vertebrate camera-type eye (distinct classes are provided for each)
Note that whilst this is classified as an organ, it is in fact more of a unit composed of different structures: in Drosophila, it includes the interommatidial bristle as a part; we consider here the vertebrate eye to include the eyeball/eye proper as a part, with the eye having as parts (when present): eyelids, conjuctiva,
An organism subdivision that extends from the head to the pectoral girdle, encompassing the cervical vertebral column.
true necks are considered to be present when the pectoral girdle is separate from the skull - Tiktaalik is the earliest known fish to have a true neck.
Anatomical cluster that consists of two or more adjacent skeletal structures, which may be interconnected by various types of tissue[VSAO].
Anatomical cluster that consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[VSAO]
Anatomical cluster which consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[TAO]
The part of the central nervous system lying between the medulla oblongata and the midbrain, ventral to the cerebellum.
The pons is not present in zebrafish. In this ontology we currently have some structures which are applicable to zebrafish appearing as parts of the pons. Currently we only include the weaker dubious_for_taxon relationship ubtil this is resolved
The part of the central nervous system lying between the medulla oblongata and the midbrain, ventral to the cerebellum. [TFD][VHOG]
During the embryonic development of birds and mammals, neuroblasts migrate from the cerebellum into the ventral part of the rhombencephalon and differentiate into pontine and other nuclei, which relay information from between the cerebrum and cerebellum, and a conspicuous band of transverse fibers. This region is known as the pons. A pons does not differentiate in reptiles and anamniotes (...).[well established][VHOG]
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.474
Anatomical system that has as its parts the organs concerned with reproduction.
consider splitting genitalia from reproductive system
Anatomical system which consists of organs and tissues associated with sexual reproduction of the organism.[AAO]
Arguably, one of the most important aspects of urbilaterian organogenesis would have been gonadogenesis, since Urbilateria must have successfully generated gametes and developed a strategy for extrusion and fertilization, in order to be the ancestor of all living Bilateria.[well established][VHOG]
PMID:21672850 Extavour CGM, Gray anatomy: phylogenetic patterns of somatic gonad structures and reproductive strategies across Bilateria. Integrative and Comparative Biology (2007)
Reproductive organ that produces and releases eggs (ovary) or sperm (testis).
Anatomical structure which produces gametes as well as certain sex hormones controlled by the pituitary gonadotropins.[AAO]
The part of the reproductive system that produces and releases eggs (ovary) or sperm (testis).[TAO]
Examination of different vertebrate species shows that the adult gonad is remarkably similar in its morphology across different phylogenetic classes. Surprisingly, however, the cellular and molecular programs employed to create similar organs are not evolutionarily conserved.[uncertain][VHOG]
DOI:10.1146/annurev.cellbio.042308.13350 DeFalco T, Capel B, Gonad morphogenesis in vertebrates: divergent means to a convergent end. Annual review of cell and developmental biology (2009)
the gonad of a female organism which contains germ cells
Either of paired female reproductive organs involved in production of ova and female sex hormones.[AAO]
(...) while it is likely that Urbilateria lacked a complex somatic reproductive system, it is at present impossible to speculate on whether or not it possessed a true gonad, let alone any other somatic adaptations for reproduction (reference 1); Examination of different vertebrate species shows that the adult gonad is remarkably similar in its morphology across different phylogenetic classes. Surprisingly, however, the cellular and molecular programs employed to create similar organs are not evolutionarily conserved (reference 2).[uncertain][VHOG]
Ovaries of some kind are found in the female reproductive system of many animals that employ sexual reproduction, including invertebrates. However, they develop in a very different way in most invertebrates than they do in vertebrates, and are not truly homologous. Many of the features found in human ovaries are common to all vertebrates, including the presence of follicular cells, tunica albuginea, and so on. However, many species produce a far greater number of eggs during their lifetime than do humans, so that, in fish and amphibians, there may be hundreds, or even millions of fertile eggs present in the ovary at any given time. In these species, fresh eggs may be developing from the germinal epithelium throughout life. Corpora lutea are found only in mammals, and in some elasmobranch fish; in other species, the remnants of the follicle are quickly resorbed by the ovary. In birds, reptiles, and monotremes, the egg is relatively large, filling the follicle, and distorting the shape of the ovary at maturity. Amphibians and reptiles have no ovarian medulla; the central part of the ovary is a hollow, lymph-filled space. The ovary of teleosts is also often hollow, but in this case, the eggs are shed into the cavity, which opens into the oviduct. Although most normal female vertebrates have two ovaries, this is not the case in all species. In birds and platypuses, the right ovary never matures, so that only the left is functional. In some elasmobranchs, the reverse is true, with only the right ovary fully developing. In the primitive jawless fish, and some teleosts, there is only one ovary, formed by the fusion of the paired organs in the embryo
female organism reproductive system gonad
female organism reproductive system gonada
gonad of female organism reproductive system
gonad of reproductive system of female organism
gonada of female organism reproductive system
gonada of reproductive system of female organism
reproductive system of female organism gonad
reproductive system of female organism gonada
female gonad
雌性生殖腺
DOI:10.1093/icb/icm052 Extavour CGM, Gray anatomy: phylogenetic patterns of somatic gonad structures and reproductive strategies across the Bilateria. Integrative and Comparative Biology (2007), DOI:10.1146/annurev.cellbio.042308.13350 DeFalco T and Capel B, Gonad morphogenesis in vertebrates: divergent means to a convergent end. Annual review of cell and developmental biology (2009)
A tube or collection of tubes in an animal from the ovaries to the outside of the body.
sometimes oviduct is used interchangeably with follaopian tube. Here they are different - the oviduct connects the gonad to the outside in a variety of animals. The mammal-class fallopian tube is derived from the mullerian duct and connects the gonads/infubdibulum to the uterus
A passage through which ova leave the maternal body or pass to an organ communicating with the exterior of the body. [TFD][VHOG]
In all remaining vertebrates (i.e., coelacanths, lungfishes, amphibians, reptiles, birds, and mammals), the oviduct arises in ontogeny as a longitudinal, groovelike invagination of the coelomic epithelium on the lateral surface of the mesonephros.[well established][VHOG]
The only female vertebrates to lack oviducts are the jawless fishes. In these species, the single fused ovary releases eggs directly into the body cavity. The fish eventually extrudes the eggs through small genital pores towards the rear of the body[WP]
in birds divided into infundibulum, magnum, isthmus, uterus, and vagina
tubular parts of female reproductive system
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.687-688
the female muscular organ of gestation in which the developing embryo or fetus is nourished until birth
The hollow muscular organ in female mammals in which the blastocyst normally becomes embedded and in which the developing embryo and fetus is nourished. Its cavity opens into the vagina below and into a uterine tube on either side. [TFD][VHOG]
An infundibulum, uterine tube, uterus, and vagina also differentiate along the oviducts of eutherian mammals.[well established][VHOG]
Most animals that lay eggs, such as birds and reptiles, have an oviduct instead of a uterus. In monotremes, mammals which lay eggs and include the platypus, either the term uterus or oviduct is used to describe the same organ, but the egg does not develop a placenta within the mother and thus does not receive further nourishment after formation and fertilization. Marsupials have two uteruses, each of which connect to a lateral vagina and which both use a third, middle 'vagina' which functions as the birth canal. Marsupial embryos form a choriovitelline 'placenta' (which can be thought of as something between a monotreme egg and a 'true' placenta), in which the egg's yolk sac supplies a large part of the embryo's nutrition but also attaches to the uterine wall and takes nutrients from the mother's bloodstream.
Two uteruses usually form initially in a female fetus, and in placental mammals they may partially or completely fuse into a single uterus depending on the species. In many species with two uteruses, only one is functional. Humans and other higher primates such as chimpanzees, along with horses, usually have a single completely fused uterus, although in some individuals the uteruses may not have completely fused [Wikipedia:Uterus]
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.678
A fibromuscular tubular tract leading from the uterus to the exterior of the body in female placental mammals and marsupials, or to the cloaca in female birds, monotremes, and some reptiles[WP].
Organ with organ cavity which connects the cervical canal of uterus to the vestibule of vagina.[FMA]
The genital canal in the female, leading from the opening of the vulva to the cervix of the uterus. [TFD][VHOG]
The distal end of the oviducts differentiates as a vagina in Metatheria and Eutheria.[well established][VHOG]
'The distal end of the oviducts differentiates as a vagina in Metatheria and Eutheria.' Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective, Third Edition (2001) Orlando Fla.: Harcourt College Publishers, p.688
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.688
The outer epithelial layer of the skin that is superficial to the dermis.
A cellular, multilayered epithelium derived from the ectoderm. Zebrafish epidermis consists only of living cells unlike terrestrial vertebrates in which dead, keratinized cells are present. Le Guellec et al, 2004.[TAO]
The outer epithelial layer of the external integument of the body that is derived from the embryonic epiblast.[AAO]
relationship loss: subclass external integument structures (AAO:0000961)[AAO]
(...) outer epithelia in all metazoan animals are homologous. (...) The ancestor of all metazoans likely had an epidermis with a basal extracellular matrix (ECM), an apical extracellular glycocalyx, and one cilium with a striated rootlet per cell.[well established][VHOG]
Zebrafish epidermis consists only of living cells unlike terrestrial vertebrates in which dead, keratinized cells are present. In terrestrial vertebrates the epidermis often forms an outer keratinized or cornified layer, the stratum corneum. Interaction between the epideris and dermis gives rise to feathers (birds), hair and mammary glands (mammals), teeth and scales (placoid: chondrichthyans; cosmoids, ganoid, cycloid in bony fishes).
ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.71-72
Functional system which consists of structures involved in respiration.
The anatomical system in which the exchange of oxygen and carbon dioxide between the organism and its environment.[AAO]
There is no doubt that the primitive pattern of vertebrate air-breathing is the buccal pulse pump found in actinopterygian fishes.[well established][VHOG]
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.599 and Figure 18-23
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
The renal system in an anatomical system that maintains fluid balance and contributes to electrolyte balance, acid/base balance, and disposal of nitrogenous waste products..
In various sources such as Encyclopedia Britannica, the excretory and urinary systems are indeed the same system (see wikipedia talk page); we merge two BTO classes here
An anatomical system which consists of organs and tissues which produce, store, and excrete urine.[AAO]
Evolution of vertebrate renal anatomy appears quite conservative when compared, for example, to evolution of respiratory and cardiovascular systems in vertebrates. Major anatomical changes in vertebrates kidneys separate those of birds and mammals from kidneys of lower vertebrates. General increase in animal size from fish to mammals is reflected by an increase in total number of nephrons per kidney, rather than by constant change in tubular dimensions.[well established][VHOG]
In humans, the renal system comprises a pair of kidneys, a pair of ureters, urinary bladder, urethra, sphincter muscle and associated blood vessels
This definition is inclusive of the organs of the vertebrate renal system, as well as the Malpighian tubules of insects, and allows for future incorporation of structures such as the antennal glands of crustaceans
ISBN:978-3540428541 Kapoor BG, Bhavna Khanna, Ichthyology Handbook (2004) p.406
organ system that passes nutrients (such as amino acids and electrolytes), gases, hormones, blood cells, etc. to and from cells in the body to help fight diseases and help stabilize body temperature and pH to maintain homeostasis[WP].
the cardiovascular system and the lymphatic system are parts of the circulatory system
Anatomical system of ion binding, a pumping mechanism, and an efficient vascular system; consisting of the blood, heart, and blood and lymph vessels, respectively.[AAO]
We should divest ourselves of the view that earlier vertebrate groups were 'on their way' to becoming mammals, as clearly they were not such visionaries. Neither were their systems 'imperfect' as earlier anatomists thought. Instead, their circulatory systems served them well to address the ecological demands arising from their lifestyles.[well established][VHOG]
WBbt coelomocyte currently classified as circulating cell
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.493
Portion of connective tissue composed of adipocytes enmeshed in areolar tissue
Connective tissue in which fat is stored.[TAO]
Tissue that contains adipocytes, used for cushioning, thermal insulation, lubrication (primarily in the pericardium) and energy storage.[AAO]
relationship loss: subclass connective tissue proper (AAO:0000099)[AAO]
Adipose tissue is unique to vertebrates. It is found in mostmammals, birds, reptiles and amphibians, and a variety is found in some species of fish. Furthermore, in insects the fat body found in larvae as well as in adults shares some homology with adipose tissue.[well established][VHOG]
In humans, adipose tissue is located beneath the skin (subcutaneous fat), around internal organs (visceral fat), in bone marrow (yellow bone marrow) and in breast tissue. Adipose tissue is found in specific locations, which are referred to as adipose depots. Adipose tissue contains several cell types, with the highest percentage of cells being adipocytes, which contain fat droplets. Other cell types include fibroblasts, macrophages, and endothelial cells. Adipose tissue contains many small blood vessels.; Mice have eight major adipose depots, four of which are within the abdominal cavity. The paired gonadal depots are attached to the uterus and ovaries in females and the epididymis and testes in males; the paired retroperitoneal depots are found along the dorsal wall of the abdomen, surrounding the kidney, and, when massive, extend into the pelvis. The mesenteric depot forms a glue-like web that supports the intestines, and the omental depot, which originates near the stomach and spleen, and, when massive, extends into the ventral abdomen.
in FMA this is dense irregular connective tissue
DOI:10.1017/S0029665107005423 Haugen F, Drevon CA, The interplay between nutrients and the adipose tissue. The Proceedings of the Nutrition Society (2007)
A subdivision of the muscular system corresponding to a subdisivision of an organism.
In FMA this is classified as a set of organs. ZFA musculature system has subtypes, so it is classified here. WBbt muscular system has subtypes so it goes here. Note that we use the MA term set of skeletal muscles here as it seems most appropriate (*not* MA:musculature). AAO is generally confused here.
The nervous system is an organ system containing predominantly neuron and glial cells. In bilaterally symmetrical organism, it is arranged in a network of tree-like structures connected to a central body. The main functions of the nervous system are to regulate and control body functions, and to receive sensory input, process this information, and generate behavior [CUMBO].
A regulatory system of the body that consists of neurons and neuroglial cells. The nervous system is divided into two parts, the central nervous system (CNS) and the peripheral nervous system (PNS). (Source: BioGlossary, www.Biology-Text.com)[TAO]
Anatomical system consisting of nerve bodies and nerve fibers which regulate the response of the body to external and internal stimuli.[AAO]
Nervous systems evolved in the ancestor of Eumetazoa.[well established][VHOG]
ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.117
The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the neural tube derivatives: the brain and spinal cord. In invertebrates it includes central ganglia plus nerve cord.
Part of the nervous system which includes the brain and spinal cord.[AAO]
The brain and spinal cord. Kimmel et al, 1995.[TAO]
The central nervous system (CNS) is the part of the nervous system which includes the brain, spinal cord, and nerve cell layer of the retina (CUMBO).
(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2); Taken together, our data make a very strong case that the complex molecular mediolateral architecture of the developing trunk CNS (central nervous system), as shared between Platynereis and vertebrates, was already present in their last common ancestor, Urbilateria. The concept of bilaterian nervous system centralization implies that neuron types concentrate on one side of the trunk, as is the case in vertebrates and many invertebrates including Platynereis, where they segregate and become spatially organized (as opposed to a diffuse nerve net). Our data reveal that a large part of the spatial organization of the annelid and vertebrate CNS was already present in their last common ancestor, which implies that Urbilateria had already possessed a CNS (reference 3).[well established][VHOG]
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 (reference 1), ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.165 (reference 2), DOI:10.1016/j.cell.2007.02.040 Denes AS, Jekely G, Steinmetz PRH, Raible F, Snyman H, Prud'homme B, Ferrier DEK, Balavoine G and Arendt D, Molecular architecture of annelid nerve cord supports common origin of nervous system centralization in Bilateria. Cell (2007) (reference 3)
An enclosed, cable-like bundle of axons in the peripheral nervous system originating in a nerve root in the central nervous system (or a condensed nervous structure) connecting with peripheral structures.
A portion of tissue which is a fasiculated group of axons.[TAO]
A nerve that transmits from sensory receptors on the surface of the body to the central nervous system.
Anatomical system that overlaps the nervous system and is responsible for receiving and processing sensory information.
An early step in the evolution of neural crest, therefore, may have been the origin of a specific dorsal neural cell population contributing to sensory processing; this would predate the divergence of the amphioxus and vertebrate lineages.[well established][VHOG]
note the distinct between entire sensory system and individual system. this reconciles is_a and part_of distinctions between ssAOs
DOI:10.1073/pnas.97.9.4449 Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000)
The sensory system for the sense of taste.
The sensory system for the sense of taste[NIFSTD:nlx_anat_090803].
The sensory system used for the sense of taste.[AAO]
in ZFA and MA this is a subtype of sensory system. we should change sensory system to disambiguate parts and wholes
Anterior subdivision of a digestive tract.
Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future. In vertebrates the term may refer to a developmental structure
The anterior portion of the primitive digestive tube of the embryo that lies cephalic to the junction of the yolk stalk, consists of endodermal tissue, and gives rise to the the pharynx, lower respiratory system, esophagus, stomach, duodenum proximal to the biliary tract, liver, pancreas, biliary tract, and gall bladder.
The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG]
ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.203, ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11
A portion of the respiratory and digestive tracts; its distal limit is the superior part of the esophagus and it connects the nasal and oral cavities with the esophagus and larynx; it contains the valleculae and the pyriform recesses; its upper limits are the nasal cavity and cranial base.[FEED].
A funnel-shaped fibromuscular tube that conducts food to the ESOPHAGUS, and air to the LARYNYX and LUNGS. It is located posterior to the NASAL CAVITY; ORAL CAVITY; and LARYNX, and extends from the SKULL BASE to the inferior border of the CRICOID CARTILAGE anteriorly and to the inferior border of the C6 vertebra posteriorly. It is divided into the NASOPHARYNX; OROPHARYNX; and HYPOPHARYNX (laryngopharynx)[MESH:A03.867].
Anatomical cavity bounded by the derivatives of the branchial arches.[AAO]
Swollen region of the anterior foregut, posterior to the mouth and anterior to the liver; its walls form the jaws and gills. Kimmel et al, 1995.[TAO]
Swollen region of the anterior foregut, posterior to the mouth and anterior to the liver; its walls form the jaws and gills[ZFA:0000056, ZFIN:ZDB-PUB-961014-576].
The portion of the alimentary canal between the mouth and the oesophagus. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
relationship type change: part_of_proxy respiratory system (AAO:0000541) CHANGED TO: develops_from respiratory system (UBERON:0001004)[AAO]
relationship type change: part_of_proxy respiratory system (AAO:0000541) CHANGED TO: part_of respiratory system (UBERON:0001004)[AAO]
(...) the earliest vertebrates possessed unjointed internal and external branchial arches, and musculature encircling the pharynx.[well established][VHOG]
MA/FMA pharynx not part of digestive/alimentary system, we are consistent with this scheme
Consider generalizing to deuterostome pharynx
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) Box essay 13.1 and Box figure I, p.502-503
Middle subdivision of a digestive tract[CJM]. In vertebrates: The middle part of the alimentary canal from the stomach, or entrance of the bile duct, to, or including, the large intestine[GO].
Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future. We may explicitly make this a developmental class
In humans: originates from the foregut at the opening of the bile duct into the duodenum and continues through the small intestine and much of the large intestine until the transition to the hindgut about two-thirds of the way through the transverse colon
in FMA this represents an embryonic region.
The caudalmost subdivision of a digestive tract.
Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future (vertebrates have some contribution from NC - https://github.com/obophenotype/uberon/wiki/The-neural-crest). We may explicitly make this a developmental class
the caudal portion of the primitive digestive tube of the embryo
in FMA this class has no children. In MA it has a single child hindgut epithelium
Primordia are populations of contiguous cells that are morphologically distinct and already correspond in extent to a later organ/tissue[FBbt, Hartenstein, V. (2004)].
In the developing vertebrate, the neural tube is the embryo's precursor to the central nervous system, which comprises the brain and spinal cord. The neural groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or neural canal (which strictly speaking is the center of the neural tube), the ectodermal wall of which forms the rudiment of the nervous system. [WP,unvetted].
Hollow epithelial tube on dorsal side of the embryo that develops into the central nervous system.[AAO]
The dorsal tubular structure in the vertebrate embryo that develops into the brain and spinal cord. [TFD][VHOG]
(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]
The mature structure of the neural tube exists when the tube has been segmented into the forebrain, midbrain, hindbrain and spinal cord regions. In addition neural crest has budded away from the epithelium
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28
the terminal portion of the intestinal tube, terminating with the anus
The terminal portion of the large intestine between the ileo-pelvic colon and the anus. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
In the lungfish, sharks and rays the rectum opens into the cloaca which also receives wastes (urine) from the kidneys and material from the reproductive organs. In bony fish the rectum reaches the outside environment through the anus, which is normally situated just in front the urinary and reproductive openings. However in some fish the digestive tract may be curled back on itself, and in the Electric Eel (Electrophorus electricus) the anus is situated in the fish's throat. -- http://www.earthlife.net/fish/digestion.html
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.
A zone of skin that is part of a back [Automatically generated definition].
TODO - distinguish between entire skin of region and arbitrary zone of skin on region
A terminal branch of the left or right common carotid artery which supplies oxygenated blood to to the throat, neck glands, tongue, face, mouth, ear, scalp and dura mater of the meninges[MP]
not homologous to the external carotid of zebrafish (Goodrich, 1958) - http://zfish.nichd.nih.gov/zfatlas/Intro%20Page/comparative.html; check XAO
It ascends beneath the anterior margin of the trapezius, distributing branches to it, and to the neighboring muscles and lymph glands in the neck, and anastomosing with the superficial branch of the descending branch of the occipital artery.
superficial branch of transverse cervical artery
The transverse cervical artery splits into two branches, a superficial one and a deep one[WP]
A vein that carries deoxygenated blood from the lower half of the body into the right atrium of the heart.
Trunk of systemic vein which is formed by the union of the right common iliac vein and the left common iliac vein and terminates in the right atrium[FMA].
Phylogenetic modifications within this basic pattern of arteries and veins are largely correlated with functional changes. In the transition from water to land, gills gave way to lungs, accompanied by the establishment of a pulmonary circulation. In some fishes and certainly in tetrapods, the cardinal veins become less involved in blood return. Instead, the composite, prominent postcava (posterior vena cava) arose to drain the posterior part of the body and the precava (anterior vena cava) developed to drain the anterior part of the body.[well established][VHOG]
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.454-455
Endocardium that is part of the cardiac ventricle.
Muscular layer of the cardiac ventricle composed of a compact myocardial layer surrounding the trabecular layer.
Muscular layer of the cardiac ventricle composed of a compact myocardial layer surrounding the trabecular layer Hu et al. 2001.[TAO]
As noted, the hearts of birds and mammals have four chambers that arises from the two chambers (atrium and ventricle) of the fish heart.[uncertain][VHOG]
A zone of skin that is part of a head [Automatically generated definition].
A zone of skin that is part of a trunk [Automatically generated definition].
Excretion that is the output of a kidney
kidney excreta from some taxa (e.g. in aves) may not be liquid
Joint fluid is a transudate of plasma that is actively secreted by synovial cells.
Portion of organism substance that is a clear fluid that occupies the space in synovial joints.[TAO]
It provides nutrients and lubrication for articular cartilage
The fluid contains hyaluronan secreted by fibroblast-like cells in the synovial membrane, lubricin (proteoglycan 4; PRG4) secreted by the surface chondrocytes of the articular cartilage and interstitial fluid filtered from the blood plasma
Muscle tissue composed of cardiac muscle cells, forming the muscles of the heart[ZFA,modified].
check relationship with myocardium. part_of in MA - but we also have a more specific class 'cardiac muscle tissue of myocardium'. Check ncit
Muscle tissue that consists primarily of skeletal muscle fibers.
TODO - add skeletal muscle organ? See GO:0060538 skeletal muscle organ development. Todo - group FBbt:00005073 - somatic muscle.
Muscle, composed of long cylindrical, multinucleated cells that attaches to the skeleton via tendons.[TAO]
Tissue which consists of skeletal muscle fibers surrounded by endomysium. Examples: Skeletal muscle tissue of biceps, Skeletal muscle tissue of diaphragm[FMA]
This result implies the following views in terms of evolutionary differentiation: (1) Arthropod striated muscle and vertebrate skeletal and cardiac muscles share a common ancestor. In other words, they did not evolve independently (...) (5) The divergence of vertebrate skeletal and cardiac muscles/vertebrate smooth muscle and nonmuscle is at least before that of vertebrates/arthropods. In other words, emergence of skeletal and cardiac musle type tissues preceded the vertebrate/arthropod divergence (ca. 700 MYA).[well established][VHOG]
PMID:10368962 Oota S, Saitou N, Phylogenetic relationship of muscle tissues deduced from superimposition of gene trees. Mol Biol Evol (1999)
Muscle tissue which is unstriated, composed primarily of smooth muscle fibers surrounded by a reticulum of collagen and elastic fibers. Smooth muscle differs from striated muscle in the much higher actin/myosin ratio, the absence of conspicuous sarcomeres and the ability to contract to a much smaller fraction of its resting length[GO].
A non-striated muscle that is composed of spindle-shaped cells. Smooth muscle usually is organized into sheets that line cavitated organs.[TAO]
Involuntary muscle tissue consisting of uninucleate spindle-shaped fibers.[AAO]
(...) the first bilateral animals possessed only smooth muscles with the molecular repertoire necessary to build a striated muscle. (...) it is more parsimonious to regard striated muscle cells as a sister cell type to the smooth muscle cells. In this scenario, striated and smooth muscles would have arisen in the stem lineage that led to the Nephrozoa (i.e. all Bilateria exclusive the acoelomorphs) (Hejnol et al., 2009), from an 'acoel-like' smooth muscle, by segregation and divergence of functions and through differential recruitment of additional genes[well established][VHOG]
GO uses visceral and smooth interchangeably. However visceral can also be used in the sense of the viscera. Many fly annotations to smooth muscle terms. If we want to be inclusive of insects have to have a general definition of tissue that includes cells.
textus muscularis levis; textus muscularis nonstriatus
DOI:10.1002/jez.b.21416 Chiodin M, Achatz JG, Wanninger A, Martinez P, Molecular architecture of muscles in an acoel and its evolutionary implications. Journal of Experimental Zoology (2011)
Simple squamous epithelium of mesodermal origin which lines serous membranes. Examples: mesothelium of pleura, mesothelium of peritoneum[FMA]. http://en.wikipedia.org/wiki/ The mesothelium is a membrane that forms the lining of several body cavities: the pleura (thoracal cavity), peritoneum (abdominal cavity including the mesentery) and pericardium (heart sac). Mesothelial tissue also surrounds the male internal reproductive organs (the tunica vaginalis testis) and covers the internal reproductive organs of women (the tunica serosa uteri).
A major subdivision of an organism that is the entire part of the organism dorsal to a horizontal plane and bounded on one side by the same transverse plane. In vertebrares this includes the vertebral column..
In humans, called the back, a large posterior area of the human body, rising from the top of the buttocks to the back of the neck and the shoulders. It is the surface opposite to the chest, its height being defined by the vertebral column (commonly referred to as the spine or backbone) and its breadth being supported by the ribcage and shoulders. The spinal canal runs through the spine and provides nerves to the rest of the body
Either of the pair of major vessels which arise from the renal hilus and return blood from the kidneys, suprarenal gland and the ureter to the inferior vena cava.
The renal veins are veins that drain the kidney. They connect the kidney to the inferior vena cava. It is usually singular to each kidney, except in the condition 'multiple renal veins'. It also divides into 2 divisions upon entering the kidney: the anterior branch which receives blood from the anterior portion of the kidney and, the posterior branch which receives blood from the posterior portion. Often, each renal vein will have a branch that receives blood from the ureter. [WP,unvetted][Wikipedia:Renal_vein].
in EHDAA2, the renal vein is part of the kidney
A renal vein that drains the right kidney
A vein that drains blood from the right kidney into the inferior vena cava[ncithesaurus].
A renal vein that drains the left kidney
A vein that drains blood from the left kidney into the inferior vena cava[ncithesaurus].
A vein that carries deoxygenated blood from its corresponding ovary to inferior vena cava or one of its tributaries.
gonad of female reproductive system vein
gonada of female reproductive system vein
vein of female reproductive system gonad
vein of female reproductive system gonada
vein of gonad of female reproductive system
vein of gonada of female reproductive system
Last portion of the large intestine before it becomes the rectum.
TODO - abstract this such that it legitimately covers all vertebrates
The last portion of the digestive system, it extracts water and salt from solid wastes before they are eliminated from the body.[AAO]
The posterior intestine has short longitudinally arranged epithelial folds which are similar to the colon of higher vertebrates. Wallace et al, 2005.[TAO]
Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG]
In mammals, the colon consists of four sections: the ascending colon, the transverse colon, the descending colon, and the sigmoid colon[WP]
In zebrafish, the posterior intestine has short longitudinally arranged epithelial folds which are similar to the colon of higher vertebrates[ZFIN]
it extracts water and salt from solid wastes before they are eliminated from the body[WP]
colon
结肠
ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11
The part of the large intestine that is closest to the rectum and anus. It forms a loop that averages about 40 cm. in length, and normally lies within the pelvis, but on account of its freedom of movement it is liable to be displaced into the abdominal cavity.
the layered structure that makes up the stomach, typiclly consists of a serous coat, a muscular coat, a mucous membrane, and other tissue layers in between
An anatomical wall that is part of a large intestine [Automatically generated definition].
One of two laterally paired arteries that supplies the kidneys. These are large arteries that branch from the dorsal aorta in primitive vertebrates.
renal arteries vary widely even in humans. Sub-structures should be checked for taxon variability.
Artery which supplies blood via branches to the gonads, oviducts, and kidneys.[AAO]
The renal arteries normally arise off the side of the abdominal aorta, immediately below the superior mesenteric artery, and supply the kidneys with blood. Each is directed across the crus of the diaphragm, so as to form nearly a right angle with the aorta. The renal arteries carry a large portion of total blood flow to the kidneys. Up to a third of total cardiac output can pass through the renal arteries to be filtered by the kidneys. The arterial supply of the kidneys is variable and there may be one or more renal arteries supplying each kidney. It is located above the renal vein. It has a radius of approximately 0.25cm, 0.26 cm at the root. The measured mean diameter can differ depending on the imaging method used. For example, the diameter was found to be 5.04 ± 0.74 mm using ultrasound, but 5.68 ± 1.19 mm using angiography. [WP,unvetted].[Wikipedia]
Renal artery that supplies the right kidney
The right [renal artery] passes behind the inferior vena cava, the right renal vein, the head of the pancreas, and the descending part of the duodenum[WP]
Renal artery that supplies the left kidney
The left [renal artery] is somewhat higher than the right; it lies behind the left renal vein, the body of the pancreas and the splenic vein, and is crossed by the inferior mesenteric vein[WP]
In human anatomy, the ovarian artery is a blood vessel that supplies oxygenated blood to the ovary. It arises from the abdominal aorta below the renal artery, and does not pass out of the abdomiproperty_value external_definitioncavity. It can be found in the suspensory ligament of the ovary. [WP].
The mucosal layer that lines the stomach.
The gastric mucosa is the mucous membrane layer of the stomach which contains the glands and the gastric pits. In men it is about 1 mm thick and its surface is smooth, soft, and velvety. It consists of epithelium, lamina propria, and the muscularis mucosae. In its fresh state, it is of a pinkish tinge at the pyloric end and of a red or reddish-brown color over the rest of its surface. In infancy it is of a brighter hue, the vascular redness being more marked. It is thin at the cardiac extremity, but thicker toward the pylorus. During the contracted state of the organ it is thrown into numerous plaits or rugae, which, for the most part, have a longitudinal direction, and are most marked toward the pyloric end of the stomach, and along the greater curvature. These folds are entirely obliterated when the organ becomes distended. When examined with a lens, the inner surface of the mucous membrane presents a peculiar honeycomb appearance from being covered with funnel-like depressions or foveolae of a polygonal or hexagonal form, which vary from 0.12 to 0.25 mm. in diameter. These are the ducts of the gastric glands, and at the bottom of each may be seen one or more minute orifices, the openings of the gland tubes. Gastric glands are simple or branched tubular glands that emerge on the deeper part of the gastric foveola, inside the gastric areas and outlined by the folds of the mucosa. There are three types of glands: cardiac glands (in the proximal part of the stomach), oxyntic glands (the dominating type of gland), and pyloric glands. The cardiac glands mainly contain mucus producing cells. The bottom part of the oxyntic glands is dominated by zymogen (chief) cells that produce pepsinogen (an inactive precursor of the pepsin enzyme). Parietal cells, which secrete hydrochloric acid are scattered in the glands, with most of them in the middle part. The upper part of the glands consist of mucous neck cells; in this part the dividing cells are seen. The pyloric glands contain mucus-secreting cells. Several types of endocrine cells are found in all regions of the gastric mucosa. In the pyloric glands contain gastrin producing cells (G cells); this hormone stimulates acid production from the parietal cells. ECL (enterochromaffine-like) cells, found in the oxyntic glands release histamine, which also is a powerful stimulant of the acid secretion. The A cells produce glucagon, which mobilizes the hepatic glycogen, and the enterochromaffin cells that produce serotonin, which stimulates the contraction of the smooth muscles. The surface of the mucous membrane is covered by a single layer of columnar epithelium . This epithelium commences very abruptly at the cardiac orifice, where there is a sudden transition from the stratified epithelium of the esophagus. The epithelial lining of the gland ducts is of the same character and is continuous with the general lining of the stomach. [WP,unvetted][Wikipedia:Gastric_mucosa].
the fibrous connective tissue layer beneath the stomach mucosa
the outermost layer of the stomach wall, consisting of layers of connective tissue continuous with the peritoneum
anatomical wall of stomach serous membrane
anatomical wall of ventriculus serous membrane
serosa of anatomical wall of ventriculus
serous membrane of anatomical wall of stomach
serous membrane of anatomical wall of ventriculus
serous membrane of stomach anatomical wall
serous membrane of ventriculus anatomical wall
ventriculus anatomical wall serous membrane
A mucosa that is part of a large intestine [Automatically generated definition].
A submucosa that is part of a large intestine [Automatically generated definition].
A serous membrane that is part of a large intestine [Automatically generated definition].
A blood vessel that drains blood from the large intestine that usually terminates when reaching the splenic vein, which goes on to form the portal vein with the superior mesenteric vein (SMV). Anatomical variations include the IMV draining into the confluence of the SMV and splenic vein and the IMV draining in the SMV. The IMV lies to the right of the similarly name artery, the inferior mesenteric artery, which originates from the abdominal aorta. [WP,unvetted].
An ureter that is part of a right side of organism [Automatically generated definition].
An ureter that is part of a left side of organism [Automatically generated definition].
A funnel shaped proximal portion of the ureter that is formed by convergence of the major calices [MP].
In this ontology, the renal pelvis is represented as the area of part-overlap between the kidney and the ureter
A serous membrane that is part of a wall of intestine [Automatically generated definition].
anatomical wall of bowel serous membrane
anatomical wall of intestine serous membrane
intestine anatomical wall serous membrane
serous membrane of anatomical wall of bowel
serous membrane of anatomical wall of intestine
serous membrane of bowel anatomical wall
serous membrane of intestine anatomical wall
Orifice at the opposite end of an animal's digestive tract from the mouth. Its function is to expel feces, unwanted semi-solid matter produced during digestion, which, depending on the type of animal, may be one or more of: matter which the animal cannot digest, such as bones; food material after all the nutrients have been extracted, for example cellulose or lignin; ingested matter which would be toxic if it remained in the digestive tract; and dead or excess gut bacteria and other endosymbionts.
opening of terminal part of digestive tract
distensible musculomembranous organ situated in the anterior part of the pelvic cavity in which urine collects before excretion[MP].
A saccular organ in which urine accumulates before discharge from the body. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-29, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]
Anatomical structure which consists of a membranous sac used to temporarily store urine until it is excreted from the body.[AAO]
In tetrapods, the urinary bladder arises as an outpocketing of the cloaca. (...) The tetrapod urinary bladder appears first among amphibians and is present in Sphenodon, turtles, most lizards, ostriches among birds, and all mammals.[well established][VHOG]
The urinary bladder evolved in tetrapods. Birds to not possess a true urinary bladder, although Palaeognathae have an undifferentiated cloacal outpocketing that serves a similar function[https://github.com/obophenotype/uberon/issues/454]
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.577-78
An anatomical wall that lines the insider of a urinary bladder.
The constricted portion of the urinary bladder, formed by the meeting of its inferolateral surfaces proximal to the opening of the urethra[MP].
the mucous membrane lining the urinary bladder
A serous membrane that is part of a urinary bladder [Automatically generated definition].
An anatomical wall that is part of a intestine [Automatically generated definition].
we place two MA classes here due to the official ncit2ma mapping to intestinal wall tissue; not clear how bowel and intestine are different
The organism subdivision that includes the pelvic girdle skeleton and associated soft tissue. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). Examples: There are only two instances in an organism, right and left pectoral girdle regions.
this class describes the subdivision of the limb/fin, NOT the skeleton within. See also: skeleton of pectoral girdle (UBERON:0007831). See also comments on obo-anatomy mail list. Note that even though the class includes soft tissue it is more restrictive than 'pelvis' which also includes structures in cavities etc. TODO this needs to be better documented
Subdivision of lower limb or fin which links the limb/fin to the body[FMA,modified]. There is only one instance of the pelvic girdle region per organism.[VSAO]
in FMA this is classified as simple columnar, MA divides this into squamous and glandular
Epithelial layer that lines the intestine.
Simple columnar epithelium that lines the intestine, sometimes pseudostratified, with absorptive brush-border cells and mucous goblet cells clearly visible. Crosnier et al. 2005[TAO]
An epithelium that is part of a large intestine [Automatically generated definition].
the glandular mucous membrane lining of the uterine cavity that is hormonally responsive during the estrous/menstrual cycle and during pregnancy
The mucous membrane lining the uterus. [TFD][VHOG]
The maternal part of the placenta (of eutherian mammals) is the vascularized and glandular uterine lining, or endometrium.[well established][VHOG]
Animals that have estrous cycles reabsorb the endometrium if conception does not occur during that cycle. Animals that have menstrual cycles shed the endometrium through menstruation instead
in FMA this is subdivided into basal and outer
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.144
TODO - check for parallel structure with peritoneum
A fallopian tube that is part of a right side of organism [Automatically generated definition].
non-functional in monotremes[ISBN-13:978-0226870137]
A fallopian tube that is part of a left side of organism [Automatically generated definition].
An artery that supplies blood to the upper urinary bladder.
The first part of the superior vesical artery represents the terminal section of the previous portion of the umbilical artery (fetal hypogastric artery)[WP]
A vein that begins near the upper part of the greater sciatic foramen, passes upward behind and slightly medial to the hypogastric artery and, at the brim of the pelvis, joins with the external iliac to form the common iliac vein. [WP,unvetted].
One the veins that drains the vaginal venous plexus, into the hypogastric veins. [WP,modified].
Muscle (organ) which is a part of the pelvis. Examples: levator ani,
A urethra that is part of a female reproductive system.
Any of the numerous small mucous-secreting glands located in the wall of the male or female urethra that help protect the epithelium from the corrosive urine
NCIT:C12339 paraurethral gland belongs here
FMA: nonkeratinizing stratified squamous epithelium; BTO: Vaginal epithelium is stratified squamous epithelium having a thickness of 15-200 microns; MA has single subclass (squamous)
The anus and surrounding regions. Encompasses both internal and external regions, where present
A zone of skin that is part of a pelvis [Automatically generated definition].
A zone of skin that is part of an abdomen [Automatically generated definition].
A zone of skin that is part of a neck [Automatically generated definition].
A zone of skin that is part of a thorax [Automatically generated definition].
An organism subdivision that includes the pectoral girdle skeleton and associated soft tissue. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). Examples: There are only two instances in an organism, right and left pectoral girdle regions.
this class describes the organism subdivision, NOT the skeleton within. See also: skeleton of pectoral girdle (UBERON:0007831).
An organism subdivision that includes the pectoral girdle skeleton. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). There is only one instance of the pectoral girdle region per organism.[VSAO]
Note that this class describes the central subdivision of the pectoral girdle complex, NOT the skeleton within.[VSAO]
Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system.
Anatomical system consisting of multiple elements and tissues that provides physical support.[TAO]
Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system.[VSAO]
System that provides physical support to the organism.[AAO]
By taking a holistic approach, integration of the evidence from molecular and developmental features of model organisms, the phylogenetic distribution in the 'new animal phylogeny' and the earliest fossilized remains of mineralized animal skeletons suggests independent origins of the skeleton at the phylum level.[debated][VHOG]
GO defines skeletal system very generically: The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton) GO:0001501; however, all annotations are to vertebrates
DOI:10.1159/000324245 Donoghue PCJ, Sansom IJ, Origin and early evolution of vertebrate skeletonization. Microscopy research and technique (2002)
A subdivision of the head that has as parts the layers deep to the surface of the anterior surface, including the mouth, eyes, and nose (when present). In vertebrates, this includes the facial skeleton and structures superficial to the facial skeleton (cheeks, mouth, eyeballs, skin of face, etc).
Subdivision of head which consists of the viscerocranium and all layers superficial to it. Examples: There is only one face.
The area that extends from the median ocellus to the oral foramen[HAO].
The face develops from outward growth of tissue located rostral to the cranium & pharynx. The lower jaw and most of the upper jaw are formed by growth of the first pharyngeal (branchial) arch. The upper incisor region and the nose and forehead (frontal region) are formed from tissue located rostral to the neural tube (frontonasal prominence)
A zone of skin that is part of a lip [Automatically generated definition].
Skeletal element that is composed of bone tissue.
Also called osseous tissue, (Latin: os). Is a type of hard endoskeletal connective tissue found in many vertebrate animals. Bone is the main tissue of body organs that support body structures, protect internal organs, (in conjunction with muscles) facilitate movement; and are involved with cell formation, calcium metabolism, and mineral storage.[AAO]
Portion of tissue which is calcified connective tissue making up the structural elements of the skeletal system.[TAO]
Skeletal element that is composed of bone tissue.[VSAO]
The 'new animal phylogeny' reveals that many of the groups known to biomineralize sit among close relatives that do not, and it favours an interpretation of convergent or parallel evolution for biomineralization in animals. (...) Whether this 'biomineralization toolkit'of genes reflects a parallel co-option of a common suite of genes or the inheritance of a skeletogenic gene regulatory network from a biomineralizing common ancestor remains an open debate.[debated][VHOG]
DOI:10.1159/000324245 Murdock DJ, Donoghue PC, Evolutionary Origins of Animal Skeletal Biomineralization. Cells Tissues Organs (2011)
An articular capsule (or joint capsule) is an envelope surrounding a synovial joint. [WP,unvetted].
Any muscle organ that is part of a pelvic girdle [Automatically generated definition].
Note that in MA, this is a subclass of pelvis muscle; in FMA this is a hindlimb muscle, but recall in FMA hindlimb includes the girdle.
The descending aorta is the portion of the aorta in a two-pass circulatory system from the arch of aorta to the point where it divides into the common iliac arteries[GO]. The descending aorta is part of the aorta, the largest artery in the body. The descending aorta is the part of the aorta beginning at the aortic arch that runs down through the chest and abdomen. The descending aorta is divided into two portions, the thoracic and abdominal, in correspondence with the two great cavities of the trunk in which it is situated. Within the abdomen, the descending aorta branches into the two common iliac arteries which serve the legs. [WP,unvetted].
results from fusion of left and right dorsal aortae
the part of the aorta that extends from the origin at the heart to the diaphragm, and from which arises numerous branches that supply oxygenated blood to the chest cage and the organs within the chest
Abdominal part of aorta: the distal part of the descending aorta, which is the continuation of the thoracic part and gives rise to the inferior phrenic, lumbar, median sacral, superior and inferior mesenteric, middle suprarenal, renal, and testicular or ovarian arteries, and celiac trunk[BTO]. The abdominal aorta is the largest artery in the abdominal cavity. As part of the aorta, it is a direct continuation of descending aorta(of the thorax). [WP,unvetted].
Many of the branches of the abdominal aorta in mammals may be branches of the dorsal aorta in other vertebrates
A bilaterally paired branched artery that originates from the aortic arches and divides into and includes as parts the internal and external carotid arteries[cjm].
we follow the FMA and treat the artery as a tree-structure - here we include the internal and external as parts. For the part that excludes the branches, see 'trunk of common carotid artery'
This class represents the adult and developing structures'
in birds and reptiles, develops from arch III and parts of ventral and dorsal aortae
A tube extending from the mouth to the anus.
The alimentary or digestive tract, and associated organs.[TAO]
FMA also has a term 'gastrointestinal tract', but this includes the liver.
we place the MA and EMAPA class here, although the intent is probably a smaller region. See https://github.com/obophenotype/uberon/issues/509
we following Kardong in naming the entire tube from mouth to anus the alimentary canal. Kardong calls the portion of this tract that excludes buccal cavity and pharynx the 'alimentary canal', consider adding an extra class for this
Subdivision of urinary system which consists of the urinary bladder and the urethra.
The segment of the respiratory tract that starts proximally with the nose and ends distally with the cricoid cartilage, before continuing to the trachea.
Some specify that the glottis (vocal cords) is the defining line between the upper and lower respiratory tracts;[2] yet even others make the line at the cricoid cartilage. The FMA includes nose, nasopharynx, oropharynx and larynx[WP]
The segment of the respiratory tract that starts proximally with the trachea and includes all distal structures including the lungs[WP,modified]
A vein that carries deoxygenated blood from the upper half of the body into the right atrium of the heart.
The mouse has both left and right anterior vena cava. adult humans only have a right. Postnatally the left regresses and becomes non-functional (Wessels and Sedmera 2003). In the mouse, The right pulmonary vein passes dorsal to the right superior vena cava, the left pulmonary dorsal to the left superior vena cava (Biology of the Laboratory Mouse, Green).
One of two jugular veins that collect the blood from the brain, the superficial parts of the face, and the neck. [WP,unvetted].
Vein which receives many veins draining the palate, brain, and the orbital, nasal, and auditory regions.[AAO]
The bronchial veins are small vessels that return blood from the larger bronchi and structures at the roots of the lungs. The right side drains into the azygos vein, while the left side drains into the left superior intercostal vein or the accessory hemiazygos vein. The bronchial veins are counterparts to the bronchial arteries. The veins, however, do not return all of the blood supplied by the arteries; much of the blood that is carried in the bronchial arteries is returned to the heart via the pulmonary veins. [WP,unvetted].
The ciliary muscle is a ring of smooth muscle in the middle layer of the eye that controls the eye's accommodation for viewing objects at varying distances and regulates the flow of aqueous humour through Schlemm's canal. [WP,unvetted].
The muscle cells of the iris are smooth muscle in mammals and amphibians, but are striated muscle in birds and reptiles. Many fish have neither, and, as a result, their irides are unable to dilate and contract, so that the pupil always remains of a fixed size[Romer, via WP]
in aves, stromal mesenchymal cells may migrate to the iris and become skeletal
A branch of the external carotid artery that supplies structures of the face. [WP,unvetted].
An artery that supplies deep structures of the face. It comes just out behind the neck of the mandible. [WP,unvetted].
...1st pair undergoes partial regression, the remnants of which becomes part of the maxillary arteries
Organ consisting of a tissue made up of various elongated cells that are specialized to contract and thus to produce movement and mechanical work[GO].
Portion of tissue composed of contractile fibers.[TAO]
It seems clear that the metazoan ancestor inherited from its unicellular descendants an actin cytoskeleton and motor-proteins of the myosin superfamily. Within metazoans, these two molecules were arranged into effective contractile units, the muscles. The basic trends for muscle evolution are already expressed in the diploblastic taxa.[well established][VHOG]
ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.75
An epithelial tube or tree of tibes that transports blood away from the heart[modified from AEO definition].
Note that in FMA an artery is a tree, whereas AEO/JB defines it as a tube; FMA includes a separate class for what it calls the trunk. Classification in this ontology may currently (Jan 2012) represent a mix of both schemes, although we are gradually revising in the direction of the AEO scheme.
Part of the circulatory system composed of blood vessels which carry oxygenated blood away from the heart to the rest of the body.[AAO]
The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]
DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2006)
Any of the tubular branching vessels that carry blood from the capillaries toward the heart.
TODO - check with MA - vein vs venous blood vessel
Part of the circulatory system composed of blood vessels which carry blood from other organs, tissues, and cells to the heart.[AAO]
Cranial nerve that has three branches - the ophthalmic (supplying the skin of the nose and upper jaw), the maxillary and the mandibular (supplying the lower jaw).
Nerve consists of motor and sensory components. Ganglion cells of the sensory component form the proximal part of the trigeminal (Gasserian) ganglion. From the ganglion 3 major rami innervate jaws, snout, and buccal roof.[AAO]
We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...) (reference 1); Phylogenetically, the cranial nerves are thought to have evolved from dorsal and ventral nerves of a few anterior spinal nerves that became incorporated into the braincase. Dorsal and ventral nerves fuse in the trunk but not in the head, and they produce two series: dorsal cranial nerves (V, VII, IX, and X) and ventral cranial nerves (III, IV, VI, and XIII) (reference 2).[well established][VHOG]
the ophthalmic usually usually merges with the other two. In some vertebrates, the ophthalmic emerges from the brain separately[Kardong] The trigeminal nerve has 3 branches in mammals - similar branches are present in nonmammalian vertebrates, but in some a separate profundus nerve that corresponds to opthalmic branch in mammls
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.625
Cranial nerve that branches into the supraorbital (supplying the skin of the eye region and the lateral line organs here), the palatine (to the roof of the buccal cavity), and the hyomandibular (dividing into the jugular and mental branches).
Slender nerve composed of branchiomotor and visceral efferent fibers innervating the mouth and various muscles within the jaw. Sensory components innervate the bucccal roof and somatomotor components innervate the depressor musculature and muscle interhyoideus.[AAO]
Cranial nerve that branches into the ramus communicans (to the skin), the pretrematic (to the walls of the pharynx and mouth, viscero-sensory fibers), and the larval post-trematic branch (lost in the adult).
Small nerve consisting of branchiomotor and visceral efferent and afferent fibers which innervate the m. subarculais rectus I, dorsal buccal mucosa, and the tongue.[AAO]
The pulmonary artery that supplies the right lung.
TODO - add class 'pulmonary artery tree organ'
The pulmonary artery that supplies the left lung.
The anterior facial vein (facial vein) commences at the side of the root of the nose, and is a direct continuation of the angular vein where it also receives a small nasal branch. It lies behind the facial artery and follows a less tortuous course. It receives blood from the external palatine vein before it either joins the anterior branch of the retromandibular vein to form the common facial vein, or drains directly into the internal jugular vein. [WP,unvetted].
Vein which collects blood from muscles of the head and drains into the external jugular vein.[AAO]
MA and NCITA also has 'anterior facial vein'
The cranial ganglion that is associated with and extends fibers into the trigeminal nerve.
consider renaming this 'trigeminal ganglion complex'. The complex may be fused (amniotes) partially fused (xenopus) or separate (sharks)
A prominent collection of touch-sensory neurons of the trigeminal or fifth cranial nerve, positioned beside the brain between the eye and the ear. Kimmel et al, 1995.[TAO]
In Xenopus, the profundal and the trigeminal ganglia are separate distally but fused at their proximal end as they condense around NF stage 24.
the bone at the lower, posterior part of the skull
formed from the sclerotome of the occipital somites. It is not present in living or fossil agnathans or cartilaginous fishes, but appears to have arisen in parallel in many bony fishes. Incorporation of the occipital ver- tebrae into the skull was associated with the annexation of the upper part of the spinal cord into the brain, together with the first 2 spinal nerves as cranial nerves XI and XII
fusion of basi-, exo- and supra-occipitals (and maybe tabular)
basi paired exo and supra occipital bones
the large, irregular bone located at the base and side of the skull; consists of three parts at birth: squamous, tympanic, and petrous
In many mammals, as in humans, the petrosal, ectotympanic and squamosal bones synostose to form the temporal bone + styloid process
fusion of squamosal + angular (tympanic annulus) [derm.] + petrosal (prootic + opisthotic)
The temporal bone consists of four parts: * Squama temporalis * Mastoid portion * Petrous portion (Petrosal ridge) * Tympanic part[WP].
Note the Temporal bone is not explicitly categorized to a part of the cranium in FMA
Sense organ in vertebrates that is specialized for the detection of sound, and the maintenance of balance. Includes the outer ear and middle ear, which collect and transmit sound waves; and the inner ear, which contains the organs of balance and (except in fish) hearing. Also includes the pinna, the visible part of the outer ear, present in some mammals.
The organ of hearing and of equilibrium. [TFD][VHOG]
Both vertebrate and invertebrate auditory organs are thought to have evolved from primitive mechanosensors, but the nature of the ancestral structure and the evolutionary trajectories followed in distinct animal lineages remain unknown. In particular, we do not know how many types of mechanosensor existed in the protostome-deuterostome ancestor from which insects and vertebrates evolved or whether the PDA had an auditory organ.[well established][VHOG]
DOI:10.1002/dvdy.20207 Boekhoff-Falk G, Hearing in Drosophila: Development of Johnston's organ and emerging parallels to vertebrate ear development. Developmental Dynamics (2005)
the group of sensory neuron cell bodies associated with the facial nerve (seventh cranial nerve)
resolve facial VII vs geniculate (see EHDAA2)
These (the epibranchial placodes) are focal thickenings of the embryonic ectoderm that form immediately dorsal and caudal of the clefts between the pharyngeal arches in all vertebrates, and they produce the neuroblasts which migrate and condense to form the distal cranial ganglia: the geniculate, petrosal and nodose ganglia. (...) The one substantial difference between the vertebrate pharyngeal arches and those of the protochordates is the presence of the epibranchial placodes but the evolution of these structures was undoubtedly driven by the endoderm.[well established][VHOG]
DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001)
The group of neuron cell bodies associated with the ninth cranial nerve.
Subdivision of skeletal system that surrounds and protects the brain. Includes the skull base, sensory capsules and the central part of the skull roof.
Anatomical cluster that consists of the cartilages and bones that surround the brain.[TAO]
It includes the following bones: Ethmoid bone, Frontal bone, Occipital bone, Parietal bone, Sphenoid bone, Temporal bone. The term cranium can be ambiguous, in that it can refer to the neurocranium, or the neurocranium and the Facial skeleton
The cartilaginous parts of the neurocranium undergo endochondral ossification in most species; ossification has been lost in cartilaginous fishes, but the cartilaginous condition of the skull of lampreys is considered to be primitive (Kardong, 1995)[PMID:11523816]. The neurocranium arises from paraxial mesoderm in the head (first five somites and the unsegmented somitomeres rostral to the first somite) and from ectoderm via the neural crest. In Chondrichthyes and other cartilaginous vertebrates this portion of the cranium does not ossify; it is not replaced via endochondral ossification[WP].
It seems MA uses 'neurocranium' as a synonym for chondrocranium. Note there are currently some structures part of both viscero and neurocranium - ethmoid, zyogomatic, ...
An anatomical cavity that is part of the olfactory apparatus. This includes the space bounded anteriorly by the nares and posteriorly by the choanae, when these structures are present.
define the boundaries of this cavity for a variety of species and check that parthood relations are not too strong.
Saclike space internal to the nasal capsule lined by respiratory and sensory epithelium and glandular tissue.[AAO]
a large air filled space above and behind the nose in the middle of the face[WP][Wikipedia:Nasal_cavity].
Despite significant modification to the nasal cavity within Archosauria and its extreme hypertrophy and supraorbital development in Lambeosaurinae, the neural olfactory system and the olfactory region of the nasal cavity proper retain their plesiomorphic positions and associations, suggesting that this system is highly conserved in vertebrate evolution.[well established][VHOG]
in humans, the cavity includes and starts at the nares and reaches all the way through to the and includes the choanae, the posterior nasal apertures
DOI:10.1666/0094-8373(2006)032[0109:NCHACC]2.0.CO;2 Evans DC, Nasal cavity homologies and cranial crest function in lambeosaurine dinosaurs. Paleobiology (2006)
Subdivision of skeleton which includes upper and lower jaw skeletons.
TODO - move ZFA:0001227 (it is the entire jaw skeleton).
Skeletal and cartilage elements of the first pharyngeal arch.[TAO]
There are cellular contributions from all three embryonic germ layers: pharyngeal mesoderm, endoderm and neural crest that migrates out of the ectoderm (Noden, 1983).
in FMA, the jaw is an organism subdivision cluster, and includes mucosal tissue such as the gingiva as parts. It appears to be skeletal in MA (and has teeth as parts). It is reasonable to assume that ZFA and XAO consider the upper and lower jaws to be skeletal elements or clusters. EHDAA2 also considers these clusters. TODO - follow EHDAA2 model. These arbitrary differences in terminology and classification have to be reconciled with the genuine well-known biological differences in the skeletal elements across vertebrates
Subdivision of head that consists of the lower jaw skeletal elements plus associated soft tissue (skin, lips, muscle)[cjm].
Inferior mandibular arch located on the anterior and lateral sides of the skull.[AAO]
Subsequent vertebrate evolution has also involved major alterations to the pharynx; perhaps the most notable occurred with the evolution of the gnathostomes. This involved substantial modifications to the most anterior pharyngeal segments, with the jaw forming from the first, anterior, pharyngeal segment, while the second formed its supporting apparatus, the hyoid.[well established][VHOG]
See notes for jaw w.r.t skeletal element vs subdivision of head
the groups of nerve cell bodies associated with the twelve cranial nerves
Ganglion which is located in the head.[TAO]
cranial ganglion part of peripheral nervous system
A specialized receptor organ that is a collection of cells spanning the gustatory epithelium.
One of a number of receptor cell nests located in the epithelium of the papillae of the tongue and in the soft palate, epiglottis, and pharynx that mediate the sense of taste. [TFD][VHOG]
Experients in amphibia have shown that an intrinsic feature of the pharyngeal endoderm is its ability to generate taste buds and this capacity must have been acquired by the endoderm at the origin of the vertebrates.[well established][VHOG]
In humans, saste buds may be found on the tongue, soft palatte, epiglottis and upper pharynx. In other species they may be found in more unusual places, such as the trunk, or on the barbels or fins of fish.
arise by inductive interactions between epithelial cells and invading gustatory cells from chorda tympani (facial), glossophrayngeal and vagues nerves ISBN10:1607950324 (todo - request cell terms from CL)
A anatomical space that is enclosed by a pharynx.
See notes for pharynx - as a grouping class this is probably too bad. We exclude WBbt:0005790 (pharyngeal lumen) because of the developmental relationship
A continuation of the pharynx that is involved in breathing, sound production, and protecting the trachea against food aspiration.
An anatomical cluster consisting of the epiglottus, the arytenoid cartilages, the thyroid cartilage, the cricoid cartilage and the muscles, membranes, and ligaments connecting them, and also of the mucosal covering these structures.[FEED]
Anatomical structure consisting of a narrowly triangular chamber supported by a series of semicircular cartilages in which part of the sound-production system is located.[AAO]
(In anura) a dorsal pair of arytenoid cartilages (...), which support vocal cords, and a ventral pair (often fused) of cricoid cartilage (...). These cartilages are regarded as derivatives of posterior visceral arches of ancestors. Together they constitute the larynx, a structure characteristic of tetrapods. (...) (In mammals) Paired arytenoid cartilages help support and control the vocal cords. The cricoid cartilage is single. Two additional cartilages are present that are lacking in other vertebrates: a large ventral thyroid cartilage (...) and a cartilage in the epiglottis.[well established][VHOG]
ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.239-241
The cartilaginous structures that support the larynx.
Cranial nerve that branches into the lateral (to body sense organs) and the intestino-accessorial (to the skin, muscles of shoulder, hyoid, larynx, gut, lungs, and heart).
Nerve consisting of branchiomotor and visceral efferent fibers which branch and innervate the smooth muscles and glands of the heart, lungs, esophagus, and stomach as well as some throat muscles. Sensory fibers supply mucosa of the mouth and pharynx.[AAO]
the space in the eye, filled with aqueous humor, and bounded anteriorly by the cornea and a small portion of the sclera and posteriorly by a small portion of the ciliary body, the iris, and part of the crystalline lens
The part of the eyeball between the cornea and the iris, filled with aqueous humor. [TFD][VHOG]
space in EHDAA2 - consider adding Cavity of anterior chamber of eyeball
the pigmented middle of the three concentric layers that make up an eye, consisting of the iris, ciliary body and choroid[WP,edited].
TODO - check child terms, isa vs partof. See also MA:0001284 ! tunica vasculosa plexus
the adjustable membrane, composed of the stroma and pigmented epithelium, located just in front of the crystalline lens within the eye
The opaque muscular contractile diaphragm suspended in the aqueous humour in front of the lens of the eye. The organ is perforated by the pupil and continues peripherally with the ciliary body. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
The avian iris and ciliary body undergoes a transition from smooth-to-striated muscle during embryonic development [doi:dx.doi.org/10.1006/dbio.1998.9019]
the smooth stratified squamous epithelium that covers the outer surface of the cornea
Portion of tissue comprised of four to six layers of nonkeratinized, stratified squamous cells and represents approximately 60% of the thickness of the cornea.[TAO]
In Humans: It consists of several layers of cells. The cells of the deepest layer are columnar; then follow two or three layers of polyhedral cells, the majority of which are prickle cells similar to those found in the stratum mucosum of the cuticle. Lastly, there are three or four layers of squamous cells, with flattened nuclei
In zebrafish: nonpigmented, stratified squamous nonkeratinizing epithelial cells, attached to a thick basement membrane that is considered to be analogous to the Bowman's membrane in mammals
Opaque fibrous outer layer of the eyeball[ZFA,Kardong,WP].
The sclera, also known as the white part of the eye, is the opaque (usually white, though certain animals, such as horses and lizards, can have black sclera), fibrous, protective, outer layer of the eye containing collagen and elastic fiber. It is derived from the neural crest. In children, it is thinner and shows some of the underlying pigment, appearing slightly blue. In the elderly, however, fatty deposits on the sclera can make it appear slightly yellow. The sclera forms the posterior five sixths of the connective tissue coat of the globe. It is continuous with the dura mater and the cornea, and maintains the shape of the globe, offering resistance to internal and external forces, and provides an attachment for the extraocular muscle insertions. The sclera is perforated by plenty of nerves and vessels passing through the posterior scleral foramen, the hole that is formed by the optic nerve. At the optic disk the outer two-thirds of the sclera continues with the dura mater (outer coat of the brain) via the dural sheath of the optic nerve. The inner third joins with some choroidal tissue to form a plate (lamina cribrosa) across the optic nerve with perforations through which the optic fibers (fasciculi). The thickness of the sclera varies from 1mm at the posterior pole to 0.3 mm just behind the rectus muscle insertions. The sclera's blood vessels are mainly on the surface, and together with the conjunctiva (which lies on top) This is a thin layer covering the sclera. Along with the vessels of the conjunctiva, those of the sclera renders the inflamed eye bright red. [WP,unvetted][Wikipedia:Sclera].
The tough, usually white, outer coat of the eyeball, covering all the posterior surface and continuous anteriorly with the cornea. [TFD][VHOG]
in fish, reptiles and monotremes the connective tissue of the sclera is skeletal
continuous with the dura mater and the cornea; The sclera forms the posterior five-sixths of the connective tissue coat of the globe.
Majority derives from NC that surrounds optic cup of neurectoderm; a small temporal portion develops from the mesoderm that contributes to striated extra-ocular muscles and vascular endothelia[Rada&Johnson].
Seko et al demonstrate chondrogenic potential and identify this as connective tissue[doi:10.1371/journal.pone.0003709].
Disease notes: implicated in rheumatoid arthritis.
A skeletal muscle organ that is part of the trunk region.
Note that this class excludes smooth muscle elements in the trunk region, such as the internal anal sphincter. This appears to be consistent with other ontologies such as FMA and ZFA which appear to only include skeletal muscles here. In fact the MA class 'trunk muscle' is classified as a 'set of skeletal muscles'.
Many ontologies do not appear to have a coherent distinction between an individual muscle and the musculature (i.e. the set of muscles in a region), so we group all together here.
the thickened portion of the vascular tunic, which lies between the choroid and the iris, composed of ciliary muscle and ciliary processes
vascular layer containing connective tissue, of the eye lying between the retina and the sclera. The choroid provides oxygen and nourishment to the outer layers of the retina. Along with the ciliary body and iris, the choroid forms the uveal tract[WP].
check choroid vs choroid layer; check ZFA/TAO placement - no homology assertion in VHOG. Note this is entirely in the posterior region of eyeball in ZFA
MP treats posterior uvea and optic choroid as distinct
A double layer covering the ciliary body that produces aqueous humor.
the any of the paired peripheral nerves formed by the union of the dorsal and ventral spinal roots from each spinal cord segment[MP,modified]
Any of the paired nerves emerging from the spinal cord, each attached to the cord by two roots: ventral and dorsal, and passing out between the vertebrae. [TFD][VHOG]
Any of the layers that make up the retina[MP].
MA does not treat internal/external limiting memranes as layers - these are classified as laminae. Here we follow other ontologies in grouping with other layers. MA also treats retinal pigment epithelium and neural retina epithelium as distinct from the layers. We follow ontologies such as FMA and ZFA in first dividing into pigmented and neural layers - these are also classified as layers, giving us over the usual 10 layers
Cranial nerves are nerves that emerge directly from the brain, in contrast to spinal nerves, which emerge from segments of the spinal cord.
classified as neural tree organ, not nerve in FMA. CN II poses a challenge here as it is not strictly a nerve, yet is expected to be classified under CN.
Twelve pairs of cranial nerves exit/enter the cranium through openings in the skull. The nerves contain efferent axons with motor and glandular functions, as well as afferent axons from cranial ganglia with sensory functions. The nerves are numbered in a rostral to caudal sequence, with the exception of the lateral line nerves.[TAO]
We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...).[well established][VHOG]
See https://github.com/obophenotype/mouse-anatomy-ontology/issues/6
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43
A thick watery refractive medium that fills the space between the lens and the cornea[WP].
The fluid produced by the ciliary process in the eye and occupying the anterior and posterior chambers. It provides nourishment for the lens and cornea and maintains the ocular pressure, and hence the optical integrity of the eyeball. [TFD][VHOG]
(...) we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya (reference 1); Although the eye varies greatly in adaptative details among vertebrates, its basic structure is the same in all. The human eye is representative of the design typical for a tetrapod. (...) A watery aqueous humor fills the spaces in the eye in front of the lens (...) (reference 2).[well established][VHOG]
FMA says A+P chambers, and MA states A chamber. ZFA states A chamber and tha it is produced primarily by dorsal ciliary epithelial cells.To be investigated across taxa.
DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007), ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.424 and p.426 and p.429 and Figure 12-24
The clusters of neurons in the somatic peripheral nervous system which contain the cell bodies of sensory nerve axons, interneurons and non-neuronal supporting cells.
any of the parts of the eye that lie in front of, or ventral to, the lens (inclusive)
any of the parts of the eye that lie in back of, or dorsal to, the lens (but not inclusive)
A layer of epithelial cells that is part of the eye.
this class is the superclass of the anterior epithelium and equatorial epithlium, although the term 'lens epithelium' may refer specifically to the former
the elastic, clear, membrane-like structure, that is outer most layer of the lens
The transparent membrane which surrounds the lens of the eye. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
synthesized by the lens epithelium and its main components are Type IV collagen and sulfated glycosaminoglycans (GAGs). [Wikipedia:Capsule_of_lens
FMA classifies this is a capsule and hence an organ part. In contrast we classify this as acellular
ganglion that has dendrites that form a junction between autonomic nerves originating from the central nervous system and autonomic nerves innervating their target organs in the periphery. There are two subtypes, sympathetic ganglion and parasympathetic ganglion.
A ganglion of the sympathetic nervous system. Examples: paravertebral and the prevertebral ganglia, which include the sympathetic chain ganglia, the superior, middle, and inferior cervical ganglia, and the aorticorenal, celiac, and stellate ganglia
ganglion of sympathetic part of autonomic division of nervous system
sympathetic part of autonomic division of nervous system ganglion
One of the cartilage structures in the nose that provide form and support[WP].
The mucous lining of the larynx, which is composed of squamous epithelium in the upper larynx and ciliated columnar epithelium in the lower larynx.
The mucous membrane that lines the nasal cavity[MP].
TODO - check lining vs part of. split olfactory and nasal mucosa?
One of the two fleshy folds which surround the opening of the mouth.
Surface structure that is one of the two fleshy folds surrounding the opening of the mouth.[TAO]
Lip that covers the lower portion of the mouth.[TAO].
Complex labyrinthine structure that comprises sensory endorgans specialized for vestibular, auditory, and acoustico-vestibular sensation.
The auditory (hearing) and vestibular (balance) organ of the fish, equivalent to the inner ear of amniotes. (See Anatomical Atlas entry for ear by T. Whitfield.)[TAO]
The labyrinth, or inner ear, evolved very early in vertebrate history and, with many variations in configuration but none of basic design and function, has been retained by all vertebrates.[well established][VHOG]
ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.366
The midbrain is the middle division of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes a ventral part containing the cerebral peduncles and a dorsal tectum containing the corpora quadrigemina and that surrounds the aqueduct of Sylvius connecting the third and fourth ventricles)[GO].
developmental relationships need revised
Middle part of the brain composed of the optic tectum and penducular region.[AAO]
The brain region between the forebrain anteriorly and the hindbrain posteriorly, including the tectum dorsally and the midbrain tegmentum ventrally. Kimmel et al, 1995.[TAO]
Fine structural, computerized three-dimensional (3D) mapping of cell connectivity in the amphioxus nervous system and comparative molecular genetic studies of amphioxus and tunicates have provided recent insights into the phylogenetic origin of the vertebrate nervous system. The results suggest that several of the genetic mechanisms for establishing and patterning the vertebrate nervous system already operated in the ancestral chordate and that the nerve cord of the proximate invertebrate ancestor of the vertebrates included a diencephalon, midbrain, hindbrain, and spinal cord.[well established][VHOG]
part of brainstem in ABA - we reject this in favor of ISBN10:0471888893 which has an implicit overlaps relationships
DOI:10.1016/S0959-4388(99)00003-3 Holland LZ and Holland ND, Chordate origins of the vertebrate central nervous system. Current Opinion in Neurobiology (1999)
A segment of the developing hindbrain[ZFA]. In the vertebrate embryo, a rhombomere is a transiently divided segment of the developing neural tube, within the hindbrain region (a neuromere) in the area that will eventually become the rhombencephalon. The rhombomeres appear as a series of slightly constricted swellings in the neural tube, caudal to the cephalic flexure.[WP].
A segment of the developing hindbrain. Kimmel et al, 1995.[TAO]
Rhombomeric segmentation is found in all living vertebrates and is of fundamental importance to the development of the vertebrate head.[well established][VHOG]
In human embryonic development, the rhombomeres are present by day 29
DHBA divides this into A(1-3),B(4),C(5-7) and D(8)
DOI:10.1006/dbio.2002.0831 Mazet F, Shimeld SM, The Evolution of Chordate Neural Segmentation. Developmental Biology (2002)
Rostral segment of the hindbrain that has as its parts the pons (where present) and the cerebellum[WP,modified].
Anterior part of the hindbrain ventral to the cerebellum[NIFSTD:birnlex_965].
The anterior of two brain vesicles formed by specialization of the rhombencephalon in the developing embryo. It gives rise to cerebellum and pons. [TFD][VHOG]
The early development of most vertebrate brains is similar (...). The zebrafish neural tube follows the same basic differentiation pattern as the mammalian neural tube (reference 1); The brain develops from three embryonic enlargements of the neural tube, which later differentiate into five regions. A forebrain differentiates into telencephalon and diencephalon. The midbrain, or mesencephalon, remains undivided. The hindbrain divides into the metencephalon and myelencephalon. Cavities within the brain enlarge to form a series of interconnected ventricles (reference 2).[well established][VHOG]
the terms metencephalon and myelencephalon are only meaningful in mammals and birds[Neuroanatomy of the Zebrafish Brain]. In zebrafish, with the exception of the cerebellum, the ventral remainder of the metencephalon can be separated only arbitrarily from the more caudal myelencephalic portion of the medulla oblongata and thus these are not distinguished in ZFA[ZFA].
ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) p.381-382, ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.500
Organ component of neuraxis that has as its parts the medullary reticular formation, inferior olivary complex and cochlear nuclear complex, among other structures[FMA]. The medulla oblongata lies directly above the spinal cord and controls vital autonomic functions such as digestion, breathing and the control of heart rate[GO].
Posterior portion of the hindbrain which controls respiration, heartbeat, digestion, and swallowing as well as some locomotor responses.[AAO]
The posterior region of the brain that is continuous with the spinal cord. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-17, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]
Classical anatomical studies subdivided the vertebrate rhombencephalon into pons and medulla oblongata. (...) The medulla oblongata appears therefore as a tagma, that is, a group of segmental units (pseudorhombomeres, in this case) sharing some morphological and molecular characteristics, and in some aspects different from the segmental units present in adjoining brain regions, pons and spinal cord.[well established][VHOG]
DOI:10.1016/j.ydbio.2008.08.017 Marin F, Aroca P, Puelles L, Hox gene colinear expression in the avian medulla oblongata is correlated with pseudorhombomeric domains. Developmental Biology (2008)
the epithelial lining of the trachea which contains numerous ciliated cells
An endothelium that is part of a capillary [Automatically generated definition].
An endothelium that is part of an arteriole [Automatically generated definition].
An endothelium that is part of an artery [Automatically generated definition].
The endothelium is the thin layer of cells that lines the interior surface of blood vessels, forming an interface between circulating blood in the lumen and the rest of the vessel wall.[AAO]
Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG]
ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.207
An endothelium that is part of a venule [Automatically generated definition].
An endothelium that is part of a vein [Automatically generated definition].
Ventral part of the midbrain, separated from the hindbrain by the isthmus[ISBN10:0471888893]. Subdivision of the midbrain lying anterior to the tectum and posterior to the substantia nigra and cerebral peduncle[FMA] The part of the midbrain extending from the substantia nigra to the cerebral aqueduct in a horizontal section of the midbrain. It forms the floor of the midbrain that surrounds the cerebral aqueduct[WP].
Together, our results reveal a shared basic organization in the tegmental domains of the diencephalon and midbrain of developing lamprey, indicating early appearance of the domain in vertebrate phylogeny.[well established][VHOG]
'tegmentum' is used generically for the ventral part of the brainstem (ISBN10:0471888893). We use the label 'midbrain tegmentum' to denote the midbrain structure. In NIFSTD tegmentum is a composite structure and there is a separate class for midbrain tegmentum and pontine tegmentum
DOI:10.1016/j.brainresbull.2005.05.001 Villar-Cheda B, Abalo XM, Anadon R, Rodicio MC, The tegmental proliferation region in the sea lamprey. Brain Research Bulletin (2005)
A multi-tissue structure that is part of a spinal cord.
The hyaline cartilaginous structures that support the bronchi, present as irregular rings in the larger bronchi (and not as regular as in the trachea), and as small plates and islands in the smaller bronchi; as the branching continues through the bronchial tree, the amount of hyaline cartilage in the walls decreases until it is absent in the smallest bronchioles[MP].
A submucosa that is part of a bronchus [Automatically generated definition].
The liquid component of blood, in which erythrocytes are suspended.
One of the minute vessels that collect deoxygenated blood from the capillary plexuses returns it to the veins
Multi-tissue structure part of the blood vasculature formed by the anastomosis of capillaries. Venules carry blood toward the heart.[TAO]
The smallest division of the artery located between the muscular arteries and the capillaries[GO].
Multi-tissue structure part of the blood vasculature, feeds into capillaries. Arterioles carry blood away from the heart.[TAO]
Small, terminal branch of an artery which generally connects to capillaries.[AAO]
A vessel through which blood circulates in the body.
consider adopting the EMAPA superclass 'vascular element', which includes microvasculature (e.g. capillaries), vascular plexus
Any of the vessels through which blood circulates in the body. [XAO:0001011_][VHOG]
Any of the vessels through which blood circulates in the body.[AAO]
annelids have blood vessels, but this class is not applicable to annelids.
FMA:63183 Blood vessel is categorized as 'general anatomical term'. Suggestion to map to region of vascular tree from Terry H at JAX
Any of the smallest blood vessels connecting arterioles with venules.
not all sources agree capillary is a blood vessel - consider adopting EMAPA superclass of vascular element
Any of the tiny blood vessels connecting the arterioles to the venules.[AAO]
capillaries lack tunica media and tunica adventitia; only the endothelial wall of the tunica intima belongs
A monolayer of specialized, flattened, mitochondria-rich cells that lines the posterior surface of the cornea and faces the anterior chamber of the eye[WP].
A layer of epithelium that lines the heart, blood vessels (endothelium, vascular), lymph vessels (endothelium, lymphatic), and the serous cavities of the body[MESH]. Simple squamous epithelium which lines blood and lymphatic vessels and the heart[FMA]
The term 'endothelium' has been either restricted to the continuous cell layer of the vertebrates, as we are assuming here, or applied to all the cells able to adhere to the luminal surface of the vascular basement membrane (Casley-Smith 1980)
Portion of semisolid bodily waste discharged through the anus[MW,modified]
Excretion in semisolid state processed by the intestine.[FMA]
Cartilage tissue primarily composed of type II collagen (thin fibrils) and a glassy appearance.
Cartilage (tissue) which consists of chondrocytes and collagen, the intercellular matrix of which is an amorphous gel with a perichondrium[FMA:64783].
Cartilage tissue primarily composed of type II collagen (thin fibrils) and a glassy appearance.[VSAO]
An artery that carries deoxygenated blood from heart to the lungs. They are the only arteries (other than umbilical arteries in the fetus) that carry deoxygenated blood..
Major artery which supplies blood to the lungs.[AAO]
One of two arteries, leaving from the heart, the left one supplying the left lung and the right one supplying the right lung. [TFD][VHOG]
On the other hand, in the sister clade of the actinopterygians, the sarcopterygians, the gill circulation is supplemented with lung ventilation. As a result, the pulmonary artery and vein and a functional ductus arteriosus arose as a major evolutionary innovation from the sixth arch, giving the organism a flexible shunt to balance blood supply to and from gills and lungs according to environmental conditions.[well established][VHOG]
In the human heart, the pulmonary trunk (pulmonary artery or main pulmonary artery) begins at the base of the right ventricle. It is short and wide - approximately 5 cm (2 inches) in length and 3 cm (1.2 inches) in diameter. It then branches into two pulmonary arteries (left and right), which deliver deoxygenated blood to the corresponding lung[WP]
the tough fibrous layer surrounding the kidney which is covered in a thick layer of perirenal adipose tissue that functions to provide some protection from trauma and damage
provides some protection from trauma and damage.
The renal capsule relates to the other layers in the following order (moving from innermost to outermost): renal medulla renal cortex renal capsule perinephric fat (or 'perirenal fat') renal fascia paranephric fat (or 'pararenal fat') peritoneum (anteriorly), and transversalis fascia (posteriorly).[Wikipedia:Kidney_capsule]
Pulmonary veins are blood vessels that transport blood from the lungs to the heart[GO].
Any of the veins which collect blood from the lungs and some small vesicles received from the esophagus.[AAO]
One of two pairs of large vessels that return oxygenated blood from each lung to the left atrium of the heart. [TFD][VHOG]
the veins that return oxygenated blood from the lungs to the left atrium of the heart
A cranial nerve that originates from neurons in the medulla and in the cervical spinal cord.
A small motor nerve which emerges from the lateral wall of the medulla with the roots of the vagus nerve, and innervates a single pectoral suspensory muscle, the m.cucullaris.
Cranial nerve that innervates the sternocleidomastoid and trapezius complex of muscles. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-1, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]
Small motor nerve which innervates a single pectoral suspensory muscle, the m. cucullaris.[AAO]
Cranial nerves XI and XII evolved in the common ancestor to amniotes (non-amphibian tetrapods) thus totalling twelve pairs.[well established][VHOG]
In mice, the spinal branch of this motor nerve innervates the trapezius and the sternocleidomastoid muscles. The cranial branch joins the vagus nerve and innervates the same targets as the vagus nerve
FMA has distinct cranial and spinal parts - WP says 'Traditional descriptions of the accessory nerve divide it into two parts: a spinal part and a cranial part.[1] However, because the cranial component rapidly joins the vagus nerve, becoming an integral part of said nerve, modern descriptions often consider the cranial component to be part of the vagus nerve and not part of the accessory nerve proper.[2]
A nervous system structure composed primarily of nerve cell bodies (somas). May also include dendrites and the initial unmyelinated portion of axons.
Multi-tissue comprised of neurons, dendrites, axon terminals, glial cells, and capillaries.[TAO]
The most posterior of the three principal regions of the brain. In mammals and birds the hindbrain is divided into a rostral metencephalon and a caudal myelencephalon. In zebrafish, with the exception of the cerebellum, the ventral remainder of the metencephalon can be separated only arbitrarily from the more caudal myelencephalic portion of the medulla oblongata (From: Neuroanatomy of the Zebrafish Brain)[ZFA]. Organ component of neuraxis that has as its parts the pons, cerebellum and medulla oblongata[FMA].
Posterior part of the brain consisting of the cerebellum and medulla oblongata.[AAO]
The most posterior of the three principal regions of the brain, forming the rhombencephalon and all or most of the metencephalon. Kimmel et al, 1995.[TAO]
relationship loss: develops_from hindbrain neural tube (TAO:0007043)[TAO]
in MA, brainstem and hindbrain and part-of siblings under brain, consistent with FMA and NIF. See also notes for cerebellum. We weaken the relation in ABA to overlaps
An epithelium that is part of a bronchus [Automatically generated definition].
Muscle tissue that contains fibers that are divided by transverse bands into striations.
Voluntary muscle tissue arranged in bundles of fibers.[AAO]
A systemic artery that supplies the lung with with oxygenated blood.
rami bronchiales partis thoracicae aortae
Although there is much variation, there are usually two bronchial arteries that run to the left lung, and one to the right lung.
The pontine raphe nucleus is one of the raphe nuclei. It is located in the pontine tegmentum. [WP,unvetted].
Respiration organ that develops as an oupocketing of the esophagus.
Either of two organs which allow gas exchange absorbing oxygen from inhaled air and releasing carbon dioxide with exhaled air.[AAO]
Lungs had already developed as paired ventral pockets from the intestine in the ancestor of Osteognathostomata. (...) In actinopterygian fishes, apart from Cladistia, the ventral intestinal pocket migrates dorsally and becomes the swim-bladder, a mainly hydrostatical organ (reference 1); Comparative transcriptome analyses indicate molecular homology of zebrafish swimbladder and Mammalian lung (reference 2).[well established][VHOG]
respiration organ in all air-breathing animals, including most tetrapods, a few fish and a few snails. In mammals and the more complex life forms, the two lungs are located in the chest on either side of the heart. Their principal function is to transport oxygen from the atmosphere into the bloodstream, and to release carbon dioxide from the bloodstream into the atmosphere. This exchange of gases is accomplished in the mosaic of specialized cells that form millions of tiny, exceptionally thin-walled air sacs called alveoli. // Avian lungs do not have alveoli as mammalian lungs do, they have Faveolar lungs. They contain millions of tiny passages known as para-bronchi, connected at both ends by the dorsobronchi
Snakes and limbless lizards typically possess only the right lung as a major respiratory organ; the left lung is greatly reduced, or even absent. Amphisbaenians, however, have the opposite arrangement, with a major left lung, and a reduced or absent right lung [WP]
ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.210, DOI:10.1371/journal.pone.0024019 Zheng W, Wang Z, Collins JE, Andrews RM, Stemple D, Gong Z, Comparative transcriptome analyses indicate molecular homology of zebrafish swimbladder and Mammalian lung. PLoS One (2011)
An interconnected tubular multi-tissue structure contains fluid that is actively transported around the organism[ZFA]. Examples: vasculature of lung, vasculature of face.
see also: vascular system. Consider merging?
Anatomical structure that is part of an embryo.
Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[AAO]
Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[TAO]
Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[VSAO]
The truncus arteriosus and bulbus cordis are divided by the aorticopulmonary septum. The truncus arteriosus gives rise to the ascending aorta and the pulmonary trunk. The bulbus cordis gives rise to the smooth parts (outflow tract) of the left and right ventricles.
The dermis is a layer of skin between the epidermis (with which it makes up the skin) and subcutaneous tissues, and is composed of two layers, the papillary and reticular dermis[WP].
Consider adding a layer-of-skin grouping class for all skin layers
A collagenous layer of the skin subjacent to the epidermis and covering the hypodermis. It contains various types of cells (e.g. fibroblasts, pigment cells, nerve, blood vessels and scales. Le Guellec et al, 2004.[TAO]
When approaching controversies surrounding skin evolution, we need to remember that the skin consists of two layers, an epidermis and a dermis, not a single evolving structure. (...) It is little wonder that controversies about homology exist. If we think of the epidermis, the dermis, and their interactions as an evolving unit, then their specialized products (hair, feathers, and reptilian scales) are broadly homologous.[well established][VHOG]
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.231-232 see also p.209 and p.228 and Figure 6-1
Lowermost layer of the integumentary system in vertebrates. Types of cells that are found in the hypodermis are fibroblasts, adipose cells, and macrophages. It is derived from the mesoderm, but unlike the dermis, it is not derived from the dermatome region of the mesoderm. The hypodermis is used mainly for fat storage[WP].
A layer separating the inner face of the dermis from the subjacent muscle cells. It is covered on both sides by a basement membrane. It contains pigment cells. Le Guellec et al, 2004.[TAO]
A layer separating the inner face of the dermis from the subjacent muscle cells. It is covered on both sides by a basement membrane. It contains pigment cells[FMA:70544].
BTO has 'subcutis', as part of dermis. We follow FMA in having distinct classes for hypodermis and superficial fascia, and including these as part of the non-skin intgeument.
An organ that is located within the body cavity (or in its extension, in the scrotum); it consists of organ parts that are embryologically derived from endoderm, splanchnic mesoderm or intermediate mesoderm; together with other organs, the viscus constitutes the respiratory, gastrointestinal, urinary, reproductive and immune systems, or is the central organ of the cardiovascular system. Examples: heart, lung, esophagus, kidney, ovary, spleen.
An internal organ of the body; especially: one (as the heart, liver, or intestine) located in the great cavity of the trunk proper.[AAO]
general anatomical term in FMA. Note that we place the MA class here temporarily, although properly systems should be distinguished from organs.
A cardiac ventricle that is in the right side of the heart.
The muscular chamber on the right and in front of the left ventricle. It generally receives venous blood from the right atrium and conveys it into the pulmonary artery. [(1988)_Dorian_AF, Amsterdam, Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B._Anatomy, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier's_Encyclopaedic_Dictionary_of_Medicine][VHOG]
In mammals continuous with the pulmonary arteries
Cardiac chamber through which blood leaves the heart.
A chamber of the heart that receives blood from one or more atria and pumps it by muscular contraction into the arteries.[AAO]
In the primitive vertebrate heart the four chambers are: 1. Sinus venosus (...) 2. Atrium (...) 3. Ventricle (...) 4. Conus arteriosus (...)[well established][VHOG]
ISBN:978-0721676678 Romer AS, Vertebrate body (1970) p.428
A cardiac ventricle that is in the left side of the heart.
Thick-walled muscular chamber constituting the left border and apex of the heart. It receives oxygenated blood from the left atrium through the mitral orifice and send it off into the aorta. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
The vertebrate heart initially forms as a tube from a population of precursor cells termed the first heart field (FHF). Cells from the adjacent second heart field (SHF) are then progressively added to the developing heart. In avian and mammalian hearts, the FHF contributes mainly to the left ventricle, whereas the SHF gives rise to the outflow tract and large portions of the right ventricle and atria. Both fields arise from common mesodermal progenitors, although the detailed lineage relationships between FHF and SHF remain uncertain.[well established][VHOG]
DOI:10.1126/science.1190181 Stolfi A, Gainous TB, Young JJ, Mori A, Levine M, Christiaen L, Early chordate origins of the vertebrate second heart field. Science (2010)
The postcranial subdivision of skeleton structural components forming the long axis of the vertebrate body; in Danio, consisting of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins; in human consists of the bones of the vertebral column, the thoracic cage and the pelvis[ZFA+FMA].
Skeletal subdivision of the central body axis including vertebrae, notochord, ribs, and sternum.[VSAO]
The axial skeleton is formed by the vertebral column, a metameric, semi-flexible, arched bar located in the dorsal part of the trunk, and is formed by a series of cartilaginous or bony vertebrae. It provides suspension for the appendicular skeleton and protection for the spinal nerve cord.[AAO]
The post-cranial structural components forming the long axis of the vertebrate body; usually consists of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins.[TAO]
The axial musculoskeletal system represents the plesiomorphic locomotor engine of the vertebrate body, playing a central role in locomotion. In craniates, the evolution of the postcranial skeleton is characterized by two major transformations. First, the axial skeleton became increasingly functionally and morphologically regionalized. Second, the axial-based locomotion plesiomorphic for craniates became progressively appendage-based with the evolution of extremities in tetrapods.[well established][VHOG]
previous some AOs had used the term 'axial skeleton' to include the skull. This is being resolved (see tracker items above). Status: MA - fixed.
DOI:10.1186/1742-9994-8-4 Schilling N, Evolution of the axial system in craniates: morphology and function of the perivertebral musculature. Frontiers in Zoology (2011)
Subdivision of skeleton which which consists of all the skeletal elements in in the pectoral and pelvic appendage complexes[cjm].
Skeletal subdivision consisting of all the skeletal elements in the pectoral and pelvic appendage complexes.[VSAO]
Skeletal system that consists of the paired fins (pectoral or pelvic fins).[TAO]
The pectoral and pelvic girdles, which articulate with the axial skeleton, together with their associated limbs, the forelimbs and hind limbs, form the appendicular skeleton.[AAO]
ontologies differ in whether they treat the term appendicular skeleton as being the entire set of bones in the limbs, or whether the fore and hind limbs/fins are treated as seperate appendicular skeletons. Here we follow FMA, and treat the appendicular skeleton as the sum total of skeletal elements in the organism (this is evidenced by the fact that in FMA, skeleton of left/right upper/lower limb is part_of a appendicular skeleton, and subtypes of 'subdivision of appendicular skeleton'). We have separate classes such as 'skeleton of limb', and 'skeleton of hindlimb' for the 4 parts of the appendicular skeleton. In future the ZFA/TAO classes may be moved.
Cardiac septum which separates the right ventricle from the left ventricle.[FMA]
The partition separating the right and left ventricles of the heart. [TFD][VHOG]
The two most progressive vertebrate classes, the birds and mammals, have completed the ventricular septum and at long last have completely separated the two blood streams along the length of the major heart chambers. This development has obviously been brought about independently in the two cases, since mammals and birds have evolved independently from primitive reptiles.[well established][VHOG]
involves the recruitment of myocardial cells as well as of non- muscular mesenchymal cells (Kaufman and Bard, 1999)
ISBN:978-0721676678 Romer AS, Vertebrate body (1970) p.430
The organ covering the body that consists of the dermis and epidermis.
consider 'integumentary system' for invertebrates
MA uses the term skin to refer to what is called here: zone of skin
The thin membranous structure between the two heart atria or the thick muscular structure between the two heart ventricles.
'Terrestrial vertebrates have divided hearts in which septae separate the oxygenated and deoxygenated blood within the pulmonary and systemic circulations'
in GO, septum morphogenesis is part of cardiac chamber morphogenesis; need to add axioms to infer this
Organism subdivision which is the part of the body posterior to the cervical region (or head, when cervical region not present) and anterior to the caudal region. Includes the sacrum when present.
Organism subdivision that is the part of the body posterior to the head and anterior to the tail.[AAO]
Organism subdivision which is the part of the body posterior to the head and anterior to the tail.[TAO]
The sensory system subserving the sense of vision.
Sensory system responsible for the perception of spatial orientation and auditory stimuli.
The sensory system used for balance and hearing.[AAO]
A portion of smooth muscle tissue that is part of an artery [Automatically generated definition].
A paired organ of the urinary tract which has the production of urine as its primary function.
One of either of a pair of structures lying on either side of the dorsal aorta in which fluid balance is regulated and waste is excreted out in the form of urine.[AAO]
kidney
An ovary that is part of a right side of organism [Automatically generated definition].
An ovary that is part of a left side of organism [Automatically generated definition].
In some elasmobranchs, the left ovary does not mature, with only the right ovary fully developing. In the primitive jawless fish, and some teleosts, there is only one ovary, formed by the fusion of the paired organs in the embryo
In mammals, the pronephros is the first of the three embryonic kidneys to be established and exists only transiently. In lower vertebrates such as fish and amphibia, the pronephros is the fully functional embryonic kidney and is indispensible for larval life[GO].
A kidney formed of nephric tubules arising in the anterior region of the nephric ridge; forms only as a transient embryonic structure. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Kardong_KV, Vertebrates:_Comparative_Anatomy, p.748][VHOG]
Organ that serves as a transient kidney, providing osmoregulation during early developmental stages and then degenerating during metamorphosis.[AAO]
The embryonic kidney, present at the level of the third somite, is composed of two glomeruli fused at the midline, two pronephric tubules, and paired bilateral pronephric ducts that modify the composition of the blood filtrate before delivering it to the cloaca for excretion.Kimmel et al, 1995.[TAO]
In all vertebrate embryos, the kidney begins with the differentiation of a few renal tubules from the anterior end of the nephric ridge overlying the pericardial cavity. (...) This early-developing embryonic kidney is called the pronephros.[well established][VHOG]
Once the more complex mesonephros forms the pronephros undergoes apoptosis in amphibians. In fishes the nephron degenerates but the organ remains and becomes a component of the immune system[Wikipedia:Pronephros]. // TODO - check developmental relationships. Note that we previously include the ZFA/XAO terms under the more specific 'pronephric kidney', but these are now merged. TODO GCI: relationship: capable_of GO:0030104
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.637
A a collection of brainstem nuclei that functions in multiple aspects of hearing and is an important component of the ascending and descending auditory pathways of the auditory system.
In mice, the superior olivary nucleus is a small cylindrical mass on the dorsal surface of the lateral part of the trapezoid body of the pons, and it is situated immediately above the inferior olivary nucleus. It receives projections from the cochlear nucleus and thus is involved in the perception of sound[GO:0021718]
The SOC displays a significant interspecies variation, being largest in bats and rodents and smaller in primates.
superior olivary nucleus (Barr & Kiernan)
The locus ceruleus is a dense cluster of neurons within the dorsorostral pons. This nucleus is the major location of neurons that release norepinephrine throughout the brain, and is responsible for physiological responses to stress and panic[GO]. Bluish region in the superior angle of the fourth ventricle floor, corresponding to melanin-like pigmented nerve cells which lie lateral to the ponto-mesencephalic central gray (griseum centrale). It is also known as nucleus pigmentosus pontis[GAID].
TODO - check ZFA/pons. also GO says part of dorsorostral pons
Nucleus containing parasympathetic neurons giving rise to the parasympathetic division of the facial nerve, innervating the salivary glands (Brodal, Neurological Anatomy, 3rd ed., 1981, pg 703).
The endocardium is an anatomical structure comprised of an endothelium and an extracellular matrix that forms the innermost layer of tissue of the heart, and lines the heart chambers[GO].
Layer that lines the lumen of the heart.[TAO]
Part of the heart comprised of thin serous membrane, composed of endothelial tissue, that lines the interior of the heart.[AAO]
Tunica intima which has as its parts the endothelium of endocardium and the fibroelastic connective tissue that surrounds the cavity of a cardiac chamber.
fixed in GO to reflect FMA. See email to David/Varsha June 18 2010
Lung which consists of the right upper lobe, middle lobe and right lower lobe.[FMA]
Lungs had already developed as paired ventral pockets from the intestine in the ancestor of Osteognathostomata.[well established][VHOG]
ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.210
Lung which consists of the left upper lobe and left lower lobe.[FMA]
the upper conducting airways of the lung; these airways arise from the terminus of the trachea
Each of the two primary divisions of the trachea leading respectively into the right and the left lung. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
In humans, the main bronchus is histologically identical to trachea; 2ary and 3ary bronchi are not; epithelium becomes simple columnar, goblet cell number decreases, elastic fibers in lamina propria increases, distribution more uniform. Muscular layer between mucosa and submucosa appears. cartilage rings become discontinuous plates connected by fibrous connective tissue
A portion of adipose tissue that is part of the hypodermis, beneath the dermis.
the superficial portion of the subcutaneous tissue which is specialized for fat storage[MP:0011156]
Anatomical cluster consisting of the hematopoietic system and the lymphoid system, or its analogs.
in FMA intergument = skin+superficial fascia(hypodermis), skin=dermis+epidermis+hair_nail. Note that the definition provided here excludes the more general sense of the term 'integument' used in invertebrates; consider 'integumental system'. Note that the VSAO class appears to include adnexa by its definition.
Anatomical system that protects the body from damage, comprising the skin and its appendages.[AAO]
Surface structure that is the outer protective covering of the body.[VSAO]
The outer protective barrier that separates the animal from its aquatic environment. Le Guellec et al, 2004.[TAO]
Vasculature that is part of a head [Automatically generated definition].
A vasculature that is part of a trunk [Automatically generated definition].
Vasculature that is part of the eye region.
not part of the eye in ZFA. Note this changed to a blood vessel in ZFA
Anatomical system that consists of the muscular and skeletal systems.
Anatomical system that provides locomotion and physical support to the organism.[AAO]
There are more than 50,000 extant vertebrate species, representing over 500 million years of evolution. During that time, the vertebrate musculoskeletal systems have adapted to aquatic, terrestrial, fossorial, and arboreal lifestyles, while simultaneously retaining functionally integrated axial and appendicular skeletal systems.[well established][VHOG]
DOI:10.1002/jez.b.21246 Shearman RM, Burke AC, The lateral somitic frontier in ontogeny and phylogeny. Journal of Experimental Zoology (2009)
Nonsynovial joint in which the articulating bones or cartilages are connected by cartilage. Examples: Spheno-occipital synchondrosis, first sternocostal joint, pubic symphysis.[FMA]
Joint in which the articulating bones or cartilages are connected by an articular capsule which encloses a synovial membrane and a synovial cavity. Examples: Temporomandibular joint, knee joint.[FMA]
Is a joint that is located at the point of contact of articulating bones allowing movement. The joint has a capsule containing synovial fluid surrounding the articulating bone surfaces.[TAO]
The part of the coelemic cavity lumen that is enclosed by the walls of the thorax.
In many species, the diaphragm separates thoracic and abdominal cavities
Part of the central nervous system located in the vertebral canal continuous with and caudal to the brain; demarcated from brain by plane of foramen magnum. It is composed of an inner core of gray matter in which nerve cells predominate, and an outer layer of white matter in which myelinated nerve fibers predominate, and surrounds the central canal. (CUMBO)
TODO - add superclass to unify with VNC?
Part of the central nervous system which descends from the hindbrain within the vertebral column.[AAO]
Endoskeletal elements that encase the brain, nose, inner ear[cjm]. that part of the neurocranium formed by endochondral ossification and comprising the bones of the base of the skull[TFD].
we follow the standard evolutionary classification and treat this as endoskeletal. This means what MA calls 'chondrocranium' must in fact be neurocranium, as it includes parts of the dermatocranium (e.g. frontal, parietal)
Anatomical cluster that is part of the cranium and composed of cartilage and cartilage replacement bones.[AAO]
Anatomical cluster that is part of the cranium and composed of cartilage and cartilage replacement bones.[TAO]
covers the brain dorsally in chondrichthyans
An organ that houses olfactory neurons and is responsible for the sense of smell. Examples include the vertebrate nose and the Drosophila dorsal organ.
An olfactory organ overlaps with the olfactory system, because some parts of the nose (e.g. nasal skeleton) are parts of the skeletal system, which is spatially disjoint
fma general anatomical term. xao has no subtypes (but Johnstons organ develops from this). An olfactory organ overlaps with the olfactory system, because some parts of the nose (e.g. nasal skeleton) are parts of the skeletal system, which is spatially disjoint
A composite substructure of the brainstem that consists of the midbrain reticular formation, the pontine reticular formation and the medullary reticular formation ( Carpenter-1983 ).
this class denotes the generic structure, and not a specific one such as medullary or pontine reticular formation.
It is essential for governing some of the basic functions of higher organisms, and is one of the phylogenetically oldest portions of the brain.
FMA has a spinal cord reticular formation but we follow NNs (classical) to restrict this to brainstem structures. This means we also include the MA class for brainstem reticular formation here. FMA has subtypes of reticular formation but we treat this as a composite structure
Stalk-like part of the brain that includes amongst its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain[ZFA,MP,generalized].
Multi-tissue structure that has as its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain.[TAO]
Multi-tissue structure that has as its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain[ZFA,adopted][ZFA:0001707].
the stalk-like part of the brain that comprises the midbrain (aka mesencephalon), the pons (aka pons Varolii), and the medulla oblongata, and connects the cerebral hemispheres with the cervical spinal cord[MP]
'brainstem' is a loose term that sometimes refers to the ventral parts o the brain except for any part of the telencephalon - sometimes it includes the diencephalon or subpallial telencephalon structures (ISBN10:0471888893). Here we use it in a more restriced sense, to include only the medulla oblongata, pons (when present) and the midbrain tegmentum (following the ZFA definitions).
A neural nucleus that is part of the brain.
The ridge-shaped grey matter of the spinal cord that extends longitudunally through the center of each half of the spinal cord, and are largely or entirely composed of nerve cell bodies and their dendrites and some supportive tissue.
The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities.
check the FMA placement here; ncit placement of body cavity here probably not correct
Anatomical space, part of the trunk that contains the pericardial and pleuroperitoneal cavities[ZFA].
The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities[BTO].
In mammals it forms the peritoneal, pleural, and pericardial cavities
Any muscle organ that is part of a back [Automatically generated definition].
The urethra is a renal system organ that carries urine from the bladder to outside the body. The epithelium is the tubular, planar layer of cells through which the urine passes..
A flexible rod-shaped body found in embryos of all chordates. It is composed of cells derived from the mesoderm and defines the primitive axis of the embryo. In some chordates, it persists throughout life as the main axial support of the body, while in most vertebrates it becomes the nucleus pulposus of the intervertebral disc. The notochord is found ventral to the neural tube.
Avascular multi-tissue structure composed of large vacuolated epithelial cells (chordablasts) and perichordal fibrous tissue.[VSAO]
Rod-like principal supportive element of the embryo and larva, present in the midline just ventral to the neural tube, and differentiating during the segmentation period to form large vacuolated epithelial cells and a surrounding a sheath of fibrous and elastic layers. Layering of the sheath may differ in structure, thickness and development among groups; in cypriniforms there are actually three very thin layers to the sheath. A functional, well developed notochord is present throughout life in certain basal fish groups but not in cypriniforms. Kimmel et al, 1995.[TAO]
Slender rod of fibrous connective tissue surrounding a core of fluid-filled cells of mesodermal origin; it lies above the gut and directly beneath the spinal cord. The notochord is present during early development and in a few cases it is retained through life; however, usually the notochord is replaced by the vertebral column.[AAO]
relationship type change: differentiates_from mesoderm (AAO:0000304) CHANGED TO: develops_from mesoderm (UBERON:0000926)[AAO]
(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (3) a stiff, longitudinal rod of turgid cells along the dorsal part of the body that is called a notochord (...).[well established][VHOG]
In between vertebra the notochord becomes the nucleus pulposus, under it degenerates, and at anterior end in some species its tissue merges with some of the cranial bones.. Some organisms retain a post-embryonic notochord.
The notochord appears early in embryogeny and plays an important role in promoting or organizing the embryonic development of nearby structures. In most adult chordates the notochord disappears or becomes highly modified. In some non-vertebrate chordates and fishes the notochord persists as a laterally flexible but incompressible skeletal rod that prevents telescopic collapse of the body during swimming[TOLWEB]
Somites are spheres of epithelial cells that form sequentially along the anterior-posterior axis of the embryo through mesenchymal to epithelial transition of the presomitic mesoderm.
currently classified as an epithelial vesicle, consistent with EHDAA2 and https://github.com/obophenotype/uberon/wiki/The-neural-crest. Consider making 'somitic mesoderm' a separate term and correlate with regionalization processes. Consider moving ZFA term to 'trunk somite' as it is part of the trunk
Post-cranial axial segments which form sclerotome and dermomyotome.[AAO]
Undifferentiated mesodermal components of early trunk or tail segments or metameres, derived from paraxial mesoderm; forms myotomes, sclerotomes and perhaps dermatomes. Kimmel et al, 1995.[TAO]
relationship loss: develops_from paraxial mesenchyme (TAO:0000942)[TAO]
relationship type change: OBO_REL:part_of trunk (TAO:0001115) CHANGED TO: develops_from trunk (UBERON:0002100)[TAO]
relationship type change: part_of paraxial mesoderm (AAO:0010568) CHANGED TO: develops_from paraxial mesoderm (UBERON:0003077)[AAO]
(...) cephalocordates and craniates belong to a group known as Somitichordata. Somitichordate synapomorphies include (1) somites (...) (reference 1); The idea that the last common ancestor of bilaterian animals (Urbilateria) was segmented has been raised recently on evidence coming from comparative molecular embryology (reference 2).[well established][VHOG]
When the somite becomes segmented from the segmental plate, it is composed of an epithelial sac enclosing mesenchymal somitocoel cells. Thereafter the somite differentiates into two parts, the ventro-medial mesenchymal sclerotome and the dorso-lateral epithelial dermomyotome. This change in the epithelial somite depends on surrounding tissue [PMID:15906248]
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.40, DOI:10.1093/icb/43.1.137 Balavoine G, Adoutte A, The segmented urbilateria: a testable scenario. Integrative and Comparative Biology (2003)
Anatomical system that consists of the glands and parts of glands that produce exocrine secretions and help to integrate and control bodily metabolic activity. Exocrine glands are glands that secrete their products (hormones) into ducts (duct glands). They are the counterparts to endocrine glands, which secrete their products (hormones) directly into the bloodstream (ductless glands) or release hormones (paracrines) that affect only target cells nearby the release site. [Wikipedia].
An arterial trunk which is continuous with the heart and branches into the pulmonary arteries.
An arterial trunk with origin from the right ventricle of the heart, and dividing into the right and left pulmonary arteries, which enter the corresponding lungs and branch with the bronchi. [TFD][VHOG]
As in birds, the conus arteriosus split during embryonic development in mammals to produce the pulmonary trunk and single aortic trunk of the adult.[well established][VHOG]
A specialized region of ectoderm found between the neural ectoderm (neural plate) and non-neural ectoderm and composed of highly migratory pluripotent cells that delaminate in early embryonic development from the dorsal neural tube and give rise to an astounding variety of differentiated cell types[MP].
consider including subclasses for pre- and post- migratory (e.g. sheets/paths/streams).
A cell population arising from the dorsolateral aspect of the central nervous system primordium during the segmentation period, and later migrating along stereotyped pathways to give rise to a diverse and well-defined set of cell types including pigment cells, peripheral neurons and glia, and head cartilage. Kimmel et al, 1995.[TAO]
Migratory cell population which delaminates from neural tube, borders surface ectoderm and neural ectoderm, and gives rise to many different tissue types.[AAO]
A well developed neural crest population is present in lampreys (Horigome et al. 1999 ; Tomsa & Langeland, 1999) and gnathostomes. chordate fossils from the early Cambrian (Yunnanozoan and Haikouella) with apparent neural-crest derived structures (pharyngeal denticles and pharyngeal skeletons resembling the striped mucocartilage of the branchial bars in lamprey ammocoete larvae), suggests that neural crest arose very early in vertebrate evolution (Chen et al. 1999; Holland & Chen, 2001). The invertebrate chordates apparently lack defini- tive neural crest. One marker of migrating neural crest in some vertebrates, the antibody HNK1, does not recognize any cells in amphioxus embryos (Holland, unpublished). Even so, in both amphioxus and tunicates, cells at the edges of the neural plate and adjacent nonneural ectoderm share some properties of neural crest[PMID:11523831]
We conclude that the neural crest is a vertebrate novelty, but that neural crest cells and their derivatives evolved and diversified in a step-wise fashion - first by elaboration of neural plate border cells, then by the innovation or co-option of new or ancient metazoan cell fates.[well established][VHOG]
Gene notes: Many factors and genes, such as Pax3 (Tremblay et al., 1995), slug (Nieto et al., 1994), AP-2 (Zhang et al., 1996; Schorle et al., 1996), and Wnt-1/3a (Ikeya et al., 1997) are expressed in the dorsal most region of the neural tube, and have been shown to be involved in the generation of neural crest cells.
DOI:10.1111/j.1469-7580.2012.01495.x Hall BK, Gillis JA, Incremental evolution of the neural crest, neural crest cells and neural crest-derived skeletal tissues. J Anat (2012)
distinction between abdomen muscle and abdomen musculature
Embryonic ectoderm that gives rise to nervous tissue.
(...) the ability of ectoderm to produce neuronal cells is a general metazoan feature.[well established][VHOG]
we prefer neurectoderm to neural ectoderm since placodal ectoderm is not classified here
epithelium tubi neuralis; neuroectoderma
the middle layer of the heart, comprised mainly of striated cardiac muscle fibers
TODO - check 'Myocardum proper' in FMA. We superclass the more generic class for now. FMA has is_a muscle layer - should we add this? ZFA and BTO both have is_a 'cardiac muscle' (tissue?). But in U we also follow FMA and have cardiac muscle tissue of myocardium (there is also Fibrocollagenous connective tissue of myocardium), which would be identical (see issue-10). Note that GO also treats left/right ventricular cardiac muscle tissue synonymous with ventricular myocardium
Robust muscular tunic of the heart which forms the basic part of its walls. Its external surface is covered by the pericardium and its internal one by the endocardium. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
The middle layer of the heart, consisting of cardiac muscle.[AAO]
The cardiac conduction system consists of specialized cardiomyocytes that regulate the frequency of heart beat[GO]
EHDAA2 divides the system from the tissue
The fish heart displays clear polarity of contraction in a posterior-to-anterior direction. The contraction waves originate in the sinus venosus and terminate in the conus arteriosus. The nodal phenotype persists in the inflow region of the heart, varying from the venosinus to the sinoatrial junctional areas in different species . Similar to the mammalian situation, pacemaker tissue with a lower intrinsic rhythmicity is also found at the atrioventricular junction.[uncertain][VHOG]
DOI:10.1152/physrev.00006.2003 Moorman AFM, Christoffels VM, Cardiac Chamber Formation: Development, Genes, and Evolution. Physiological Reviews (2003)
The lower segment of the trunk, inferioposterior to the abdomen proper, in the transition area between the trunk and the lower limbs.
MA and FMA differ in what they consider to be parts of the pelvis. MA includes ureter, urethra, urinary bladder, reproductive organs
A gland that secretes products (excluding hormones and other chemical messengers) into ducts (duct glands) which lead directly into the external environment[WP]. Typical exocrine glands include sweat glands, salivary glands, mammary glands, stomach, liver, pancreas
Currently this is logically defined by the system it belongs to, but a better system may be base this on presence/absence of ducts. However, the dual nature of the liver should be taken into consideration here. Consider adding subclasses
Endocrine glands are glands of the endocrine system that secrete their products directly into the circulatory system rather than through a duct.[WP, modified].
Any skeletal muscle that is part of the head region.
defined generically so could in theory encompass FBbt:00003260 'skeletal muscle of head', or the muscle of a starfish Aristotle's lantern, but we restrict this to craniates. Skeletal muscles of the head originate from the non-segmented head mesoderm (Noden, 1983; Wachtler et al., 1984)
Any muscle that is part of the cervical (neck) region.
Muscle (organ) which is a part of the abdomen. Examples: external oblique, rectus abdominis.
Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance.
One of the four types of tissue in traditional classifications. It is largely a category of exclusion rather than one with a precise definition, but there are certain characteristics shared by all or most tissues in this category, such as involvement in structure and support, derived from mesoderm, and characterized largely by the traits of non-living tissue.[AAO]
Portion of tissue that consists of mesodermally derived cells and intercellular matrix comprised of protein fibers and carbohydrates, which supports, ensheathes and binds together other tissues.[TAO]
Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance.[VSAO]
Muscle tissue is a contractile tissue made up of actin and myosin fibers[GO].
One of the four types of tissue in traditional classifications. Tissue that contains cells with contractile filaments that move past each other and change the size of the cell. Muscle tissue also is separated into three distinct categories.[AAO]
Vertebrate muscle is categorized into three major muscle types defined by their structural and functional properties: skeletal, cardiac and smooth. In Dmel the counterparts are somatic, heart/cardiac and visceral. Here we take a cell type based approach.
Anatomical system that is involved in the production of hematopoietic cells.
Anatomical system that consists of the blood and blood forming tissues.[AAO]
Zebrafish developmental hematopoiesis shows close correspondence to the development of the mammalian hematopoietic system and is regulated by conserved molecular pathways.[well established][VHOG]
In humans this is primarily the bone marrow, spleen, tonsils, and lymph nodes
DOI:10.1016/j.coph.2010.05.004 Ellett F, Lieschke GJ, Zebrafish as a model for vertebrate hematopoiesis. Current Opinion in Pharmacology (2010)
The autonomic nervous system is composed of neurons that are not under conscious control, and is comprised of two antagonistic components, the sympathetic and parasympathetic nervous systems. The autonomic nervous system regulates key functions including the activity of the cardiac (heart) muscle, smooth muscles (e.g. of the gut), and glands[GO].
Nervous system including a portion of the central and peripheral systems and presiding over the control and coordination of the vegetative functions of the organism. It innervates smooth and cardiac muscles and glandular tissues and is responsible for many actions which are more or less automatic (e.g. secretion, vasoconstriction etc.). It consists of the sympathetic and parasympathetic nervous systems. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
Part of the peripheral nervous system which regulates involuntary functions of the body and consists of the sympathetic and parasympathetic system.[AAO]
From comparative analyses of craniate brains, a morphotype of the brain in the earliest craniate stock can be constructed. In marked contrast to cephalochordates, the ancestral craniate morphotype had a plethora of unique features, which included a telencephalon with pallial and subpallial parts, paired olfactory bulbs with substantial projections to most or all of the telencephalic pallium, paired lateral eyes and ears, a lateral line system for both electroreception and mechanoreception, spinal cord dorsal root ganglia, and an autonomic nervous system.[well established][VHOG]
FMA splits this into peripheral and nervous parts; GO has ANS directly under NS; PNS is a sib
autonomic division of peripheral nervous system
autonomic part of peripheral nervous system
divisio autonomica systematis nervosi peripherici
pars autonomica systematis nervosi peripherici
DOI:10.1002/1097-0185(20000615)261:3<111::AID-AR6>3.0.CO;2-F Butler AB, Chordate evolution and the origin of craniates: An old brain in a new head. AnaT Rec (New Anat) (2000)
Connected anatomical system that forms a barrier between an animal and its environment. In vertebrates, the integumental system consists of the epidermis, dermis plus associated glands and adnexa such as hair and scales. In invertebrates, the integumental system may include cuticle.
(...) the integument of many tetrapods is reinforced by a morphologically and structurally diverse assemblage of skeletal elements. These elements are widely understood to be derivatives of the once all-encompassing dermal skeleton of stem-gnathostomes (...).[well established][VHOG]
Skeletal tissue that is avascular, rich in glycosaminoglycans (GAGs) and typically includes chondrocytes within isolated lacunae. Cartilage tissue is deposited by chondroblasts.
A type of dense connective tissue. It is composed of cells called chondrocytes which are dispersed in a firm gel-like ground substance, called the matrix. Cartilage is avascular (contains no blood vessels) and nutrients are diffused through the matrix. Cartilage is found in the joints, the rib cage, the ear, the nose, in the throat and between intervertebral disks. It makes up virtually the entire skeleton in chondrichthyes.[AAO]
Portion of tissue which is connective tissue composed of collagen and/or elastin fibers and chondrocytes. Cartilage is avascular and provides both skeletal functions and a framework upon which bone is deposited.[TAO]
Skeletal tissue that is avascular, rich in glycosaminoglycans (GAGs) and typically includes chondrocytes within isolated lacunae. Cartilage tissue is deposited by chondroblasts.[VSAO]
Phylogenetic analysis suggests that cartilage arose independently in cnidarians, hemichordates, vertebrates, arthropods, annelids, brachiopods, and molluscs - or a common ancestor of brachiopods and molluscs (...). Analyses of cartilage as a tissue and of the development of invertebrate cartilages are consistent with homology between invertebrate and vertebrate cartilage. From the discussion above, it will be clear that understanding genetic changes underlying cartilage evolution is key to determining whether the multiple origins of cartilage represent parallel evolution.[well established][VHOG]
Previous: "A portion of connective tissue dominated by extracellular matrix containing collagen type II and large amounts of proteoglycan, particularly chondroitin sulfate[GO]. Regular connective tissue, which consists of chondrocytes and related cells, the intercellular matrix of which is chondrified. Examples: hyaline cartilage, fibrocartilage, elastic cartilage[FMA]. an avascular supporting and articular skeletal tissue. It also functions as the primary endoskeletal support in vertebrate embryos. Cartilage is deposited by and is composed of chondroblasts and chondrocytes separated by an extracellular matrix, which may or may not mineralize depending on cartilage type, age, or taxon[Hall and Witten]." See also FMA:71500 Set of cartilages, FMA:55107 Cartilage organ, FMA:12264 Articular cartilage. // elements made from cartilage, cartilage-like, or chondroid tissues evolved in invertebrates[H&W]
DOI:10.1111/j.1525-142X.2011.00520.x Hall BK, Parallelism, deep homology, and evo-devo. Evolution and Development (2012)
A gland that is part of a skin of body [Automatically generated definition].
check FMA, use plural for now as general class not there
An epithelium that is part of the mouth and lines the oral cavity, typically stratified squamous, and may be para-, ortho- or non- keratinized. Primary barrier between oral environment and deeper tissues
consider including separate class for developmental structure (adult human is stratified; in EHDAA2 is unilaminar)
The epithelium that lines the oral cavity. The oral epithelium epithelial cells with many short microvilli as well as mucous cells, rodlet cells and taste buds[ZFIN:ZDB-PUB-060921-12, ZFIN:ZDB-PUB-091204-24].
the avian oral epithelium has the developmental capacity to initiate tooth developmental programs with underlying grafts of non-avian oral ectomesenchyme
A blood vessel that is part of a choroid [Automatically generated definition].
cannot find singular in FMA, using Set class
The mucous secreting gland associated with the mucuous membrane lining the uterus.
A tributary of the iliac vein that drains the urinary bladder.
Clear to pale yellow watery secretions from the glands lining the small intestine walls. Secretion is stimulated by the mechanical pressure of partly digested food in the intestine.
Skeletal tissue with a collagen-rich extracellular matrix vascularized, mineralized with hydroxyapatite and typically including osteocytes located in lacunae that communicate with one another by cell processes (in canaliculi). Bone is deposited by osteoblasts.
see https://github.com/obophenotype/uberon/issues/27
Skeletal tissue with a collagen-rich extracellular matrix vascularized, mineralized with hydroxyapatite and typically including osteocytes located in lacunae that communicate with one another by cell processes (in canaliculi). Bone is deposited by osteoblasts.[VSAO]
An epithelium that is part of a iris [Automatically generated definition].
Replacement bone that forms within cartilage.
Replacement bone that forms within cartilage.[VSAO]
some structures, e.g. in ZFA are both intramembrane and endochondral
Connective tissue composed of elastic fibers.
The middle layer of an artery or vein. [WP,unvetted].
May be composed of smooth muscle and elastic tissue
The innermost layer of a blood vessel which is a lining of endothelial cells facing the lumen[Kardong].
the FMA class represents a more generic layer which is the superclass of the layer found in both blood vessels and lymph vessels (and also endocardium) - we should probably follow this structure
the FMA class represents a structure which may have both epithelium and fibroelastic connective tissue as parts
The tunica intima (or just intima) is the innermost layer of an artery or vein. It is made up of one layer of endothelial cells and is supported by an internal elastic lamina. The endothelial cells are in direct contact with the blood flow. The inner coat (tunica intima) can be separated from the middle by a little maceration, or it may be stripped off in small pieces; but, on account of its friability, it cannot be separated as a complete membrane. It is a fine, transparent, colorless structure which is highly elastic, and, after death, is commonly corrugated into longitudinal wrinkles. The inner coat consists of: A layer of pavement endothelium, the cells of which are polygonal, oval, or fusiform, and have very distinct round or oval nuclei. This endothelium is brought into view most distinctly by staining with silver nitrate. A subendothelial layer, consisting of delicate connective tissue with branched cells lying in the interspaces of the tissue; in arteries of less than 2 mm. in diameter the subendothelial layer consists of a single stratum of stellate cells, and the connective tissue is only largely developed in vessels of a considerable size. An elastic or fenestrated layer, which consists of a membrane containing a net-work of elastic fibers, having principally a longitudinal direction, and in which, under the microscope, small elongated apertures or perforations may be seen, giving it a fenestrated appearance. It was therefore called by Henle the fenestrated membrane. This membrane forms the chief thickness of the inner coat, and can be separated into several layers, some of which present the appearance of a network of longitudinal elastic fibers, and others a more membranous character, marked by pale lines having a longitudinal direction. In minute arteries the fenestrated membrane is a very thin layer; but in the larger arteries, and especially in the aorta, it has a very considerable thickness. [WP,unvetted].[Wikipedia]
an organ that functions as a secretory or excretory organ
In amniote animal embryology, the epiblast is a tissue type derived either from the inner cell mass in mammals or the blastodisc in birds and reptiles. It lies above the hypoblast. In mammalian embryogenesis, the columnar cells of the epiblast are adjacent to the trophoblast, while the cuboidal cells of the hypoblast are closer to the blastocoele. The epiblast, whilst referred to as the primary ectoderm, differentiates to form all three layers of the trilaminar germ disc in a process called gastrulation[WP]. The outer of the two layers of the blastoderm that form during gastrulation, corresponding to primitive ectoderm during gastrulation and to the definitive ectoderm after gastrulation[ZFA]
MP says - tissue that gives rise to the ectoderm, endoderm and mesoderm of the embryo proper. In HOG, epiblast is part of primitive streak/blastpore, which is inconsistent with the MP definition of primitive streak as a ridge of the epiblast. Note that these terms, epiblast and hypoblast, are also used to describe layers of the avian embryonic blastoderm, but the layers so-named seem to be altogether different in these two kinds of vertebrate embryos(CVS). Consider obsoleting this as a grouping class
In pregastrula zebrafish embryos, the epiblast is an inverted cup of cells that sits on top of a large yolk cell. (...) In amniote embryos (mammals and birds), gastrulation initiates in an epithelial layer called the epiblast. Cells in the epiblast undergo an epithelial to mesenchymal transition (EMT), migrate through the primitive streak (PS), and incorporate in the middle (mesoderm) or outer (endoderm) layer. The presumptive definitive endoderm (DE) cells invade and displace an outer layer of extraembryonic tissue cells, the hypoblast in chick and the visceral endoderm (VE) in mouse, which form supporting structures such as the yolk sac.[uncertain][VHOG]
DOI:10.1146/annurev.cellbio.042308.113344 Zorn AM, Wells JM, Vertebrate endoderm development and organ formation. Annual Review of Cell Developmental Biology (2009)
One of a series of paired bulges that develop along the lateral walls of the foregut. The pharyngeal arches have developmental contributions from endoderm, mesoderm, and neural crest cells and are separated by anterior lateral endoderm out-pockets known as pharyngeal pouches.
One of a series of bony or cartilaginous arches that develop in the walls of the mouth cavity and pharynx of the embryo.[AAO]
A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down.[well established][VHOG]
Numbered cranial to caudal. different in mammals. branchial arch = ZFA:0001613 pharyngeal arch 3-7. generally gill arch 1 = pharyngeal arch 3. terminology varies as to whether branchial arch follows gill or pharyngeal numbering
DOI:10.1111/j.1469-7580.2005.00472.x Graham A, Okabe M and Quinlan R, The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat (2005)
Ectodermal placode that develops in the head into a part of the sensory nervous system. With a few exceptions (lens, adenohypophyseal), cranial placodes are neurogenic.
Comparisons of developmental gene expression suggest that the anterior ectoderm in amphioxus may be homologous to the vertebrate olfactory placode, the only vertebrate placode with primary, not secondary, neurons
The term placode or placodes also applies to developing organs such as teeth, mammary glands, hair follicles, feathers and scales. We include a separate parent class for this. to avoid confusion, we include neurogenic placode as a subclass
Anatomical space which contains portions of one or more body substances and is bounded by the internal surface of one maximally connected anatomical structure. Examples: cranial cavity, pharyngeal recess space, nasal cavity, tooth socket, cavity of serous sac, lumen of stomach, lumen of artery, fornix of vagina.
The cavity that is enclosed by the central nervous system. In vertebrates this is the cavity that includes as parts ventricular cavities and the central canal of the spinal cord that develops from the lumen of the neura tube
cavity of ventricular system of neuraxis
Anatomical divisons of the brain according to one or more criteria, e.g. cytoarchitectural, gross anatomy. Parts may be contiguous in 3D or not, e.g., basal ganglia.
A nucleus of brain that is part of a trigeminal nuclear complex.
massive inconsistencies between GO, MA, wikipedia. Part of pons in MA, but this leads to inconsistencies with ABA.
nucleus tractus mesencephali nervi trigeminalis
A sensory epithelium that is part of a gustatory system.
Dorsal portion of the pons, containing cranial nervee nuclei, ascending and descending tracts and reticular nuclei. It is continuous with the reticular formation of the medulla (Carpenter, A Core Text of Neuroanatomy, 3rd ed, 1985, pg 133).
involved in the initiation of REM sleep [Wikipedia:Pontine_tegmentum]
A wall, dividing a cavity or structure into smaller ones[WP].
A thick plate of cells derived from the neural ectoderm in the head region of the embryo that develops into the olfactory region of the nasal cavity.
We conclude this section by listing some of the many synapomorphies of craniates, including (...) (2) neurogenic placodes (...).[well established][VHOG]
Olfactory placodes are the only ectodermal placodes to produce glia, a cell type typically derived from neural crest // Note that NBK53171 classifies this as non-neurogenic
An epithelial sac of invaginated ectoderm formed from the otic placode that gives rise to the structures of the inner ear[MP]
Epithelial sac present beside the fifth rhombomere; forms the semicircular canals dorsally and the otolith organs ventrally, and houses the acoustico-vestibular sensory epithelia (maculae) of hair cells. Kimmel et al, 1995. (Also see Anatomical Atlas entry for ear by T. Whitfield.)[TAO]
One of the paired sacs of invaginated ectoderm that develop into the membranous labyrinth of the internal ear. [Biology_online][VHOG]
The inner ear develops embryonically in all vertebrates as an invagination of the ectodermal otic placode to form an otic vesicle.[well established][VHOG]
MP defines as epithelial sac, but EHDAA defines as multi-tissue; See https://github.com/obophenotype/uberon/issues/1305
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.413
The part of the brain that is the morphological boundary between the midbrain and hindbrain and that is the location of an organizing center which patterns the midbrain and hindbrain primordia of the neural plate.
consider adding class for organizer. Consider adding separate class for isthmus as a structure
Lampreys also have an MHB [midbrain hindbrain boundary], expressing a similar repertoire of regulatory gene cognates as in gnathostomes.[well established][VHOG]
DOI:10.1016/j.ydbio.2005.02.008 Murakami Y, Uchida K, Rijli FM and Kuratani S, Evolution of the brain developmental plan: Insights from agnathans. Developmental Biology (2005)
A temporary epithelium that derives from the outer layer of the ectdoerm and is shed once the inner layer differentiates to form a true epidermis.
The outermost epidermal layer covering the fish at embryonic stages; derived from the EVL and thought to eventually be replaced by the superficial stratum of the epidermis. Sometimes used synonymously with EVL. Le Guellec et al, 2004.[TAO]
relationship type change: OBO_REL:part_of ectoderm (TAO:0000016) CHANGED TO: develops_from ectoderm (UBERON:0000924)[TAO]
In mice, the first non-basal layer formed at ~E9.5; it is a temporary structure composed of simple squamous epithelium that serves as the first barrier to the embryo's physical environment, exists throughout the entire keratinocyte stratification process, and sheds off at ~E17, when it is replaced by corneocytes[MP]
In some mammals, Eyelid Fusion is thought to be driven by a population of cells which are derived from the periderm, the outermost layer of the developing epidermis
Originally the epidermis is one layer thick, in most vertebrates it soon becomes a two-layered structure. The outer layer gives rise to the periderm. The periderm goes through distinct developmental phases and is ultimately sloughed into the amniotic fluid when differentiation of the underlying epidermal layers is complete. The function of the periderm is not known, but is thought to be related to transport/exchange between the fetus and the amniotic fluid (http://courses.washington.edu/hubio567/devbio/periderm.html)
The portion of neural plate anterior to the mid-hindbrain junction.
The portion of neural plate posterior to the mid-hindbrain junction.
Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form.
Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. Kimmel et al, 1995.[TAO]
It is reasonable to assume that the proximate invertebrate ancestor of the vertebrates had an amphioxus-like tail bud in its larval stage. This archetypal tail bud would have (...) (3) lacked any component of mesenchyme cells, (4) budded off new mesodermal segments directly, without any intervening zone of presomitic mesoderm (...). Then, early in vertebrate evolution, epithelium-to-mesenchyme interconversions (and the gene networks for effecting them) became prominent features of development. (...) In any case, conspicuous mesenchymal components tended to be added to the vertebrate tail bud itself. In addition, a mesenchymatous presomitic mesoderm (not a part of the tail bud proper) came to intervene between the tail bud and the forming somites.[well established][VHOG]
DOI:10.1006/dbio.2001.0460 Schubert M, Holland LZ, Dale Stokes M and Holland ND, Three Amphoxius Wnt Genes (AmphiWnt3, AmphiWnt5, and AmphiWnt6) Associated with the Tail Bud: the Evolution of Somitogenesis in Chordates. Developmental Biology (2001)
In mammals, the pronephric duct is the predecessor of the Wolffian duct[WP].
Duct of the embryonic kidney, present bilaterally ventral to the somites and leading to the anal region where it empties separately from, and just posterior to the anus. Kimmel et al, 1995.[TAO]
The first-formed kidney duct, which drains the kidney of most anamniotes and becomes the ductus deferens of male amniotes. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-3, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]
(...) in all craniates, the archinephric duct develops in embryogeny.[well established][VHOG]
The pronephric duct collects the filtrate from the pronephric tubules and opens to the exterior of the pronephric kidney[GOC:mtg_kidney_jan10, http://www.ncbi.nlm.nih.gov/pubmed/15647339, XAO:0000063, ZFA:0000150]
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.686
Blood islands are structures in the developing embryo which lead to many different parts of the circulatory system. They primarily derive from plexuses formed from angioblasts. Within them, vacuoles appear through liquefaction of the central part of the syncytium into plasma. The lumen of the blood vessels thus formed is probably intracellular. The flattened cells at the periphery form the endothelium. The nucleated red blood corpuscles develop either from small masses of the original angioblast left attached to the inner wall of the lumen or directly from the flat endothelial cells. In either case the syncytial mass thus formed projects from and is attached to the wall of the vessel. Such a mass is known as a blood island and hemoglobin gradually accumulates within it. Later the cells on the surface round up, giving the mass a mulberry-like appearance. Then the red blood cells break loose and are carried away in the plasma. Such free blood cells continue to divide. Blood islands have been seen in the area vasculosa in the omphalomesenteric vein and arteries, and in the dorsal aorta[WP, unvetted].
Nests of developing blood cells arising late in the segmentation period from the intermediate mass, and located in the anterior-ventral tail, just posterior to the yolk extension. Kimmel et al, 1995.[TAO]
Region located on the ventral surface of the developing embryo that is a site of hematopoiesis and that is analogous to the yolk sac blood islands of higher vertebrates.[AAO]
relationship loss: part_of intermediate cell mass of mesoderm (TAO:0000033)[TAO]
Small clusters of mesodermal cells called blood islands mark the embryonic debut of the cardiovascular system (in vertebrates) (reference 1); In birds and mammals, primitive hemangioblasts are extraembryonic, populating the yolk sac as the so-called blood islands (reference 2).[well established][VHOG]
EHDAA2 distinguishes 3 types, but does not have a superclass. The VHOG class may refer to yolk sac
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.450, DOI:10.1146/annurev.cellbio.22.010605.093317 Hartenstein V, Blood cells and blood cell development in the animal kingdom. Annual Review of Cell and Developmental Biology (2006)
A horseshoe-shaped thickening of the endoderm at the cranial (rostral) end of the primitive streak formed by the involution of Spemann's organizer cells which, together with the notochord, induces the formation of the neural plate from the overlying ectodermal cells and contributes mesodermal type cells to the surrounding tissue
TODO - check; developmental relationship to anterior hypoblast in ZFA?
Axial hypoblast located anterior to the chorda mesoderm; the polster is its most anterior region. Kimmel et al, 1995.[TAO]
Axial mesoderm that lies anterior to the notochord and that underlies the forebrain. [Amphioxus_goosecoid_and_the_evolution_of_the_head_organizer_and_prechordal_plate._Evolution_and_Development_(2008)_2(6):303-310, Neidert_AH, Panopoulou_G_and_Langeland_JA][VHOG]
There are two opposing models that can potentially explain the differences in gsc (goosecoid) expression between amphioxus and vertebrates. In one model, the vertebrate gsc expression pattern more closely resembles the common ancestral state and the amphioxus gsc expression pattern is a derivation associated with its unique morphology. (...) In an alternate model, the amphioxus gsc expression pattern most closely represents the common ancestral state and the vertebrate pattern is derived. This model suggests that the evolution of vertebrates was accompanied by the segregation of gsc expression, from a more general domain underlying the entire brain anlage to a distinct forebrain organizer domain and subsequent prechordal plate. We feel this second model is more parsimonious than the first model in that what would be novel anterior gsc expression in vertebrates directly correlates with a novel vertebrate anterior structure, the prechordal plate.[well established][VHOG]
DOI:10.1046/j.1525-142x.2000.00073.x Neidert AH, Panopoulou G and Langeland JA, Amphioxus goosecoid and the evolution of the head organizer and prechordal plate. Evolution and Development (2008)
The intermediate mesoderm is located between the lateral mesoderm and the paraxial mesoderm. It develops into the kidney and gonads.
Mesoderm between somite and lateral plate. Traditionally thought to give rise to the urogenital system.[AAO]
(...)the mesoderm of a developing vertebrate transitionally differentiates into the following sub-types: Chordamesoderm (also known as axial mesoderm) which later on gives rise to notochord in all chordates, Paraxial mesoderm, Intermediate mesoderm, Lateral plate mesoderm (reference 1); The mesoderm is present in Bilateria, therefore they are sometimes called triploblasts. Ectoderm and endoderm are usually organized as epithelial layers, while mesoderm can be epithelial or a compact, three-dimensional tissue.[well established][VHOG]
all AOs differ in the relationship between this structure and the mesoderm; in ZFA it is a subclass (and this is implied by the GO definition and GO relationships), in AAO it is part of, and in EHDAA2 it develops from the mesoderm (but in EHDAA2 the naming convention is to use 'paraxial mesenchyme', rather than 'paraxial mesoderm').
http://en.wikipedia.org/wiki/Mesoderm, ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.43
The second pharyngeal arch will form the hyoid apparatus. The cranial neural crest cells that populate the second pharyngeal arch emerge primarily from rhombomere 4 and will form skeletal elements.
The second of the series of bony or cartilaginous arches that develop in the walls of the mouth cavity and pharynx of the embryo.[AAO]
A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG]
Lateral neurogenic placodes positioned dorsal of the epibranchial placodes.
In summary, the collective term 'placodes' refers to some rather different structures, probably with different evolutionary origins. Some sensory placodes (at least the otic and olfactory) may have homologues in basal chordates. Even if this is so, it is apparent that they were elaborated considerably during early vertebrate evolution. Epibranchial and dorsolateral placodes appear to be new; we infer that their origin depended on the evolution of specific inductive signals.[well established][VHOG]
The only remaining dorsolateral placode in land vertebrates is the otic/octaval placode
The axial mesoderm includes the prechordal mesoderm and the chordamesoderm. It gives rise to the prechordal plate and to the notochord.
The portion of the mesoderm underlying the midline of the embryo. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG]
A cranial placode which, once specified, invaginates to form an otic cup, which eventually separates from the surface ectoderm to form the otic vesicle or otocyst, a rounded structure without appar- ent polarity. As the otic placode invaginates into a cup neuroblasts delaminate from the anterior ventral aspect of the otic epithelium to give rise to neurons of the vestibulocochlear (statoacoustic) ganglion of cranial nerve VIII[NBK]
Primordium of the ear epithelium before it hollows into the otic vesicle, present beside the hindbrain rudiment in the midsegmentation period. Kimmel et al, 1995. (Also see Anatomical Atlas entry for ear by T. Whitfield.)[TAO]
With the exception of the pigment cells of the stria vascularis and the secretory epithelium of the cochlea, which are of neural crest origin, all compo- nents of the inner ear derive from the otic placode. In most species the thickening of the ectoderm into a placode occurs in a region adjacent to rhombomere 5 (reviewed in Ohyama et al., 2007), while in amphibians the otic placode is centered onto rhombomere 4 (Ruiz i Altaba and Jessell, 1991).
A neurogenic placode that arises at the level of the midbrain-hindbrain boundary and develops into a trigeminal ganglion.
The ectodermal precursor of the trigeminal ganglion. The profundal and the trigeminal ganglia are separate distally but fused at their proximal end as they condense around NF stage 24.[XAO]
The ectodermal rudiment of the trigeminal ganglion, distinguishable during much of the segmentation period. Kimmel et al, 1995.[TAO]
The dorsolateral placodes (trigeminal and vestibular) develop from ectoderm lateral to the brain (...). In summary, the collective term 'placodes' refers to some rather different structures, probably with different evolutionary origins. Some sensory placodes (at least the otic and olfactory) may have homologues in basal chordates. Even if this is so, it is apparent that they were elaborated considerably during early vertebrate evolution. Epibranchial and dorsolateral placodes appear to be new; we infer that their origin depended on the evolution of specific inductive signals.[well established][VHOG]
Consider naming this 'trigeminal placode complex'. Also, Fig9-5 of ISBN10:0471888893 calls this the profundus placode; XAO says 'profundal and the trigeminal ganglia are separate distally but fused at their proximal end...'
Portion of tissue that is part of the anterior neural keel and will form the optic vesicle[ZFA]. A paired ectodermal placode that becomes invaginated to form the embryonic lens vesicles.
TODO - check that GO's optic placode is the same as ZFA's eye primordium; we may want to have separate term for ocular primordium precursor. XAO has both optic field and eye primordium.
Multi-tissue structure that is comprised of neural and non-neural epithelial layers which will form the retina and retinal pigmented epithelium of the mature eye[ZFA]. double walled structured formed by expansion and invagination of the distal end of the optic vesicle that develops into the pigmented and sensory layers of the retina while the mouth of the optic cup eventually forms the pupil of the eye[MP].
(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup.[well established][VHOG]
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429
A thickened portion of ectoderm which serves as the precursor to the lens. SOX2 and Pou2f1 are involved in its development[WP].
Ectodermal primordium of the lens of the eye. Kimmel et al, 1995.[TAO]
(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The optic cup induces the overlying surface ectoderm first to thicken as a lens placode and then to invaginate and form a lens vesicle that differentiates into the lens.[well established][VHOG]
Classical transplantation experiments using amphibian embryos suggested that the optic vesicle is the source of lens-inducing signals sufficient to generate lens tissues in competent ectoderm (reviewed in Grainger et al., 1996). More recent findings suggest a multistep model for lens induction. There is now good evidence that lens specification occurs at the neurula stage, before the optic vesicle contact the surface ectoderm, and that neural crest cell migration in the frontonasal region is required to restrict the position of the lens placode (Bailey et al., 2006)
Paired organ that connects the primitive kidney Wolffian body (or mesonephros) to the cloaca and serves as the anlage for certain male reproductive organs. the Wolffian duct is what remains of the pronephric duct after the atrophy of the pronephros[WP]. In Zebrafish: Duct of the adult kidney (mesonephros), present bilaterally ventral to the somites and leading to the cloacal chamber[ZFA].
Consider adding subclasses for male and female specific variants
TODO - mesonephric portion of the nephric duct
Anatomical structure consisting of either of a pair of longitudinal ducts which carry urine and in males, sperm, to the cloaca.[AAO]
In the male the Wolffian duct persists, and forms for example the epididymis, the ductus deferens, the ejaculatory duct, seminal vesicle and efferent ducts.
A region of embryonic ectodermal cells that lie directly above the notochord. During neurulation, they change shape and produce an infolding of the neural plate (the neural fold) that then seals to form the neural tube[XAO]. The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium[ZFA]
The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium. Kimmel et al, 1995.[TAO]
The paraxial mesoderm is the mesoderm located bilaterally adjacent to the notochord and neural tube[GO]
Mesoderm lateral to the neural tube and notochord that is divided into cranial and post-cranial portions. The trunk portions further segment into somites.[AAO]
Presently, Cephalochordata, Urochordata, and Vertebrata are placed as subphyla of the phylum Chordata, in which the overall organization of embryonic tissues (dorsal hollow nerve cord, ventral digestive tract, axial notochord, and bilateral paraxial mesoderm) is largely conserved. In contrast, the echinoderms and hemichordates are sister groups of the chordates and they lack the notochord and paraxial mesoderm. Thus, the basic mesodermal organization of vertebrates must have appeared first in the common ancestor of the chordates.[well established][VHOG]
note that all AOs differ in the relationship between this structure and the mesoderm; in ZFA it is a subclass (and this is implied by the GO definition and GO relationships), in AAO it is part of, and in EHDAA2 it develops from the mesoderm (but in EHDAA2 the naming convention is to use 'paraxial mesenchyme', rather than 'paraxial mesoderm'). Also in ZFA it is part of the trunk whereas this conflicts with the division into head and trunk in ehdaa2 (which we follow here)
DOI:10.1002/dvdy.21177 Kusakabe R and Kuratani S. Evolutionary perspectives from development of mesodermal components in the lamprey. Developmental dynamics (2007)
Focal thickenings of the embryonic ectoderm that form immediately dorsal and caudal of the clefts between the pharyngeal arches and that produce the neuroblasts that migrate and condense to form the distal cranial ganglia.
Focal thickenings of the embryonic ectoderm that form immediately dorsal and caudal of the clefts between the pharyngeal arches and that produce the neuroblasts that migrate and condense to form the distal cranial ganglia. [Graham_A, The_development_and_evolution_of_the_pharyngeal_arches._J_Anat_(2001)_199:_133-141][VHOG]
Epibranchial placodes-derived neurons innervate internal organs to transmit information such as heart rate, blood pressure, and visceral distension from the periphery to the central nervous system (Baker and Bronner-Fraser, 2001). From rostral to caudal the epibranchial placodes comprise the geniculate, petrosal, and nodose placodes, each associated in sequence with the first, second and third branchial clefts. Each placode contributes sensory neurons to cranial nerves VII (facial nerve), IX (glossopharyngeal nerve), and X (vagal nerve), respectively
in XAO this develops_from dorsolateral placode, but in NBK53175, this is a separate group
DOI:10.1046/j.1469-7580.2001.19910133.x Graham A, The development and evolution of the pharyngeal arches. J Anat (2001)
TODO - add grouping class for the anterior end of the neural tube at all stages
Portion of the middle of the three primary germ layers of the embryo that resides on the periphery of the embryo, is continuous with the extra-embryonic mesoderm, splits into two layers enclosing the intra-embryonic coelom, and gives rise to body wall structures[MP].
Portion of mesoderm traditionally thought to give rise to limb bones and parts of the girdles.[AAO]
The portion of the mesoderm of the trunk of vertebrate embryos lying lateral to the intermediate mesoderm. [...] [It] subdivides into two plates: one dorsal, called the somatopleure, and one ventral, called the splanchnopleure. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG]
A ventrolateral zone of amphioxus mesoderm grows down to surround the gut. Homology of this zone to the lateral plate mesoderm of vertebrates is supported by site of origin and fate.[well established][VHOG]
A transitional population of migrating mesenchymal cells that derive from somites and that will become muscle cells.
The term 'myotome' is also used to describe the muscles served by a single nerve root / spinal segment - consider adding new class, myomere.
Portion of the somites giving rise to body wall muscle masses. Kimmel et al, 1995.[TAO]
In all vertebrates, the skeletal muscle of the body axis is chiefly derived from an early embryonic compartment, known as the myotome.[well established][VHOG]
DOI:10.1038/sj.embor.embor920 Hollway GE, Currie PD, Myotome meanderings. Cellular morphogenesis and the making of muscle. EMBO Rep.(2003)
Trunk portion of the neural crest. The trunk neural crest lies between the vagal and sacral neural crest and gives rise to two groups of cells. One group migrates dorsolateral and populates the skin, forming pigment cells and the other migrates ventrolateral through the anterior sclerotome to become the epinephrine-producing cells of the adrenal gland and the neurons of the sympathetic nervous system. Some cells remain in the sclerotome to form the dorsal root ganglia [Wikipedia].
Post-cranial portion of the neural crest. Exact anatomical derivations not experimentally resolved in amphibians.[AAO]
We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG]
Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline to form the heart rudiment or cone.
should probably be merged with heart rudiment.
Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline between 21 and 26 somites to form the heart rudiment or cone. Stainier 2001.[TAO]
The fused aspects of ventral mesoderm, which have migrated from either side of the prechordal plate, and fused ventrally, just behind the cement gland. They will give rise to the endocardium at NF stage 27&28.[AAO]
relationship loss: develops_from lateral mesoderm (TAO:0001065)[TAO]
Ventral somitic compartment that is a precursor of the axial skeleton[XAO]. Sclerotomes eventually differentiate into the vertebrae and most of the skull. The caudal (posterior) half of one sclerotome fuses with the rostral (anterior) half of the adjacent one to form each vertebra. From their initial location within the somite, the sclerotome cells migrate medially towards the notochord. These cells meet the sclerotome cells from the other side to form the vertebral body. From this vertebral body, sclerotome cells move dorsally and surround the developing spinal cord, forming the vertebral arch[WP].
The vertebrate sclerotome has no equivalent in amphioxus and is a novelty linked with the evolution of the axial skeleton.[well established][VHOG]
neural crest cells (NCCs) originating in the anterior part of the developing embryo and residing between the mid-diencephalon and the forming hindbrain; cranial NCCs migrate dorsolaterally to form the craniofacial mesenchyme that differentiates into various craniofacial cartilages and bones, cranial neurons, glia, and connective tissues of the face; these cells enter the pharyngeal pouches and arches where they give rise to thymic cells, bones of the middle ear and jaw (mandible), and the odontoblasts of the tooth primordia; like their counterparts in the trunk, cranial NCCs also contribute to the developing peripheral nervous system, along with the pigmented cell (i.e. melanocyte) lineage.
Anterior most portion of the neural crest. Migrates in three highly conserved streams: mandibular, hyoid and branchial.[AAO]
Neural crest that is part of the head.[TAO]
Gonochoristic organism that can produce female gametes.
Anatomical structure that overlaps the outer epithelial layer and is adjacent to the space surrounding the organism.
Organism subdivision which is the collection of anatomical structures on the body surface.[ZFA]
Anatomical structure that has as its parts two or more multi-tissue structures of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona fide boundaries from other distinct anatomical structures of different types.
this class was introduced for consistency with CARO. However, in this ontology we typically classify organs directly under 'organ' rather than subdividing into compound and simple organs
Portion of tissue consisting of loosely organized undifferentiated mesodermal cells that give rise to such structures as connective tissues, blood, lymphatics, bone, and cartilage[XAO]. A mesh-like cell arrangement, less compact than an epithelium[ZFA]. The part of the embryonic mesoderm, consisting of loosely packed, unspecialized cells set in a gelatinous ground substance, from which connective tissue, bone, cartilage, and the circulatory and lymphatic systems develop[BTO].
the relationship to mesoderm is weaker than develops_from in order to have classes such as 'head mesenchyme from mesoderm' make sense
A mesh-like cell arrangement, less compact than an epithelium. Kimmel et al, 1995.[TAO]
Portion of tissue consisting of loosely organized undifferentiated mesodermal cells that give rise to such structures as connective tissues, blood, lymphatics, bone, and cartilage.[AAO]
Subdivision of skeleton that includes all dermal bones in the cranial skeleton[ZFA,modified].
wikipedia treats skull roof and dermatocranium as synonymous, but some sources treat the roof as being part of the dermatocranium - see UBERONREF:0000007
Anatomical cluster that is part of the cranium and composed of dermally derived bones.[TAO]
Anatomical cluster that is part of the cranium which consists of dermally derived bones.[AAO]
contributes to development of the cartilage of the larynx, laryngeal, pharyngeal, and soft palate muscles, superior parathyroid gland, and C-cells of the thymus
The second pharyngeal/branchial arch; arises as a thickening of the pharygeal wall between the first and second branchial clefts; contains the second aortic arch; forms part of the hyoid bone, tongue and facial musculature.[AAO]
in XAO, called branchial arch 2 and df VP4
The 6th pharyngeal arch. contributes to the development of the sternocleidomastoid and trapezius muscles
The forth in a series of paired bars in the wall of the pharynx, within which are formed the forth aortic arch and the cartilage bar of the visceral skeleton, forms and supports the gills.[AAO]
DOI:10.1111/j.1469-7580.2005.00472.x Graham A, Okabe M, Quinlan R, The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat (2005)
The vessels formed within the first pair of branchial arches in embryogenesis
Disappears early in development in tetrapods
ZFA states that The paired aortic arch 1 arteries branch off of the ventral aorta, and empty into the right and left lateral dorsal aortas
The vessels formed within the second pair of branchial arches in embryogenesis
The first and second arches disappear early, but the dorsal end of the second gives origin to the stapedial artery, a vessel which atrophies in humans but persists in some mammals. It passes through the ring of the stapes and divides into supraorbital, infraorbital, and mandibular branches which follow the three divisions of the trigeminal nerve. The infraorbital and mandibular arise from a common stem, the terminal part of which anastomoses with the external carotid. On the obliteration of the stapedial artery this anastomosis enlarges and forms the internal maxillary artery, and the branches of the stapedial artery are now branches of this vessel. The common stem of the infraorbital and mandibular branches passes between the two roots of the auriculotemporal nerve and becomes the middle meningeal artery; the original supraorbital branch of the stapedial is represented by the orbital twigs of the middle meningeal[WP][Wikipedia:Aortic_arches#Arches_1_and_2].
The second in a series paired arterial connections between the dorsal and ventral aortae. Aortic arch 2 that is part of hyoid arch.[AAO]
The vessels formed within the fourth pair of branchial arches in embryogenesis
Aortic arches 3 and 4 are not remodeled but are retained largely intact as the branchial arteries providing circulation through the gills. These areches are direct branches from the ventral aorta to the lateral dorsal aorta. Isogai et al. 2001.[TAO]
The forth in a series paired arterial connections between the dorsal and ventral aortae, lies within the 4th branchial arch. The paired aortic arch 4 arteries branch directly from the ventral aorta to the lateral dorsal aorta, and are retained as the branchial arteries providing circulation through the gills in the adult.[AAO]
The fourth right arch forms the right subclavian as far as the origin of its internal mammary branch; while the fourth left arch constitutes the arch of the aorta between the origin of the left carotid artery and the termination of the ductus arteriosus[WP][Wikipedia:Aortic_arches#Arch_4].
Normally, the left fourth arch becomes the aortic arch, the right fourth arch contributes to the innominate artery[http://emedicine.medscape.com/article/899609-overview] in birds it is the right fourth arch which forms the permanent aorta
The vessels formed within the sixth pair of branchial arches in embryogenesis
The fifth and sixth arches, which come on-line at approximately 2.5 dpf, have a common trunk from the ventral aorta and drain to the midline dorsal aorta via an independent route. The fifth and sixth aortic arches supply the trunk and tail with oxigenated blood. Isogai et al. 2001.[TAO]
The sixth in a series paired arterial connections between the dorsal and ventral aortae. Aortic arch 6 artery is paired and has a common trunk with aortic arch 5 from the ventral aorta, and drains via a separate branch of the lateral dorsal aorta. It forms part of the pulmonary arteries, and in the later embryo, the ductus arteriosis. Aortic arches 5 and 6 together supply the trunk and tail with oxygenated blood.[AAO]
The sixth right arch disappears; the sixth left arch gives off the pulmonary arteries and forms the ductus arteriosus; this duct remains pervious during the whole of fetal life, but then closes within the first few days after birth due to increased O2 concentration. Oxygen concentration causes the production of bradykinin which causes the ductus to constrict occluding all flow. Within 1-3 months, the ductus is obliterated and becomes the ligamentum arteriosus. His showed that in the early embryo the right and left arches each gives a branch to the lungs, but that later both pulmonary arteries take origin from the left arch[WP][Wikipedia:Aortic_arches#Arch_6].
the distal left sixth arch becomes the ductus arteriosus, the proximal sixth arches bilaterally contribute to the proximal branch pulmonary arteries
The trachea is the portion of the airway that attaches to the bronchi as it branches [GO:dph].
An elongated tube which carries air to and from the lungs.[AAO]
The respiratory tube between the larynx and the bronchi. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-29, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]
In primitive fishes and most tetrapods, the lungs of adults are usually paired. They lie ventral to the digestive tract and are connected to the outside environment through the trachea.[well established][VHOG]
In birds, the trachea runs from the pharynx to the syrinx, from which the primary bronchi diverge. Swans have an unusually elongated trachea, part of which is coiled beneath the sternum; this may act as a resonator to amplify sound. In some birds, the cartilagenous rings are complete, and may even be ossified. In amphibians, the trachea is normally extremely short, and leads directly into the lungs, without clear primary bronchi. A longer trachea is, however found in some long-necked salamanders, and in caecilians. While there are irregular cartilagenous nodules on the amphibian trachea, these do not form the rings found in amniotes. The only vertebrate to have lungs, but no trachea, is Polypterus, in which the lungs arise directly from the pharynx.
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.409
Upper portion of the skull that excludes the mandible (when present in the organism).
the inclusion of the FMA class here is probably not quite correct, as this class includes as parts sutures, whereas this is not part of the bones of the cranium
The term cranium can be ambiguous, in that it can refer to the neurocranium, or the neurocranium and the Facial skeleton
Anatomical structure that is part of the head consisting entirely of cranium and mandible[WP].
in FMA the skull is divided into orbit, neurocranium (8 parts), viscerocranium (26 parts). Here we have a separate overlapping division into cranium and mandible.
in many ontologies, the structure called the cranium is inclusive of the mandible/lower jaw skeleton
A skull that is missing a mandible is only a cranium; this is the source of a very commonly made error in terminology. Those animals having skulls are called craniates
GO uses genitalia for the singular organ
female organism reproductive system organ
reproductive structure of female organism
reproductive system organ of female organism
Any sense organ that functions in (some) detection of chemical stimulus involved in sensory perception of taste (GO:0050912).
Septum that divides the ovary, the basal portion of a carpel or group of fused carpels, that encloses the ovule(s)[GO].
one of the two embryological structures that give rise to the kidney (the other is the ureteric bud). The metanephric blastema mostly develops into nephrons, but can also form parts of the collecting duct system.[WP]. Metanephric mesenchyme is the tissue made up of loosely connected mesenchymal cells in the metanephros[GO]
A mass of intermediate mesodermal cells around the distal end of the ureteric bud that gives rise to nephrons in the metanephric kidney. [TFD][VHOG]
When the ureteric buds emerge from the nephric duct, they enter the metanephrogenic mesenchyme. The ureteric buds induce this mesenchymal tissue to condense around them and differentiate into the nephrons of the mammalian kidney. As this mesenchyme differentiates, it tells the ureteric bud to branch and grow.[well established][VHOG]
Genes: The positional specification of the metanephrogenic mesenchyme is negatively regulated by Foxc1 and Foxc2. Next the permanent kidney forming metanephrogenic mesenchyme is specified by Hox11 genes. The competence to respond to ureteric bud inducers is regulated by WT1. GDNF secretion restricted to posterior region by Robo2 and Sprouty1. The receptors for GDNF are synthesized in the nephric ducts and later in ureteric buds [ISBN:9780878932504 "Developmental Biology"]
ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) p.462
An epithelium that is part of a lower jaw [Automatically generated definition].
epithelial tissue of ventral mandibular arch
ventral mandibular arch epithelial tissue
An epithelium that is part of a otic placode [Automatically generated definition].
check ZFA, placemeant, appears to refer to both adult structures and primordium
An endoderm that is part of a foregut [Automatically generated definition].
An endoderm that is part of a midgut [Automatically generated definition].
An endoderm that is part of a hindgut [Automatically generated definition].
A portion of skeletal muscle tissue that is part of a eye [Automatically generated definition].
A subdivision of the skeleton that corresponds to the lower part of the mouth. The lower jaw skeleton includes the following elements, when present: lower jaw teeth, the mandible and other lower jaw bones, and Meckel's cartilage.
The ventral portion of the first pharyngeal arch, comprising the lower jaw.[TAO]
The jaw joint of all jawed vertebrates, except for mammals, involves the quadrate and articular bones, or the posterior ends of the palatoquadrate and mandibular cartilages; A correlate of the conversion of the articular and quadrate bones to the malleus and incus is that all adult mammals have a jaw joint that lies between the dentary of the lower jaw and the squamosal bone of the skull roof.[well established][VHOG]
Inclusion of the FMA class 'lower jaw' is debatable - this mostly corresponds to the lower jaw skeleton (with 'maxillary part of mouth' corresponding to the upper jaw region); however, the FMA class also includes gingiva. See also: https://github.com/obophenotype/mouse-anatomy-ontology/issues/102
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.241 and p.101
An endothelium that is part of a trachea.
A gland that is part of a foregut [Automatically generated definition].
Racemose mucous glands beneath the mucous membrane of the pharynx.
A gland that is part of a integumental system [Automatically generated definition].
A blood island that is part of a mesoderm.
in EHDAA2, gives rise to blood and dorsal aorta
Mesenchyme that is part of a developing camera-type eye.
TODO - change mesenchyme relationships to precursor_of
Mesenchyme that is part of a developing ovary [Automatically generated definition].
female reproductive system gonad mesenchyme
female reproductive system gonada mesenchyme
gonad of female reproductive system mesenchyme
gonada of female reproductive system mesenchyme
mesenchyme of female reproductive system gonad
mesenchyme of female reproductive system gonada
mesenchyme of gonad of female reproductive system
mesenchyme of gonada of female reproductive system
Mesenchyme that is part of a developing lower jaw [Automatically generated definition].
A submucosa that is part of an anal canal [Automatically generated definition].
anal canal viewed anatomically submucosa
submucosa of anal canal viewed anatomically
The submucous layer of the wall of the rectum.
A submucosa that is part of a colon [Automatically generated definition].
A serous membrane that is part of a rectum [Automatically generated definition].
A serous membrane that is part of a colon [Automatically generated definition].
A spatially aggregated collection of nerve cell bodies in the PNS, consisting of one or more subpopulations that share cell type, chemical phenotype, and connections. (CUMBO).
we follow MA in including separate classes for ganglion and peripheral nervous system, even though for vertebrates gangia are always in the PNS
A ganglion that is part of a central nervous system [Automatically generated definition].
this has no subclasses in FMA. In EHDAA2 and EMAPA it has only the cranial ganglia
A mucosa that is part of an anal canal [Automatically generated definition].
anal canal viewed anatomically mucosa of organ
anal canal viewed anatomically mucous membrane
anal canal viewed anatomically organ mucosa
mucosa of anal canal viewed anatomically
mucosa of organ of anal canal viewed anatomically
mucosa of organ of anatomical anal canal
mucous membrane of anal canal viewed anatomically
mucous membrane of anatomical anal canal
organ mucosa of anal canal viewed anatomically
A mucosa that is part of a oral opening [Automatically generated definition].
A mucosa that is part of a rectum [Automatically generated definition].
A layer of epithelial cells on the surface of the mucosa.
An epithelium that is part of a pharynx [Automatically generated definition].
Epithelium lining the pharynx consisting largely of simple columnar epithelium with a short segment (1mm) of stratified squamous epithelium on the ventral side. Chen et al, 2007.[TAO]
An epithelium that is part of a hindgut [Automatically generated definition].
An epithelium that is part of a rectum [Automatically generated definition].
An epithelium that is part of a right lung [Automatically generated definition].
An epithelium that is part of a left lung [Automatically generated definition].
An unilaminar epithelium that surrounds a pelvic appendage bud.
An unilaminar epithelium that surrounds a pectoral appendage bud.
A portion of cardiac muscle tissue that is part of a right ventricle [Automatically generated definition].
cardiac muscle tissue of right ventricle
A portion of cardiac muscle tissue that is part of a left ventricle [Automatically generated definition].
A portion of cardiac muscle tissue that is part of an interventricular septum [Automatically generated definition].
cardiac muscle of interventricular septum
cardiac muscle tissue of interventricular septum
A portion of skeletal muscle tissue that is part of a pharynx [Automatically generated definition].
any of the striated muscles that move the eye and include: superior rectus, inferior rectus, medial rectus, lateral rectus, superior oblique, inferior oblique, retractor bulbi
Not clear if we need this and intra-ocular muscle. See issue #331. MA includes ciliary and iris smooth muscle
A portion of smooth muscle tissue that is part of a trachea [Automatically generated definition].
A cartilage element that is part of a respiratory system [Automatically generated definition].
A gland that is part of a digestive tract [Automatically generated definition].
Mesenchyme that is part of a pelvic appendage bud.
Mesenchyme that is part of a pectoral appendage bud.
Mesoderm that is part of the pectoral fin bud.[TAO]
An adipose tissue that is part of a dermis [Automatically generated definition].
A nerve that is part of an abdomen [Automatically generated definition].
A nerve that is part of a neck [Automatically generated definition].
added for consistency with mouse ontologies. The term 'ciliary nerve' is usually used to denote either of the two nerves (with different origins) that innervate the iris, as well as ciliary muscles and cornea
A nerve that is part of the trunk region of the body (not to be confused with a nerve trunk).
A nerve that is located in a thoracic cavity [Automatically generated definition].
consider merging with thoracic nerve. In MA the only subclass is the phrenic nerve, which arises from a cervical nerve
A nerve that is part of a pelvis [Automatically generated definition].
A bone that is part of a head [Automatically generated definition].
Different sources vary regarding which bones are craniofacial; e.g. hyoid bone
A bone that is part of a neck [Automatically generated definition].
A bone that is part of a facial skeleton [Automatically generated definition].
test whether 'facial bone' is an exact synonym
A bone that is part of a trunk [Automatically generated definition].
The ureteral branches of renal artery are small branches which supply the ureter.
An artery that is part of a respiratory system [Automatically generated definition].
The Iinferior labial artery (inferior labial branch of facial artery) arises near the angle of the mouth; it passes upward and forward beneath the Triangularis and, penetrating the Orbicularis oris, runs in a tortuous course along the edge of the lower lip between this muscle and the mucous membrane. It supplies the labial glands, the mucous membrane, and the muscles of the lower lip; and anastomoses with the artery of the opposite side, and with the mental branch of the inferior alveolar artery.
ramus labialis inferior (arteria facialis)
ramus labialis inferior arteriae facialis
An artery that is part of a thoracic cavity[cjm].
in MA, aorta is classified here - but this is problematic because the abdominal aorta is not in the thoracic cavity
A vein that is part of a ureter [Automatically generated definition].
A vein that is part of a respiratory system [Automatically generated definition].
The inferior labial vein is the vein receiving blood from the lower lip.
A vein that is part of a thoracic cavity [Automatically generated definition].
An endothelium of capillary that is part of a respiratory system [Automatically generated definition].
apparatus respiratorius blood capillary endothelium
apparatus respiratorius capillary endothelium
apparatus respiratorius capillary vessel endothelium
apparatus respiratorius endothelium of blood capillary
apparatus respiratorius endothelium of capillary
apparatus respiratorius endothelium of capillary vessel
blood capillary endothelium of apparatus respiratorius
blood capillary endothelium of respiratory system
capillary endothelium of apparatus respiratorius
capillary endothelium of respiratory system
capillary vessel endothelium of apparatus respiratorius
capillary vessel endothelium of respiratory system
endothelium of blood capillary of apparatus respiratorius
endothelium of blood capillary of respiratory system
endothelium of capillary of apparatus respiratorius
endothelium of capillary of respiratory system
endothelium of capillary vessel of apparatus respiratorius
endothelium of capillary vessel of respiratory system
respiratory system blood capillary endothelium
respiratory system capillary vessel endothelium
respiratory system endothelium of blood capillary
respiratory system endothelium of capillary
respiratory system endothelium of capillary vessel
respiratory system capillary endothelium
A venule that is part of a respiratory system [Automatically generated definition].
An arteriole that is part of a respiratory system [Automatically generated definition].
A blood vessel that is part of a head [Automatically generated definition].
A blood vessel that is part of an abdomen [Automatically generated definition].
A blood vessel that is part of a heart [Automatically generated definition].
A blood vessel that is part of a brain [Automatically generated definition].
A blood vessel that is part of a cornea [Automatically generated definition].
A blood vessel that is part of a retina [Automatically generated definition].
blood vessel of tunica interna of eyeball
A blood vessel that is part of a neck [Automatically generated definition].
A blood vessel that is part of a respiratory system [Automatically generated definition].
A blood vessel that is part of a trachea.
A blood vessel that is part of the arterial system. Includes artery, arteriole and aorta.
only in MA - supertype of artery, arteriole, aorta.
A blood vessel that is part of a iris [Automatically generated definition].
A blood vessel that is part of a lung [Automatically generated definition].
A blood vessel that is part of a trunk [Automatically generated definition].
A blood vessel that is part of a kidney [Automatically generated definition].
A blood vessel that is part of a thoracic cavity [Automatically generated definition].
A blood vessel that is part of a pelvis [Automatically generated definition].
A capillary that is part of a respiratory system [Automatically generated definition].
apparatus respiratorius capillary vessel
blood capillary of apparatus respiratorius
capillary vessel of apparatus respiratorius
A capillary that is part of a kidney [Automatically generated definition].
A gray matter that is part of a brain [Automatically generated definition].
A portion of connective tissue that is part of a head [Automatically generated definition].
portion of connective tissue of adult head
A portion of connective tissue that is part of an abdomen [Automatically generated definition].
A portion of connective tissue that is part of a neck [Automatically generated definition].
neck (volume) portion of connective tissue
portion of connective tissue of neck (volume)
A portion of connective tissue that is part of a respiratory system [Automatically generated definition].
apparatus respiratorius connective tissue
apparatus respiratorius portion of connective tissue
apparatus respiratorius textus connectivus
connective tissue of apparatus respiratorius
portion of connective tissue of apparatus respiratorius
portion of connective tissue of respiratory system
respiratory system portion of connective tissue
textus connectivus of apparatus respiratorius
textus connectivus of respiratory system
A portion of connective tissue that is part of a trachea.
A portion of connective tissue that is part of a lower respiratory tract [Automatically generated definition].
connective tissue of lower respiratory tract
lower respiratory tract portion of connective tissue
lower respiratory tract textus connectivus
portion of connective tissue of lower respiratory tract
textus connectivus of lower respiratory tract
lower respiratory tract connective tissue
A portion of connective tissue that is part of a larynx [Automatically generated definition].
A portion of connective tissue that is part of a dermis [Automatically generated definition].
A portion of connective tissue that is part of a trunk [Automatically generated definition].
A portion of connective tissue that is part of a bronchus [Automatically generated definition].
bronchial trunk portion of connective tissue
portion of connective tissue of bronchial trunk
portion of connective tissue of bronchus
A portion of connective tissue that is part of a thoracic cavity [Automatically generated definition].
cavity of chest portion of connective tissue
cavity of thorax portion of connective tissue
chest cavity portion of connective tissue
pectoral cavity portion of connective tissue
portion of connective tissue of cavity of chest
portion of connective tissue of cavity of thorax
portion of connective tissue of chest cavity
portion of connective tissue of pectoral cavity
portion of connective tissue of thoracic cavity
thoracic cavity portion of connective tissue
A portion of connective tissue that is part of a pelvis [Automatically generated definition].
A cartilage that is part of a neck [Automatically generated definition].
A cartilage that is part of a lower respiratory tract [Automatically generated definition].
the ring-shaped cartilaginous structures that support the trachea
check whether to classify as part of splanchoncranium
in mammals the rings are incomplete, in avians the rings are complete.
A skin gland that is part of a camera-type eye [Automatically generated definition].
The dense connective tissue which contains predominantly elastic fibers and is found in the tunica media of the aorta wall.
adult aorta textus connectivus elasticus
dorsal aorta textus connectivus elasticus
elastic connective tissue of adult aorta
elastic connective tissue of dorsal aorta
elastic connective tissue of trunk of aortic tree
textus connectivus elasticus of adult aorta
textus connectivus elasticus of dorsal aorta
textus connectivus elasticus of trunk of aortic tree
trunk of aortic tree elastic connective tissue
trunk of aortic tree textus connectivus elasticus
The type of heart connective tissue found in the endocardial layer that consists mainly of elastic fibers.
An elastic tissue that is part of a respiratory system [Automatically generated definition].
apparatus respiratorius elastic connective tissue
apparatus respiratorius textus connectivus elasticus
elastic connective tissue of apparatus respiratorius
elastic connective tissue of respiratory system
elastic tissue of apparatus respiratorius
respiratory system elastic connective tissue
respiratory system textus connectivus elasticus
textus connectivus elasticus of apparatus respiratorius
textus connectivus elasticus of respiratory system
An elastic tissue that is part of a circulatory system [Automatically generated definition].
cardiovascular system elastic connective tissue
cardiovascular system textus connectivus elasticus
circulatory system elastic connective tissue
circulatory system textus connectivus elasticus
elastic connective tissue of cardiovascular system
elastic connective tissue of circulatory system
textus connectivus elasticus of cardiovascular system
textus connectivus elasticus of circulatory system
Elastic tissue layer that lines a blood vessel layer.
blood vessel textus connectivus elasticus
elastic connective tissue of blood vessel
textus connectivus elasticus of blood vessel
Elastic tissue that is part of a lung [Automatically generated definition].
An elastic tissue that is part of a bronchus [Automatically generated definition].
bronchial trunk elastic connective tissue
bronchial trunk textus connectivus elasticus
elastic connective tissue of bronchial trunk
textus connectivus elasticus of bronchial trunk
textus connectivus elasticus of bronchus
An elastic tissue that is part of a trachea [Automatically generated definition].
cartilaginous trachea elastic connective tissue
cartilaginous trachea textus connectivus elasticus
elastic connective tissue of cartilaginous trachea
elastic connective tissue of vertebrate trachea
textus connectivus elasticus of cartilaginous trachea
textus connectivus elasticus of vertebrate trachea
textus connectivus elasticus of windpipe
vertebrate trachea elastic connective tissue
vertebrate trachea textus connectivus elasticus
The middle layer of the aorta wall, containing the smooth muscle layer and elastic fibers.
The innermost layer of the aorta, containing the endothelium and an inner elastic membrane.
An arterial blood vessel that is part of a respiratory system [Automatically generated definition].
respiratory system arterial blood vessel
An arterial blood vessel that is part of a kidney [Automatically generated definition].
The part of the ventral body cavity that is within the abdomen proper (excluding the pelvic cavity).
in FMA this contains the pelvic cavity, but this is inconsistent with the concept of abdominopelvic cavity
In anatomy, in the occipital bone, the foramen magnum is one of the several oval or circular apertures in the base of the skull, through which the medulla oblongata (an extension of the spinal cord) enters and exits the skull vault. Apart from the transmission of the medulla oblongata and its membranes, the foramen magnum transmits the Spinal Accessory nerve, vertebral arteries, the anterior and posterior spinal arteries, the membrana tectoria and alar ligaments. [WP,unvetted].
Foramen in the occipital region of neurocranium to allow passage of spinal cord.[TAO]
Design pattern notes: check whether this fits the foramen design pattern
The tissues that surround the organs that are present within the abdominal cavity. The abdominal wall tissue is composed of layers of fat, parietal peritoneum, fascia, and muscles.
A vein arising from the splenic trabecular vein in the hilum of the spleen that drains into the portal vein.
Portion of tissue in the nervous system which consists of neurons and glial cells, and may also contain parts of the vasculature.
One of the four types of tissue in traditional classifications. Cells forming the brain, spinal cord and peripheral nervous system.[AAO]
The major nerves supplying sympathetic innervation to the abdomen, including the greater, lesser, and lowest (or smallest) splanchnic nerves that are formed by preganglionic fibers from the spinal cord which pass through the paravertebral ganglia and then to the celiac ganglia and plexuses and the lumbar splanchnic nerves carry fibers which pass through the lumbar paravertebral ganglia to the mesenteric and hypogastric ganglia.
All carry sympathetic fibers except for the pelvic splanchnic nerves, which carry parasympathetic fibers
A branch of the vagus nerve that supplies motor function and sensation to the larynx (voice box). It travels within the endoneurium. It is the nerve of the 6th Branchial Arch.
Branch of the vagus nerve that separates from the vagus well postcranially, then continues anteriorly to innervate the larynx[AAO:0010754].
recurrent laryngeal nerve from vagus nerve
vagus X nerve recurrent laryngeal branch
this is defined as any mucous membrane of the mouth - including palate, lips, uvula, etc. ncit split mouth/oral mucosa into lip and buccal. In future we may split into masticatory/keratinized (gingiva + hard palate) vs lining/non-keratinized (lips, cheeks, floor of mouth, soft palate). FMA distinguishes between mucosa of mouth and region of mouth (the latter including the buccal mucosa)
the mucous membrane epithelium of the mouth. It can be divided into three categories: masticatory, lining, and specialized[Wikipedia:Oral_mucosa].
A nerve that is part of a thorax [Automatically generated definition].
A nerve that is part of an abdominal segment of trunk [Automatically generated definition].
A bone that is part of a thorax [Automatically generated definition].
A bone that is part of an abdominal segment of trunk [Automatically generated definition].
bone organ of abdominal segment of trunk
Any muscle tissue that is part of the urethra.
Any muscle organ that is part of a thorax [Automatically generated definition].
Any muscle organ that is part of a respiratory system [Automatically generated definition].
A muscle organ that is part of an abdominal segment of trunk [Automatically generated definition].
muscle organ of abdominal segment of trunk
A blood vessel that is part of a thorax [Automatically generated definition].
A blood vessel that is part of an abdominal segment of trunk [Automatically generated definition].
blood vessel of abdominal segment of trunk
A skin of body that is part of an abdominal segment of trunk [Automatically generated definition].
A portion of connective tissue that is part of a thorax [Automatically generated definition].
A portion of connective tissue that is part of an abdominal segment of trunk [Automatically generated definition].
abdominal segment of trunk connective tissue
abdominal segment of trunk portion of connective tissue
abdominal segment of trunk textus connectivus
connective tissue of abdominal segment of trunk
portion of connective tissue of abdominal segment of trunk
textus connectivus of abdominal segment of trunk
An anatomical space that surrounded_by a neural tube.
In medicine, gonadal vein refers to the blood vessel that carrying blood away from the gonad (testis, ovary) toward the heart. Females : ovarian vein Males : testicular vein [WP,unvetted].
A neural crest that has_potential_to_developmentally_contribute_to a midbrain.
A neural crest that has_potential_to_developmentally_contribute_to a hindbrain.
Cranial neural crest that is part of the hindbrain.[TAO]
A neural crest that has_potential_to_developmentally_contribute_to a spinal cord.
We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...)[well established][VHOG]
A neural plate that develops_from a future spinal cord.
Neural plate that is part of the spinal cord. [Bgee_curator][VHOG]
(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...)[well established][VHOG]
Mesenchyme that is part of a developing gonad [Automatically generated definition].
A presumptive structure that has the potential to develop into a ganglion.
An anatomical cavity that has the potential to develop into a coelemic cavity lumen.
The part of the coelom in the embryo between the somatopleuric and splanchnopleuric mesoderm; the principal body cavities of the trunk (thoracic, abdominal, and pelvic) arise from this embryonic part of the coelom
consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. editor note: TODO check ZFA, which appears to be a structure present in adults
(...) I regard it unlikely that coeloms of all bilaterian animals are comparable and evolved very early. Considering all these questions, few convincing characters concerning the evolution of body cavities remain to be named. (...) A segmental coelom appears to have evolved at least two times, in Annelida and in Myomerata (Acrania and Craniota).[well established][VHOG]
ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.166
Initial section of the oviduct through which the ova pass from the ovary to the uterus
paired ducts of the embryo that run down the lateral sides of the urogenital ridge and terminate at the mullerian eminence in the primitive urogenital sinus. In the female, they will develop to form the fallopian tubes, uterus, and the upper portion of the vagina; in the male, they are lost. These ducts are made of tissue of mesodermal origin[WP]. develops either by lengthwise splitting of the archinephric duct (in chondrichthyans and some amphibians) or by a elongated invagination of the coelomic epithelium (other vertebrates) In males, the oviducts regress. The cranial end of the oviduct maintains an opening into the coelom (which primitively may have been the anteriormost coelomic funnels connecting the nephrocoel with the coelom). This opening is the ostium tubae[USM].
Either of the paired embryonic ducts developing into the uterine tubes, uterus, and vagina in the female and becoming largely obliterated in the male. [TFD][VHOG]
Transient developmental organ which gives rise to oviducts in female (documented to persist in some male frogs).[AAO]
In females, the archinephric (mesonephric) ducts tend to function only within the urinary systems. The muellerian duct arises embryologically next to the archinephric (wolffian) duct. In males, the muellerian duct regresses if it appears at all, but in females, the muellerian ducts become the oviducts of the reproductive system.[well established][VHOG]
Sertoli cells secrete anti-Mullerian hormone (AMH) inducing the demise of this duct
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.559
One of the skeletal muscles of the head and neck, spine, and ribs.
A portion of skeletal muscle tissue in the trunk.
The part of the retina that contains neurons and photoreceptor cells[GO].
(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG]
Epithelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues, with tube shape and organization varying from the single-celled excretory organ in Caenorhabditis elegans to the branching trees of the mammalian kidney and insect tracheal system.
contrast with a multi-tissue tube, which has as parts both epithelium, connective tissue, possibly muscle layers
Any endothelium that has the quality of being cylindrical [Automatically generated definition].
Kidney mesenchyme is the tissue made up of loosely connected mesenchymal cells in the kidney[GO].
A blood vessel that carries blood from the capillaries toward the heart
A duct that is part of a digestive system [Automatically generated definition].
An epithelium that lines the lumen of the digestive tract.
Epithelium lining the lumen of the gut.[TAO]
A cartilage element of chondrocranium. Example: neurocranial trabecula.
A cartilage element that is part of the cranial skeleton.
Cartilage which is part of the cranium.[TAO]
Any of the organized aggregations of cells that function as secretory or excretory organs and are associated with reproduction.
The sensory system for the sense of touch and pain.
The neural tissue involved in the transmission of sensory signals
MP defines this in a may more appropriate to somatosensory cortex
The slender connective tissue fiber in the extracellular matrix of skin tissue that is composed of microfibrils and amorphous elastin and is characterized by great elasticity
The internal feminine genital organs, including the ovaries, uterine tubes, uterus, uterine cervix, and vagina.
internal genitalia of female reproductive system
TODO: Relabel. Make distinct organ class. See https://github.com/obophenotype/uberon/issues/547
A conical pouch formed from the upper and left angle of the right ventricle in the chordate heart, from which the pulmonary artery arises[WP]. the anteriosuperior, smooth-walled portion of the cavity of the right ventricle, beginning at the supraventricular crest and terminates in the pulmonary trunk[MP].
Receives blood from the left atrium and becomes the median truncus arteriosus.[AAO]
Kardong says absent in adult tetrapods, check AAO
we use the term CA for the anterior chamber if it is composed of cardiac muscle, contractile, and contains conal valves internally
The funnel-like expansion of the abdominal extremity of the uterine tube[MP]
The third part of the uterine tube is the infundibulum. It terminates with the ostium of Fallopian tube, surrounded by fimbriae, one of which is attached to the ovary[Wikipedia:Infundibulum_of_uterine_tube].
The connection between the embryo proper and extraembryonic tissues
A transitional population of migrating mesenchymal cells that derive from somites and that will become dermal cells.
Not to be confused with 'dermatome segment of skin'.
The single layer of epithelial cells that lines the early neural tube and develops into the nervous system and into the neural crest cells
As the cells adjacent to the lumen continue to divide, the migrating cells form a second layer around the original neural tube. This layer becomes progressively thicker as more cells are added to it from the germinal neuroepithelium. This new layer is called the mantle (or intermediate) zone, and the germinal epithelium is now called the ventricular zone (and, later, the ependyma)[NCBIBook:NBK10047]
The layer of undifferentiated, proliferating cells that line the neural tube lumen that is the immediate transformation of the germinal neuroepithelium
consider merging with 'ventricular zone'; note that the MA class probably does not belong here, as this is an embryonic structure
The layer of undifferentiated, proliferating cells that line the neural tube lumen
The layer of glia and differentiating neurons that forms as a second layer around the germinal neuroepithium; as this develops it comes to lie between the ventricular and marginal layers and includes the basal and alar plates. Develops into neurons and glia forming a gray matter layer.
The outermost layer of the neural tube that consists of axons from the developing mantle layer and will form the white matter
The region of the mantle layer of the neural tube that lies ventral to the sulcus limitans and contains primarily motor neurons and interneurons.
Any of the veins that carries deoxygenated blood from a part of the body into the right atrium of the heart.
The subdivision of the face that includes the eye (eyeball plus adnexa such as eyelids) and the orbit of the skull and associated parts of the face such as the eyebrows, if present
note the FMA class is more narrow though, and is more like eye + muscles + vasculature. The FMA also has FMA:72951 orbital part of eye
Any tube, opening or passage that connects two distinct anatomical spaces.
FMA has both conduit and conduit space. In EHDAA2 this is a surface feature
A vasculature that is part of a iris [Automatically generated definition].
An anatomical structure that develops (entirely or partially) from the endoderm.
An anatomical structure that develops (entirely or partially) from the mesoderm.
An anatomical structure that develops (entirely or partially) from the ectoderm.
Anatomical system that has as its parts the organs concerned with the production and excretion of urine and those concerned with reproduction.
Anatomical system that has as its parts the organs concerned with the production and excretion of urine and those concerned with reproduction.[AAO]
relationship type change: differentiates_from intermediate mesoderm (AAO:0010575) CHANGED TO: develops_from intermediate mesoderm (UBERON:0003064)[AAO]
Kidneys and gonads (of vertebrates) develop from adjacent tissues, and after the excretory or urinary ducts have developed, the reproductive system usually taps into them or their derivatives.[well established][VHOG]
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.633
The optic vesicle is the evagination of neurectoderm that precedes formation of the optic cup[GO]. Portion of tissue that is comprised of neuroepitheium which has pinched off from the anterior neural keel and will form the optic cup[ZFA].
(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles.[well established][VHOG]
Genes: Six3, Pax6, Rx1 are expressed together in the tip of the neural plate [ISBN:9780878932504 "Developmental Biology"]. Development notes: During subsequent develop- ment, the optic vesicle invaginates and becomes a two-layered structure with an inner neural retina and outer retinal pigment epithelium. As soon as the developing optic vesicle makes contact with the overlying ectoderm, it induces the ectoderm to thicken and form the lens placode [PMID:16496288]
The first recognizable structure derived from the heart field
TODO - check plate vs rudiment vs primordium vs endocardial tube. See XAO
(In vertebrates) The embryonic mesoderm is the source of both the cardiogenic plate, giving rise to the future myocardium as well as the endocardium that will line the system on the inner side.[well established][VHOG]
PMID:15611355 Gittenberger-de Groot AC, Bartelings MM, Deruiter MC, Poelmann RE, Basics of cardiac development for the understanding of congenital heart malformations. Pediatric Research (2005)
A specific region of the lateral mesoderm that will form the primary beating heart tube. In mammals the primary heart field gives rise to the left ventricle.
this term denotes the primary heart field; GO:0003128 denotes the superclass of primary and secondary: specific region of the lateral mesoderm into the area which will form the primary beating heart tube[GO:0003138]
An epithelial tube that will give rise to the mature heart.
the paired, longitudinal, endothelial-lined channels formed from the cardiogenic mesoderm in embryonic development; angiogenic cell clusters (aka angioblastic cords) located in a horse-shoe shape configuration in the cardiogenic plate coalesce to form the right and left endocardial heart tubes which then fuse in cephalo-caudal direction to form a single primitive heart tube.
The outflow tract septum is a partition in the outflow tract
The outflow tract is the portion of the heart through which blood flows into the arteries
Depending on the species, attached at the cardiac outflow are described the conus arteriosus, the truncus arteriosus and, or the bulbus arteriosus. At the distal limit of these outflow structures, but lying outside the pericardial cavity, is the ventral aorta[PMID:20735616]
Vein of heart that drains the myocardium
A cardiac chamber surrounds an enclosed cavity within the heart
generic enough to cover FBbt:00003156 heart chamber but this is a cavity. GO defines it as the cavity. TODO - move subclasses. Note this also includes sinus venosus
The internal genitalia are the internal sex organs such as the uterine tube, the uterus and the vagina in female mammals, and the testis, seminal vesicle, ejaculatory duct and prostate in male mammals
TODO: make a subdivision of reproductive system. Relabel. See https://github.com/obophenotype/uberon/issues/547
The external genitalia are the outer sex organs, such as the penis or vulva in mammals
Organ that is part of the hematopoietic system.
consider splitting out lymph organ, compare with lymph node
the organs in which the formed elements of the blood and lymph are produced[http://encyclopedia2.thefreedictionary.com/Hematopoietic+Organs].
the FMA class 'lymphoid organ' is a general anatomical term
the nonstriated, involuntary muscle tissue located in the wall of the aorta
A portions of the gut that is derived from endoderm.
A nerve that is part of a back [Automatically generated definition].
A portion of smooth muscle tissue that is part of a urethra [Automatically generated definition].
A portion of smooth muscle tissue that is part of a large intestine [Automatically generated definition].
MA class may specifically mean muscle layer, but we treat as the sum of smooth muscle in both muscle layer and muscularis mucosa
A portion of smooth muscle tissue that is part of a intestine [Automatically generated definition].
A portion of smooth muscle tissue that is part of a stomach [Automatically generated definition].
A portion of smooth muscle tissue that is part of a vagina [Automatically generated definition].
A portion of smooth muscle tissue that is part of a respiratory system [Automatically generated definition].
A portion of smooth muscle tissue that is part of a digestive system [Automatically generated definition].
smooth muscle tissue of gastrointestinal system
the smooth muscle tissue surrounding the urothelium of the kidney pelvis
A portion of smooth muscle tissue that is part of a urinary bladder [Automatically generated definition].
A portion of smooth muscle tissue that is part of a neck of urinary bladder [Automatically generated definition].
involuntary muscle of neck of urinary bladder
involuntary muscle of urinary bladder neck
neck of urinary bladder involuntary muscle
neck of urinary bladder non-striated muscle
neck of urinary bladder smooth muscle tissue
non-striated muscle of neck of urinary bladder
non-striated muscle of urinary bladder neck
smooth muscle of neck of urinary bladder
smooth muscle tissue of neck of urinary bladder
smooth muscle tissue of urinary bladder neck
urinary bladder neck non-striated muscle
urinary bladder neck smooth muscle tissue
A portion of smooth muscle tissue that is part of an anal region [Automatically generated definition].
anal part of perineum involuntary muscle
anal part of perineum non-striated muscle
anal part of perineum smooth muscle tissue
involuntary muscle of anal part of perineum
non-striated muscle of anal part of perineum
smooth muscle tissue of anal part of perineum
A portion of smooth muscle tissue that is part of a lower respiratory tract [Automatically generated definition].
involuntary muscle of lower respiratory tract
lower respiratory tract involuntary muscle
lower respiratory tract non-striated muscle
lower respiratory tract smooth muscle tissue
non-striated muscle of lower respiratory tract
smooth muscle of lower respiratory tract
smooth muscle tissue of lower respiratory tract
A portion of smooth muscle tissue that is part of a iris [Automatically generated definition].
A portion of smooth muscle tissue that is part of an arteriole [Automatically generated definition].
smooth muscle found within, and composing the majority of the wall of blood vessels.
Vascular smooth muscle contracts or relaxes to both change the volume of blood vessels and the local blood pressure, a mechanism that is responsible for the redistribution of the blood within the body to areas where it is needed (i.e. areas with temporarily enhanced oxygen consumption). Thus the main function of vascular smooth muscle tonus is to regulate the caliber of the blood vessels in the body. Excessive vasoconstriction leads to hypertension, while excessive vasodilation as in shock leads to hypotension.
A portion of smooth muscle tissue that is part of a bronchus [Automatically generated definition].
A portion of smooth muscle tissue that is part of a fallopian tube [Automatically generated definition].
A portion of smooth muscle tissue that is part of a outflow tract [Automatically generated definition].
A bone that is part of the dorsal region of an animal.
this class may be obsoleted. See: https://github.com/obophenotype/mouse-anatomy-ontology/issues/93
Any muscle organ that is part of a skin of body [Automatically generated definition].
review as part of general integumentary system review - part of skin, or more generally, integumental system
in MA, the only skin muscle is arrector pili. The only integumental muscle is panniculus carnosus. In EMAPA, the arrector pili only
A blood vessel that is part of a back [Automatically generated definition].
A myocardium that is part of a outflow tract [Automatically generated definition].
(...) (theme) is how the vertebrate cardiovascular system differs from that of the presumptive evolutionary chordate ancestor. (...) At best we can tell there are two essential new ingredients: (1) vertebrates all have a continuous endothelial lining to the heart and vessels and (2) vertebrates have developed a second chamber in the heart, one designed for generating high systemic blood pressure.[uncertain][VHOG]
PMID:9187138 Fishman MC, Chien KR, Fashioning the vertebrate heart: earliest embryonic decisions. Development (1997)
A portion of connective tissue that is part of a back [Automatically generated definition].
A muscle that is part of the eye region.
Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body.
Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body.[VSAO]
The bilaminar epithelium formed from the myotome and dermatome.
Epithelial sheet on the external surface of the somite that gives rise to trunk, muscle and dermis. Within the dermomyotome there is also a medio-lateral difference. The central region makes dermis, the mesenchymal connective tissue of the back skin. The medial region (closest to neural tube) makes epaxial muscle, and the lateral region (furthest from neural tube) makes hypaxial muscle[http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=eurekah&part=A66768].
Epithelial sheet on the external surface of the somite that gives rise to trunk, muscle and dermis.[TAO]
Portion of somites that gives rise to dermis and muscles.[AAO]
all but the sclerotome of a mesodermal somite; the primordium of skeletal muscle and, perhaps, of the dermis.
Thus, representatives of the agnathan vertebrates, chondrichthyans, and sarcopterygians all have a layer of undifferentiated cells external to the embryonic myotome. In the amniotes, this external cell layer is the dermomyotome. The simplest interpretation of the similar position, morphology, and lack of myosin labeling is that a dermomyotome epithelium is a shared, ancestral vertebrate characteristic.[well established][VHOG]
DOI:10.1111/j.1525-142X.2006.05079.x Devoto SH, Stoiber W, Hammond CL, Steinbacher P, Haslett JR, Barresi MJF, Patterson SE, Adiarte EG and Hughes SM, Generality of vertebrate developmental patterns: evidence for a dermomyotome in fish. Evolution and Development (2006)
A cone-like structure that is formed when myocardial progenitor cells of the heart field fuse at the midline. The heart rudiment is the first structure of the heart tube.
The migrating myocardial precursors of the heart rudiment form a cone like structure between 19.5hpf and 22hpf, and eventually telescope out into the primitive heart tube at 24hpf. Stainier 2001.[TAO]
A blood vessel smooth muscle that is part of a respiratory system [Automatically generated definition].
smooth muscle tissue of blood vessel of respiratory system
respiratory system blood vessel smooth muscle
The primitive streak is a structure that forms during the early stages of avian, reptilian and mammalian embryonic development[WP]. the midline ridge of the embryonic epiblast that later develops into mesoderm and endoderm[MP]
(...) the blastopore equivalent of chordates (germ ring in fish, marginal zone/blastopore lip in frog and node/primitive streak in chick and mouse) (...) (reference 1); Indeed, the primitive streak has been considered the homologue of the blastopore since the 1870s (reference 2).[well established][VHOG]
VHOG includes a very broad grouping here based on http://www.ncbi.nlm.nih.gov/pubmed/9609826
primitive streak - blastopore - germ ring
PMID:9609826 Wu LH, Lengyel JA, Role of caudal in hindgut specification and gastrulation suggests homology between Drosophila amnioproctodeal invagination and vertebrate blastopore. Development (1998), ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.139
The embryonic structure that gives rise to the corneal ectoderm
multilayered ectodermal region at the distal tip of a limb or fin bud necessary for the proper development of the underlying mesenchyme[MP,modified]. Along with the zone of polarizing activity, it is a crucial organizing region during limb development[WP].
note that media, dorsal fins etc have AERs.
Distal ectodermal thickening which forms along the anterior-posterior limb axis. Signaling from this region influences proximal-distal patterning of the limb. Structure is missing in some lineages (salamanders, Eleutherodactylus coqui) however morphologically their indistinct distal ectoderm may still be involved in signaling.[AAO]
Proliferative region that is part of the developing fin fold or fin.[TAO]
relationship loss: subclass proliferative region (TAO:0000098)[TAO]
The AER of tetrapods regresses after specification of skeletal progenitors, the AER of teleosts form an elongating fin fold
maintaining mesenchyme in plastic proliferating state; maintaining expression of A-P axis genes; interacting with D-V proteins. Genes: AER induced by Fgf10 in mesenchyme. AER secretes Fgf8, which stimulates mitosis in the mesenchyme causing Fgf10 production - positive feedback loop
An outgrowth on the lateral trunk of the embryo that develops into a limb or paired fin. The limb/fin bud is divided into ectoderm and mesenchyme[cjm, modified from MP].
The tetrapod limb is derived from a posterior part of the fin endoskeleton of elasmobranchs and basal bony fish, the so-called metapterygium, a series of endoskeletal elements that is the first to form in the developing paired fins. (...) In addition, there is an independent endoskeletal element called the protopterygium that develops anterior to the metapterygium in many basal fishes (e.g., the bichir and sturgeon). Teleosts have lost the metapterygium whereas the sarcopterygians, on the other hand, have lost the protopterygium. Sarcopterygians thus develop all their endoskeletal structures from the metapterygium and consequently the tetrapod limb skeleton is derived from the metapterygium.[uncertain][VHOG]
Genes: In limb buds of chick and mouse, Shh expression is activated as soon as there is a morphological bud, whereas in S. canicula fin buds, consistent with reported data in other cartilaginous fishes, Shh is transcribed late in fin development[PMID:17187056]
DOI:10.1002/jez.1100 Wagner GP, Chiu C, The tetrapod limb: A hypothesis on its origin. J Exp Zool (Mol Dev Evol) (2001)
The first of the series of pharyngeal arches that develop into jaw bones or their homologs, and their associated nerves and arteries
The first of the series of bony or cartilaginous arches that develop in the walls of the mouth cavity and pharynx of the embryo.[AAO]
the first arch which contributes to development of mastication muscles, maxilla, mandible, incus, malleus, Meckel's cartilage, trigeminal nerve, and maxillary artery
One of a series of paired embryological vascular structures formed within a pharyngeal arch; in the adult, some of these vessels give rise to the great vessels[MP]
Paired vessels arching from the ventral to the dorsal aorta through the pharyngeal arches. [TFD][VHOG]
Number varies - Lampreys have 8, hagfishes 15; only up to 6 appear in embryonic development in most gnathostome fishes and all tetrapods
The third, fourth, and sixth arches, along with the seventh intersegmental arteries and the left dorsal aorta, are the primary contributors to the normal aortic arch and its major thoracic branches
A transparent homogeneous acellular layer, 6 to 9 um thick, lying between the basal lamina of the outer layer of stratified epithelium and the substantia propria of the cornea; it is considered to be a basement membrane.
Acellular anatomical structure that is the zone of collagen fibers adjacent the basement membrane of the corneal epithelium.[TAO]
Compared to terrestial animals, the cornea of zebrafish is relatively flat. It consists of nonpigmented, stratified squamous nonkeratinizing epithelial cells, attached to a thick basement membrane that is considered to be analogous to the Bowman's membrane in mammals
A bone that is part of an appendage [Automatically generated definition].
bone of free segment of appendicular skeleton
Sum of all sensory systems in an organism.
Any collection of skeletal muscles that is part of a head [Automatically generated definition].
This class is restricted to skeletal muscles that attach to the cranial skeleton. This seems to be consistent with FMA and EMAPA usage. Note that by definition this excludes invertebrate head musculature. It corresponds to the individual muscle organ term UBERON:0002376
Any collection of muscles that is part of a thorax [Automatically generated definition].
BTO and FMA do not mean precisely the same thing here. BTO thorax muscle is a pectoral muscle or diaphragm
Any collection of muscles that is part of a neck [Automatically generated definition].
Any collection of muscles that is part of a back [Automatically generated definition].
Any collection of muscles that is part of a pelvic girdle [Automatically generated definition].
A subdivision of the musculature of the body in the pectoral girdle region. Includes pectoral and shoulder muscles.
Any collection of muscles that is part of a face.
originally created to reflect the distinction drawn in FMA between a facial muscle and the entire musculature of the face. However, naming both does not serve any particular purpose
The collection of muscles that are part of the larynx.
currently defined by location rather than attachment
Any collection of muscles that is part of a trunk [Automatically generated definition].
A portion of cardiac muscle tissue that is part of a cardiac septum [Automatically generated definition].
A portion of cardiac muscle tissue that is part of a myocardium [Automatically generated definition].
Note placement of MA class based on parthood relationship
A vasculature that is part of a muscle organ [Automatically generated definition].
A vasculature that is part of a musculoskeletal system [Automatically generated definition].
Anatomical system that has as its parts the heart and blood vessels.
we treat cardiovascular as part of circulatory system, with the latter including other kinds of circulation, including lymph.
The vessels of the cardiovascular system are as varied as the diverse organs they supply. However, these variations are based on modifications of a fundamental plan of organization common to vertebrates.[well established][VHOG]
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.451
A vascular network consisting of blood vessels.
A kidney that is part of a left side of organism [Automatically generated definition].
A kidney that is part of a right side of organism [Automatically generated definition].
An eye that is part of a left side of organism [Automatically generated definition].
An eye that is part of a right side of organism [Automatically generated definition].
The part of the arterial system which carries oxygenated blood away from the heart to the body, and returns deoxygenated blood back to the heart.
The part of the cardiovascular system consisting of all arteries.
DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2005)
An artery of the systemic circulation, which is the part of the cardiovascular system which carries oxygenated blood away from the heart, to the body, and returns deoxygenated blood back to the heart.
The part of the venous system that drains the general body tissues[Kardong]
In human anatomy, the systemic venous system refers to veins that drain into the right atrium without passing through two vascular beds (i.e. they originate from a set of capillaries and do not pass through a second set of capillaries before reaching the right side of the heart). The term systemic venous system is often used to differentiate veins from veins that drain the pulmonary system (the pulmonary venous system) and veins that drain the digestive tract (the portal venous system). Large veins that are considered part of the systemic venous system are the: Superior vena cava; Inferior vena cava[WP]
Subdivision of cardiovascular system which has as its parts the right side of heart, the superior vena cava and the inferior vena cava[FMA]
The part of the cardiovascular system consisting of all venous vessels. In vertebrates with a double circulation, this can be divided into systemic and pulmonary portions.
An endothelium that lines the blood vasculature. Other endothelia may line lymph vessels, the heart
An anatomical wall that is part of an aorta, enclosing the luminal space.
the outermost layer of the aorta wall, containing connective tissue and collagen and elastic fibers
The membranous portion of the wall between the two lower chambers of the heart
The membranous septum is the upper part of ventricular septum[GO:0003149].
membranous part of interventricular septum
membranous portion of interventricular septum
pars membranacea (septi interventricularis)
pars membranacea septi interventricularis
The muscular portion of the wall between the two lower chambers of the heart
The muscular septum is the lower part of the ventricular septum[GO]
muscular part of interventricular septum
pars muscularis (septi interventricularis)
pars muscularis septi interventricularis
The raphe nuclei are thin plates of cells in and immediately adjacent to the sagittal plane.
we treat NR obscurus, NR magnus etc as parts of the raphe nuclei. This is consistent with treatment in FMA, where the class is 'set of raphe nuclei'
The costocervical trunk arises from the upper and back part of the subclavian artery, behind the scalenus anterior on the right side, and medial to that muscle on the left side. Passing backward, it splits into the deep cervical artery and the supreme intercostal artery (or the Highest intercostal artery), which descends behind the pleura in front of the necks of the first and second ribs, and anastomoses with the first aortic intercostal (3rd posterior intercostal artery). As it crosses the neck of the first rib it lies medial to the anterior division of the first thoracic nerve, and lateral to the first thoracic ganglion of the sympathetic trunk. In the first intercostal space, it gives off a branch which is distributed in a manner similar to the distribution of the aortic intercostals. The branch for the second intercostal space usually joins with one from the highest aortic intercostal artery. This branch is not constant, but is more commonly found on the right side; when absent, its place is supplied by an intercostal branch from the aorta. Each intercostal gives off a posterior branch which goes to the posterior vertebral muscles, and sends a small spinal branch through the corresponding intervertebral foramen to the medulla spinalis and its membranes. [WP,unvetted].
A portion of smooth muscle tissue that is part of an arterial system [Automatically generated definition].
A portion of smooth muscle tissue that is part of a venous system [Automatically generated definition].
An endothelium that is part of a vena cava [Automatically generated definition].
An endothelium that is part of a outflow tract [Automatically generated definition].
It is assumed that during evolution, a circulatory system composed of the heart and endothelial tubular system first formed in vertebrates, medial smooth muscle then appeared for regulation of the system, and innervation of the muscle tissue took place. This sequence of development assumed for phylogenesis is actually realized in the ontogenetic processes.[well established][VHOG]
DOI:10.1254/jjp.87.253 Shigei T, Tsuru H, Ishikawa N, Yoshioka K, Absence of endothelium in invertebrate blood vessels: significance of endothelium and sympathetic nerve/medial smooth muscle in the vertebrate vascular system. Japanese Journal of Pharmacology (2001)
An endothelium that is part of an arterial system [Automatically generated definition].
An endothelium that is part of a venous system [Automatically generated definition].
A blood vessel endothelium that is part of a respiratory system [Automatically generated definition].
respiratory system blood vessel endothelium
a transient fetal dilation of the distal (or cranial) heart tube located where the arterial trunk joins the ventral roots of the aortic arches
TODO - check relationship to bulbus arteriosus
A pear shaped chamber that functions as a capacitor, maintaining continuous blood flow into the gill arches. The bulbus arteriosus has three distinct layers. Hu et al. 2000.[TAO]
An appendage that is part of an appendage girdle complex.
this class is the union of the classes limb, pectoral fin and pelvic fin.
Paired appendage that consists of the posterior appendicular skeleton and associated soft and hard tissues, but excludes the pelvic girdle and its associated soft and hard tissues.
Paired appendage that consists of the anterior appendicular skeleton and associated soft and hard tissues, but excludes the pectoral girdle and its associated soft and hard tissues.
While the skeletons of teleost pectoral fins and tetrapod forelimbs are homologous at the level of endoskeletal radials, teleosts and tetrapods do not share homologous skeletal elements at the level of 'individuated' pro-, meso-, and metapterygia. Among osteichthyans, only basal actinopterygians retain the full complement of elements present in non-osteichthyan gnathostomes.[uncertain][VHOG]
DOI:10.1002/jmor.10264 Davis MC, Shubin NH, Force A, Pectoral fin and girdle development in the basal actinopterygians Polyodon spathula and Acipenser transmontanus. Journal of Morphology (2004)
The jugular veins are veins that bring deoxygenated blood from the head back to the heart via the superior vena cava.
The embryo and its adnexa (appendages or adjunct parts) or associated membranes (i.e. the products of conception) The conceptus includes all structures that develop from the zygote, both embryonic and extraembryonic. It includes the embryo as well as the embryonic part of the placenta and its associated membranes - amnion, chorion (gestational sac), and yolk sac[WP].
EHDAA2 places this as a subtype of organism. This leads to the inference that a conceptus is an embryo (if an embryo is defined as an organism at embryo stage), which eliminates the embryonic + extra-embryonic = conceptus
A transverse unitary subdivision of the neural tube that shares a common dorsoventral structure (floor, basal, alar, and roof plates), but each having differential molecular identities and fates; they comprise the secondary prosencephalon, diencephalon (prosomeres), the midbrain (mesomeres), and the hindbrain (rhombomeres).
We take the definition of neuromere from Puelles et al, although the existence of mesomeres and prosomeres may not be widely accepted
A metameric segment of the central nervous system.[ZFA]
Any segmental subdivision of a nervous system. Includes metameric developmental segments, such as vertebrates neuromeres.
revisit this after CARO is revised and/or we have defined metameric segment; note that with the additional of an A/P axis constraint this corresponds to what Richter at al call a neuromere (PMID:21062451)
An organ subunit that is part of a hindbrain [Automatically generated definition].
We explicitly merge the NCITA terms here
A specialized form of connective tissue in which the extracellular matrix is firm, providing the tissue with resilience, and/or mineralized and that functions in mechanical and structural support.[VSAO]
Four classes of mineralized tissues are found in vertebrates: bone, cartilage, dentine, and enamel. We think of cartilage and bone as skeletal tissues and of enamel and dentine as dental tissues, but enamel and dentine arose evolutionarily together with bone as skeletal tissues in the dermal skeleton (exoskeleton) of early vertebrates. Scales and teeth of sharks are examples of dermal skeletal elements that are still composed of the three ancient components-enamel, dentine, and bone. Cartilage, on the other hand, provided the basis for the second vertebrate skeletal system, the endoskeleton (Smith and Hall, 1990; Hall, 1998a,b). some invertebrate skeletal tissues have surprisingly bone-like features. Examples include chondrocytes interconnected by cell processes in cephalopod cartilages (Cole and Hall, 2004a,b), and the calcium phosphate layer in the shells of brachiopods (Rodland et al., 2003). However, neither bone nor mineralized cartilage have been found in invertebrates. Editors notes: TODO - develops_from
taken from version of VSAO used in TAO and used directly in Uberon
dermis-derived entity that is made of skeletal tissue.
A gland that is part of an anal canal [Automatically generated definition].
The primitive cartilagionous skeletal structure of the fetal skull that grows to envelop the rapidly growing embyonic brain. In humans, the chondrocranium begins forming at 28 days from mesenchymal condensations and is fully formed between week 7 and 9 of fetal development. While the majority of the chondrocranium is succeeded by the bony skull in most higher vertebrates, some components do persist into adulthood.[1] In Cartilagious fishes and Agnathans, the chondrocranium persist throughout life.[2] Embryologically, the chondrocranium represent the basal cranial structure, and lay the base for the formation of the endocranium in higher vertebrates[WP].
in contrast to chondrocranium, this structure is entirely cartiliginous. In Chondricthyes this is the same as the neurocranium. FMA:76621 is an undefined fetal structure, so we assume the correct placement is here. Note that this is distinct from MA:0000317 which is the uberon:neurocranium (the part of the cranium that encloses the brain)
cartiligionous skeletal structure of skull
Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles.
Organ entity that is typically involved in mechanical support and may have different skeletal tissue compositions at different stages.[VSAO]
Organ entity that may have different tissue compositions at different stages and is typically involved in mechanical support.[TAO]
Any bone that is part of the lower jaw skeleton. This includes (when present): the dentary/mandible, the articular, the splenial, the suprangular
Do not manually classify under here - bones are automatically classified
Anatomical system that consists of all the joints of the body.
A submucosa that is part of a respiratory system [Automatically generated definition].
A submucosa that is part of a larynx [Automatically generated definition].
A serous membrane that is part of a digestive system [Automatically generated definition].
serous membrane of gastrointestinal system
An anatomical wall that is part of a cardiac ventricle [Automatically generated definition].
anatomical wall of lower chamber of heart
the mucous membrane lining the respiratory tract
TODO - split respiratory tract mucosa from respiratory system mucosa
mucosa of organ of apparatus respiratorius
mucous membrane of apparatus respiratorius
A mucosa that is part of a gastrointestinal system.
The gut mucosa of amphioxus has insulin-secreting cells. http://www.ncbi.nlm.nih.gov/pubmed/16417468
A mucous gland that is part of a larynx [Automatically generated definition].
A mucous gland that is part of the skin.
Any of the tissue layers that comprise a blood vessel. Examples: tunica media, tunica adventitia.
An epithelium that is part of a uterine cervix [Automatically generated definition].
The epithelium of the cervix is varied. The ectocervix (more distal, by the vagina) is composed of nonkeratinized stratified squamous epithelium. The endocervix (more proximal, within the uterus) is composed of simple columnar epithelium
the pseudostratified ciliated epithelium that lines much of the conducting portion of the airway, including part of the nasal cavity and larynx, the trachea, and bronchi
An epithelium that is part of a oviduct [Automatically generated definition].
in FMA, epithelium of uterine tube is a subclass of ciliated columnar epithelium. MA introduces subtypes: ciliated columnar and cuboidal. We map the FMA type according to its relationships, not its label
columnar epithelium of the fallopian tube
An epithelium that is part of a respiratory system [Automatically generated definition].
apparatus respiratorius epithelial tissue
epithelial tissue of apparatus respiratorius
An epithelium that is part of a digestive system [Automatically generated definition].
epithelial tissue of gastrointestinal system
gastrointestinal system epithelial tissue
An epithelium that is part of an endometrium [Automatically generated definition].
In rodents and primates, the uterine epithelium (the endometrium) is eroded away so that maternal blood comes into direct contact with the trophoblast surface (called haemochorial)
epithelium of tunica mucosa of endometrium
An epithelium that is part of a upper respiratory tract [Automatically generated definition].
epithelial tissue of upper respiratory tract
upper respiratory tract epithelial tissue
An epithelium that is part of a lower respiratory tract [Automatically generated definition].
epithelial tissue of lower respiratory tract
lower respiratory tract epithelial tissue
An epithelium that is part of a larynx [Automatically generated definition].
composed of squamous epithelium in the upper larynx and ciliated columnar epithelium in the lower larynx [ISBN:0-397-51047-0]
the cellular avascular layer of the kidney luminar surfaces
A portion of skeletal muscle tissue that is part of a urethra [Automatically generated definition].
A portion of skeletal muscle tissue that is part of a respiratory system [Automatically generated definition].
respiratory system skeletal muscle tissue
skeletal muscle of apparatus respiratorius
skeletal muscle tissue of apparatus respiratorius
skeletal muscle tissue of respiratory system
A portion of skeletal muscle tissue that is part of an anal region [Automatically generated definition].
anal part of perineum skeletal muscle tissue
skeletal muscle of anal part of perineum
skeletal muscle tissue of anal part of perineum
A portion of skeletal muscle tissue that is part of a lip [Automatically generated definition].
this class is derived from MA. Consider re-modeling this as being a muscle that acts on the lips. See: http://en.wikipedia.org/wiki/Lip#Muscles_acting_on_the_lips
An endothelium of artery that is part of a respiratory system [Automatically generated definition].
apparatus respiratorius arterial endothelium
apparatus respiratorius artery endothelium
apparatus respiratorius endothelium of artery
arterial endothelium of apparatus respiratorius
arterial endothelium of respiratory system
artery endothelium of apparatus respiratorius
artery endothelium of respiratory system
endothelium of artery of apparatus respiratorius
endothelium of artery of respiratory system
respiratory system endothelium of artery
An endothelium of vein that is part of a respiratory system [Automatically generated definition].
apparatus respiratorius endothelium of vein
apparatus respiratorius vein endothelium
apparatus respiratorius venous endothelium
endothelium of vein of apparatus respiratorius
endothelium of vein of respiratory system
vein endothelium of apparatus respiratorius
venous endothelium of apparatus respiratorius
venous endothelium of respiratory system
the thin layer of flat cells that line the aorta and form a barrier between circulating blood in the lumen and the rest of the vessel wall
endothelium of trunk of systemic arterial tree
trunk of systemic arterial tree endothelium
An endothelium that is part of the cardiovascular system.
A connective tissue that surrounds a skeletal muscle tissue.
connective tissue of skeletal muscle tissue
portion of connective tissue of skeletal muscle
portion of connective tissue of skeletal muscle tissue
skeletal muscle portion of connective tissue
skeletal muscle tissue connective tissue
skeletal muscle tissue portion of connective tissue
skeletal muscle tissue textus connectivus
textus connectivus of skeletal muscle tissue
A gland that is part of a eye. The eye is a compound unit which depending on the species may consist of an eyeballs plus associated ducts and integumentary structures. Eye glands therefore include the various types of lacrimal gland, the various types of apocrine and sebaceous glands associated with the eyelid.
Examples: harderian gland, accessory lacrimal gland, gland of Moll, gland of Zeis, nictitating membrane glands
A vasculature that is part of a retina [Automatically generated definition].
Layer of lateral plate mesoderm that forms the circulatory system and future gut wall - overlies endoderm[WP].
We group the BILA class here. Considering adding more general class for metazoa grouping cardiogenic successors
splanchnic layer of lateral plate mesoderm
A structure created during embryogenesis when the lateral mesoderm splits into two layers - the inner (or splanchnic) layer adheres to the endoderm, and with it forms the splanchnopleure[WP].
A structure created during embryogenesis when the lateral mesoderm splits into two layers - the outer (or somatic) layer becomes applied to the inner surface of the ectoderm, and with it forms the somatopleure.[WP].
Gives rise to the paired appendages in jawed vertebrates. a persistent somatopleure through the redistribution and expansion of the lateral plate mesoderm is a synapomorphy for gnathostomes and a critical step in generating a novel developmental module with dramatic evolutionary potentia (Tulenko et al. 2012) http://burkelab.research.wesleyan.edu/current-projects/lamprey/
sources differ as to whether this is part-of or develops-from the LPM
A portion of the urogenital ridge which is the source of much of the urinary system[WP].
part_of or develops_from urogenital ridge?
One of of the pair of folds derived from the cloacal folds which give rise to a portion of the external genitalia; in male embryos they close over the urethral plate and fuse to form the spongy (penile) urethra and ventral aspect of the penis, not including the glans; failure of fusion of the urethral folds leads to hypospadias; in female embryos they fuse only anterior to the anus and form the labia minora[MP].
Less commonly, urogenital fold refers to the fold in the mesonephros which is the precursor of e.g. the suspensory ligament of the ovary. This is the case in older versions of Gray's anatomy[WP]
The central region of trunk mesoderm. This tissue forms the notochord
Notochord rudiment[ZFIN:ZDB-PUB-961014-576].
WP treats this as synonym of axial mesoderm. Induces neural tube. Gilbert: contains an anterior head process and the notochord.
The mass of tissue made up of mesenchymal cells in the lung.
The fetal urogenital sinus (from which the prostate derives) is a simple cylinder of stratified basal epithelium, surrounded by mesenchyme and positioned between the embryonic bladder and pelvic urethra
we follow EHDAA2 in dividing the UGS into epithelium and lumen
A neuron projection bundle that connects the retina or its analog in the eye with the brain. This includes the vertebrate optic nerve (not truly a nerve) as well as analogous structures such as the Bolwig nerve in Drosophila
for the vertebrate-specific structure, see UBERON:0000941 (cranial nerve II)
neuron projection bundle connecting eye with brain
Anatomical cluster that connects two or more adjacent skeletal elements or hardened body parts.
A portion of the gut that is derived from ectoderm.
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
after reasoning this should subsume the more specific germinal epithelium classes. We include the fly structure here although it is not clear if the sheath is an epithelium or a multi-tissue structure that includes epithelium as parts
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.
A part of a wall of an organ that forms a layer.
The tissue underlying the tunica mucosa of the pharynx.
A submucosa that is part of a sigmoid colon [Automatically generated definition].
The submucous layer of the wall of the urinary bladder.
A submucosa that is part of a neck of urinary bladder [Automatically generated definition].
A mucosa that is part of a ureter [Automatically generated definition].
A mucosa that is part of a vagina [Automatically generated definition].
A mucosa that is part of a sigmoid colon [Automatically generated definition].
A mucosa that is part of a right ureter [Automatically generated definition].
A mucosa that is part of a left ureter [Automatically generated definition].
A mucosa that is part of a renal pelvis [Automatically generated definition].
A mucosa that is part of a neck of urinary bladder [Automatically generated definition].
mucosa of organ of neck of urinary bladder
mucous membrane of neck of urinary bladder
A mucosa that is part of a right uterine tube [Automatically generated definition].
A mucosa that is part of a left uterine tube [Automatically generated definition].
A mucosa that is part of a female urethra [Automatically generated definition].
A mucosa that is part of a lower lip [Automatically generated definition].
A mucosa that is part of a fallopian tube [Automatically generated definition].
A mucosa that is part of a uterine tube infundibulum [Automatically generated definition].
mucosa of infundibulum of fallopian tube
mucosa of organ of uterine tube infundibulum
mucous membrane of uterine tube infundibulum
organ mucosa of uterine tube infundibulum
uterine tube infundibulum mucosa of organ
uterine tube infundibulum mucous membrane
An external genitalia that is part of a female reproductive system [Automatically generated definition].
in eutherians, this is known as the vulva in and composed of the mons pubis, the labia majora and minora, the clitoris, the vestibule of the vagina and its glands, and the opening of the urethra and of the vagina [MP:0003126]
external genitalia of female reproductive system
A gland that is part of a hemolymphoid system [Automatically generated definition].
The median dorsal longitudinal groove formed in the embryo by the neural plate after the appearance of the neural folds.
The neural groove is a shallow median groove between the neural folds of an embryo. The neural folds are two longitudinal ridges that are caused by a folding up of the ectoderm in front of the primitive streak of the developing embryo. The groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or canal, the ectodermal wall of which forms the rudiment of the nervous system. After the coalescence of the neural folds over the anterior end of the primitive streak, the blastopore no longer opens on the surface but into the closed canal of the neural tube, and thus a transitory communication, the neurenteric canal, is established between the neural tube and the primitive digestive tube. The coalescence of the neural folds occurs first in the region of the hind-brain, and from there extends forward and backward; toward the end of the third week the front opening (anterior neuropore) of the tube finally closes at the anterior end of the future brain, and forms a recess which is in contact, for a time, with the overlying ectoderm; the hinder part of the neural groove presents for a time a rhomboidal shape, and to this expanded portion the term sinus rhomboidalis has been applied. Before the neural groove is closed a ridge of ectodermal cells appears along the prominent margin of each neural fold; this is termed the neural crest or ganglion ridge, and from it the spinal and cranial nerve ganglia and the ganglia of the sympathetic nervous system are developed. By the upward growth of the mesoderm the neural tube is ultimately separated from the overlying ectoderm. The cephalic end of the neural groove exhibits several dilatations, which, when the tube is closed, assume the form of three vesicles; these constitute the three primary cerebral vesicles, and correspond respectively to the future fore-brain (prosencephalon), mid-brain (mesencephalon), and hind-brain (rhombencephalon). The walls of the vesicles are developed into the nervous tissue and neuroglia of the brain, and their cavities are modified to form its ventricles. The remainder of the tube forms the medulla spinalis or spinal cord; from its ectodermal wall the nervous and neuroglial elements of the medulla spinalis are developed while the cavity persists as the central canal[Wikipedia:Neural_groove].
One of the two elevated edges of the neural groove[GO,MP].
In front of the primitive streak two longitudinal ridges, caused by a folding up of the ectoderm, make their appearance, one on either side of the middle line. These are named the neural folds; they commence some little distance behind the anterior end of the embryonic disk, where they are continuous with each other, and from there gradually extend backward, one on either side of the anterior end of the primitive streak. Also, after differentiation it turns into the neural tubes[Wikipedia:Neural_fold].
A solid rod of neurectoderm derived from the neural keel. The neural rod is roughly circular in cross section. Neural rod formation occurs during primary neurulation in teleosts[GO]. An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube[ZFIN].
An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube. Kimmel et al, 1995.[TAO]
An anatomical boundary that adjacent_to a hindbrain and adjacent_to a spinal cord.
The portion of the ureteric bud tube that contributes to the morphogenesis of the metanephros[GO].
The portion of the ureteric bud that contributes to the morphogenesis of the ureter. The ureter ureteric bud is the initial structure that forms the ureter[GO].
An ectodermal placode is a thickening of the ectoderm that is the primordium of many structures derived from the ectoderm[GO]
consder adding placodal ectoderm as a distinct class? Also place placodal ectoderm as develops_from ectoderm; need to check taxon-appropriateness
With the exception of the adenohypophysis, homologues of the nonneurogenic placodes (e.g. placodes giving rise to the teeth, hair follicles and lens), appear to be lacking in invertebrate chordates.
in GO, covers optic, otic, olfactory, mammary, hair, tooth, sebaceous - and also insect structures
Muscle structures are contractile cells, tissues or organs that are found in multicellular organisms[GO].
in some organisms such as drosophila, muscles can be single cells. This class groups together all discrete muscle elements, from multicellular muscle organs in vertebrates, to individual single-cell muscles in drisophila
class added for consistency with GO - consider merging with kidney mesenchyme.
An epithelium that is part of a mesonephros [Automatically generated definition].
A metanephric tubule is an epithelial tube that is part of the metanephros[GO].
An epithelium is a tissue that covers the internal or external surfaces of an anatomical structure[GO].
Any smooth muscle tissue that is part of a metanephros.
The metanephric capsule is the tough fibrous layer surrounding the metanephros, covered in a thick layer of perinephric adipose tissue. It provides some protection from trauma and damage[GO].
A bud is a protrusion that forms from an epithelial sheet by localized folding.
Any anatomical structure that is part of the reproductive system.
An epithelial sheet bent on a linear axis.
A structure consisting of multiple cell components but which is not itself a cell and does not have (complete) cells as a part.
we go with the FMA classification rather than the CARO one. FMA def: 'Anatomical cluster which has as direct parts cell parts from two or more cells.'
An organ or element that is in the abdomen. Examples: spleen, intestine, kidney, abdominal mammary gland.
An organ or element that is part of the adbominal segment of the organism. This region can be further subdivided into the abdominal cavity and the pelvic region.
An organ or element that part of the dorsum of the organism. Examples: spinal cord, vertebrae, muscles of back.
An organ or element that part of the trunk region. The trunk region can be further subdividied into thoracic (including chest and thoracic cavity) and abdominal (including abdomen and pelbis) regions.
An organ or element that is in the thoracic cavity. Examples: lung, heart, longus colli.
An organ or element that is part of the pelvic region. Examples: reproductive organs (in some organisms), urinary bladder, bones of the pelvis.
An organ that part of the thoracic segment region. This region can be further subdividied chest and thoracic cavity regions.
A vein that is part of a thorax [Automatically generated definition].
A gland that is part of a larynx submucosa [Automatically generated definition].
An external ectoderm that is part of a optic eminence [Automatically generated definition].
An ectoderm that is part of a optic eminence [Automatically generated definition].
The ventral half of the developing neural tube that is the metencephalon. [Chordate_evolution_and_the_origin_of_craniates:_An_old_brain_in_a_new_head._AnaT_Rec_(New_Anat)_(2000)_261(3):_111-125, See_Butler_AB][VHOG]
An endocardium that is part of a interventricular septum [Automatically generated definition].
interventricular septum endocardial tissue
A myocardium that is part of a bulbus cordis [Automatically generated definition].
A renal pelvis that is part of a metanephros.
The ureteric bud itself forms the collecting tubules and the ureter that drain the adult kidney. This type of kidney, called the metanephros, occurs in all adult amniotes.[well established][VHOG]
Portion of primordial embryonic connective tissue of the developing head, consisting of mesenchymal cells supported in interlaminar jelly, that derive mostly from the mesoderm and contribute to head connective tissue, bone and musculature in conjunction with cranial neural crest cells.
Mesoderm that will give rise, along with cranial neural crest cells, to connective tissue, bone and musculature in the head. (Source: BioGlossary, www.Biology-Text.com)[TAO]
Mesenchyme that is part of a developing trunk.
The posterior part of the developing vertebrate hindbrain or the corresponding part of the adult brain composed of the medulla oblongata and a portion of the fourth ventricle; as well as the glossopharyngeal nerve (CN IX), vagus nerve (CN X), accessory nerve (CN XI), hypoglossal nerve (CN XII), and a portion of the vestibulocochlear nerve (CN VIII).[BTO,WP].
The posterior of the two brain vesicles formed by specialization of the rhombencephalon in the developing embryo, it comprises the medulla oblongata. [TFD][VHOG]
the terms metencephalon and myelencephalon are only meaningful in mammals and birds - Neuroanatomy of the Zebrafish Brain. Note that its not clear if this refers to the developing medulla oblongata - MA (adult) has two distinct classes
A portion of tissue that is part of an embryo.
Portion of tissue that is contiguous with the embryo and is comprised of portions of tissue or cells that will not contribute to the embryo.
The endothelial lining of the endocardium.
An pulmonary artery endothelium is an epithelium that lines the pulmonary artery[GO].
Mesonephric mesenchyme is the tissue made up of loosely connected mesenchymal cells in the mesonephros[GO].
A ventricular outflow tract is a portion of either the left ventricle or right ventricle of the heart through which blood passes in order to enter the great arteries. The right ventricular outflow tract (RVOT) is an infundibular extension of the ventricular cavity which connects to the pulmonary artery. The left ventricular outflow tract (LVOT), which connects to the aorta, is nearly indistinguishable from the rest of the ventricle[WP].
An outflow tract that is part of a aorta.
the group of sensory neuron cell bodies associated with the vagus nerve
An epithelium that lines the nasal cavity.
this class may in future be split into the embryonic precursor of the oronasal membrane and the structure that is part of the mucosa in the developed organism
An array of photoreceptors and any supporting cells found in an eye.
A transparent structure that is part of a visual sense organ, the function of which is to direct or focus light onto a photoreceptor array.
directing or focusing light onto light receptors
One of: the common carotid artery, or its branches, the external and internal carotid arteries.
This is a generic grouping class that is the superclass of the trunks/branches of the common carotid artery. Note that AOs vary widely in how they divide up and generalize arteries
Artery originating at the junction of the first two aortic arches and supplying the anterior brain. Kimmel et al, 1995.[TAO]
A sex gland that is part of a female reproductive system.
The part of the digestive system that excludes the hepatobiliary system.
the decision to split digestive and gastrointestinal in this way may be revisited. As it currently stands, this class more closely aligns what MA calls the alimentary system
The system that includes the esophagus, stomach, small and large intestine, anus, liver, biliary tract, and pancreas[ncithesaurus:Gastrointestinal_System].
All metazoans (with degenerate exceptions) have some sort of digestive cavity with a means of entrance to and exit from it.[well established][VHOG]
that many anatomy ontologies consider this 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. We have one entity that is part of both gastrointestinal and hepatobiliary systems: hepatopancreatic ampulla.
alimentary part of gastrointestinal system
ISBN:978-0721676685 Sherwood Romer A and Parsons T, Vertebrate body (1977) p.3
A limb bud that develops into a forelimb or pectoral fin.
Fin bud that develops into the pectoral fin.[TAO]
at this time we have no need to name a more specific 'pectoral fin bud' class, but we may in future
A limb bud that develops into a hindlimb or pelvic fin.
Fin bud that develops into the pelvic fin.[TAO]
Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG]
at this time we have no need to name a more specific 'pelvic fin bud' class, but we may in future
ISBN:978-0198540472 Janvier P, Early vertebrates (1996) p.268
An apical ectodermal ridge that is part of a pectoral appendage bud.
An ectodermal thickening at the end of the forelimb bud in the developing embryo. [TFD][VHOG]
Apical ectodermal ridge that is part of the pectoral fin bud.[TAO]
Pectoral and pelvic fins are homologous to the tetrapod fore and hindlimb, respectively. (...) The zebrafish AER [apical ectodermal ridge] is an apical ectodermal thickening at the distal tip of the fin bud and consists of wedge-shaped cells of the basal stratum. The AER is observed only transiently, and from 36 hpf onwards the cells of this region form the apical fold (AF), which consists of a dorsal and a ventral layer of cylindrically-shaped ectodermal cells extending from the anterior to the posterior fin margin. Despite the change in shape, the AF still carries out the same functions as the AER. Indeed, although the AER receives its name from its characteristic shape, being composed of a pseudostratified ectoderm in the chicken and a polystratified ectoderm in the mouse, this independence of AER morphology from its function is also observed in tetrapods. The AF also expresses similar molecular markers to the tetrapod AER, suggesting that it fulfills similar functions in the fin as the AER does in tetrapod limbs.[well established][VHOG]
apical ectodermal ridge pectoral fin bud
pectoral appendage apical ectodermal ridge
An apical ectodermal ridge that is part of a pelvic appendage bud.
An ectodermal thickening at the end of the hindlimb bud in the developing embryo. [TFD][VHOG]
Apical ectodermal ridge that is part of the pelvic fin bud.[TAO]
pelvic appendage apical ectodermal ridge
Portion of tissue that is the inner layer of the optic cup and will become the neural retina.
Portion of tissue that gives rise to the lens.
A vesicle formed from the lens pit of the embryo, developing into the crystalline lens. [TFD][VHOG]
the lens of zebrafish (and other teleosts) forms from delamination of cells from the lens placode; thus, there is no formation of a hollow lens vesicle, in contrast to the situation in mammals and birds (Glass and Dahm, 2004) [PMID:16496288] The lens of the zebrafish forms by delamination of lens placodal cells and not through invagination. This results in a solid spherical mass as opposed to a hollow lens vesicle. Detachment of the solid lens vesicle of zebrafish at 24b26 hpf is accomplished in part by apoptosis, similar to mammals
Portion of tissue that is part of the eye and gives rise to the mature, fully layered cornea.
Vagal neural crest is adjacent to the first seven somites gives rise to both ganglionic and ectomesenchymal derivatives[ZFA].
Vagal neural crest is adjacent to the first seven somites gives rise to both ganglionic and ectomesenchymal derivatives.[TAO]
In chicken fate mapping studies it was found to originate from neural crest residing between Somite 1-7 (S1-7); In mouse it is considered to be derived from rhombencephalic (post otic) neural crest cells and trunk neural crest cells (anterior to S5)
The dilated structure that is lined by endothelial cells and located at the arterial pole of the heart just above (distal to) the truncus arteriosus in mammalian embryos; it is the primordial vascular channel from which the aortic arches (and eventually the dorsal aortae) arise; the aortic sac is homologous to the ventral aorta of gill-bearing vertebrates
the merged ventral aortae of the embryo which supplies blood to the aortic arches[TMD][http://medical-dictionary.thefreedictionary.com/aortic+sac].
The jugular foramen is a large aperture in the base of the skull. It is located behind the carotid canal and is formed in front by the petrous portion of the temporal, and behind by the occipital; it is generally larger on the right than on the left side
Large foramen that houses the glossopharyngeal and vagus nerves and is located inside the condyloid fossa.[AAO]
One of a pair of openings between the lateral part of the occipital bone and the petrous part of the temporal bones in the skull. The foramen contains the inferior petrosal sinus; the transverse sinus; some meningeal branches of the occipital and ascending pharyngeal arteries; and the glossopharyngeal, vagus, and accessory nerves. [Free_Online_Medical_Dictionary]
relationship loss: subclass braincase and otic capsule opening (AAO:0000051)[AAO]
A longitudinal groove in the neural tube wall that divides the neural tube into dorsal (alar) and ventral (basal) halves (dorsal receives input from sensory neurons, ventral effects motor functions); stretches from the mesencephalon caudad[TMD].
neural tube lateral wall sulcus limitans
Cranial neural crest which gives rise to the glossopharyngeal ganglion.
Portion of tissue on the side of the lumen of the neural tube.
todo - epidermis? todo - track down EHDAA2 class in new release
In the early gastrula of vertebrates, factors from the organizer (e.g. noggin, chordin, and follistatin in Xenopus) antagonize the epidermalizing factor bone morphogenetic protein 4 (BMP4), thus dividing the epiblast into neuroectoderm. In Drosophila, decapentaplegic, the homologue of BMP4, interacts similarly with the protein short gastrulation, the homologue of chordin. Thus, a comparable molecular mechanism for distinguishing non-neural ectoderm from neural ectoderm was probably present in the common ancestor of all bilaterally symmetrical animals.[well established][VHOG]
After gastrulation, neural crest cells are specified at the border of the neural plate and the non-neural ectoderm.
Gene notes: One of the first genes to be expressed in nonneural ectoderm in amphioxus is BMP2/4 (Panopoulou et al. 1998). BMP2/4 homologues appear to have a very ancient role in distinguishing neural from nonneural ectoderm; in Drosophila as well as in amphioxus and vertebrates, BMP2/4 homologues are expressed in nonneural ectoderm and function in distinguishing neural from nonneural ectoderm (Francois & Bier, 1995 ; Sasai et al. 1995 ; Wilson & Hemmati-Brivanlou, 1995; Panopoulou et al. 1998). A change in level of BMP2/4 from very high in nonneural ectoderm to low in neural ectoderm appears to be a key factor in development of neural crest (Baker & Bronner-Fraser,1997a,1997b;Erickson&Reedy,1998;Marchantet al.1998 ;Selleck et al. 1998).
Multi-tissue structure that arises from the heart rudiment and will become the heart tube.
A neural tube lateral wall that is part of a rhombomere.
Cranial neural crest which gives rise to the trigeminal ganglion.
todo - compare ZFA and EHDAA2 representation
Portion of tissue that gives rise to the immature gonad.
Immature reproductive tissue that has not undergone final maturation into either testis or ovary.[TAO]
Cranial neural crest that gives rise to the facio-acoustic ganglion.
Somite located in the head region, caudal to the otic vesicle
They provide the epaxial and hypaxial muscles of the neck, the pharyngeal and laryngeal muscles that develop in the caudal branchial arches and the musculature of the tongue. Despite their localisation in the head, myogenic precursors from occipital somites essentially follow the trunk programmes (E. H. Walters and S. D., unpublished). during evolution, have been secondarily incorporated into the head (Gans and Northcutt, 1983)
EHDAA2 has both 'head somite' and 'head somite group', with part_of and develops_from for latter
A pair of lateral diverticula just over the liver rudiment representing the primordia of the lungs, formed by the floor of the foregut just anterior to the liver diverticulum.
Any of the three veins including the common, external and internal iliac veins.
A study of embryos shows that in all vertebrates six arterial arches link the ventral aorta with a pair of lateral dorsal aortae on each side of the body. The latter unite posteriorly to form a single median dorsal aorta wich takes blood to the body.[well established][VHOG]
Contributes to the arch of aorta in humans
ISBN:978-0174480198 Roberts MBV, Biology: a functional approach (1986) p.572
A layer of cuboidal epithelial cells bounded anteriorly by the capsule of the lens and posteriorly by the lens cortex.
Cells of the subcapsular epithelium (or anterior lens cells) are mitotically active. In adult individuals they only cover the anterior 'hemisphere' of the lens. As they divide, cells gradually move towards the equator of the lens where they tranform into lens fibres. The apical part of the gradually elongating cell extends between the subcapsular epithelium and adjacent lens fibres towards the anterior pole of the lens. The basal part extends towards the posterior pole. The nucleus remains close to the equatorial plane of the lens - http://www.lab.anhb.uwa.edu.au/mb140/corepages/eye/eye.htm
Arteries which arise from the abdominal aorta and distribute to most of the intestines.
includes posterior and anterior mesenteric arteries, which branch from the dorsal aorta (see Kardong), and superior and inferior mesenteric arteries
A vein that returns blood from the intestines.
In humans the inferior mesenteric vein empties into the splenic vein, the superior mesenteric vein joins the splenic vein to form the portal vein
An epithelium that is part of a anterior chamber of eyeball.
An epithelium that is part of a lens vesicle.
An ectoderm that is part of a pharyngeal arch 2.
In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG]
An ectoderm that is part of a pharyngeal arch 4.
An endoderm that is part of a pharyngeal arch 2.
An endoderm that is part of a pharyngeal arch 4.
An endothelium that is part of a right lung.
An endothelium that is part of a left lung.
An anatomical cavity that is part of a lens vesicle.
Mesenchyme that is part of a pharyngeal arch 2.
Mesenchyme that is part of a pharyngeal arch 4.
Mesenchyme that is part of a optic eminence.
A venous system that is part of a hindbrain.
A mesoderm that has the potential to develop into a pronephros.
Portion of tissue that consists of the mesenchymal precursor to the pronephric kidney and that begins to separate from the intermediate mesoderm at NF stage 21 and epithelializes by NF stage 30.[AAO]
the intermediate mesoderm of the chick embryo acquires its ability to form kidneys through its interactions with the paraxial mesoderm [ISBN:9780878932504 "Developmental Biology", http://www.ncbi.nlm.nih.gov/pubmed/10720431 "Signals from trunk paraxial mesoderm induce pronephros formation in chick intermediate mesoderm"]. These interactions induce the expression of TFs including Lim1, Pax2 and Pax6 that cause the intermediate mesoderm to form the kidney
A limb/fin field that has the potential to develop into a pectoral appendage bud mesenchyme.
Embryonic region that develops into the pectoral fin bud.[TAO]
pectoral appendage field of lateral plate mesoderm
A limb/fin field that has the potential to develop into a pelvic appendage bud mesenchyme.
Embryonic region that develops into the pelvic fin bud.[TAO]
pelvic appendage field of lateral plate mesoderm
A ring of cells capable of forming a limb or paired fin[Gilbert,modified].
we represent the field as being a part of the LPM (consistent with ZFA, Gilbert). As a consequence, the relationship between limb bud (with is ectoderm+mesenchyme) stands in a weaker has_developmental_contribution_from relation to the field - TODO implement this.
limb/fin field of lateral plate mesoderm
The outermost layer of a blood vessel, composed mainly of fibrous tissue.
TODO - note terminological problems. WP says tunica external layer of blood vessel. FMA says tunica externa = adventitia, and is FMA adventitia covers other kinds of vessels. Here we opt for a lengthier name that attempts to disambiguate. There is no precise FMA equivalent, as FMA has tunica externa of arteries, veins, genital ducts etc as siblings
The outermost layer of a blood vessel, surrounding the tunica media. It is mainly composed of collagen. The collagen serves to anchor the blood vessel to nearby organs, giving it stability[Wikipedia:Tunica_externa_%28vessels%29].
A tunica intima that is part of a artery.
An outermost connective tissue covering of an organ, vessel, or other structure[WP].
Anatomical space that is an opening in a bone, usually for passage of blood vessels or nerves.
in FMA and ZFA this is a conduit space, not a conduit. Note there may be some additional disambiguation required: foramen is used loosely in the sense of any opening (e.g. foramen primum). FMA appears to use cranial conduit (undefined) in the sense of any foramen of the skull (includes mental foramen, which is not in the cranium proper).
The metanephros develops from the most caudal part of the nephrogenic cord that is itself derived from the intermediate plate mesoderm.
The initial renal anlage that develops from the most rostral part of the nephrogenic cord is termed the pronephros.
A acellular anatomical structure that is the bounding layer of a anatomical structure.
An acellular membrane that is part of the epithelium, lies adjacent to the epithelial cells, and is the fusion of the the basal lamina and the reticular lamina.
this class represents a continuous sheet of basement membrane which can underlie multiple epithelial cells over large regions. In contrast, the GO class 'basal membrane' represents a portion of substance on the scale of a single cell.
Nephric tubules (nephrons) form embryonically along the nephric ridge. The ridge comprises three regions; anterior, middle and posterior. The functional kidney uses nephrons from only one or two regions of the ridge. A pronephric kidney uses only the nephrons from the anterior region of the ridge. A mesonephric kidney uses only the middle region, a metanephric kidney uses only the posterior region and an opisthonephric kidney uses the middle and posterior regions.
TODO - check ridge vs cord vs nephrogenic cord vs blastema
Any portion of the aorta including the ascending and descending aorta, and aortic arch or a portion of the aortic orifice of the left ventricle.
The dorsal aorta is a blood vessel in a single-pass circulatory system that carries oxygenated blood from the gills to the rest of the body. In a single-pass circulatory system blood passes once through the heart to supply the body once.
Each primitive aorta receives anteriorly a vein 'the vitelline vein' from the yolk-sac, and is prolonged backward on the lateral aspect of the notochord under the name of the dorsal aorta. The dorsal aortae give branches to the yolk-sac, and are continued backward through the body-stalk as the umbilical arteries to the villi of the chorion. The two dorsal aortae combine to become the descending aorta in later development[WP].
Principal unpaired, median artery of the trunk, leading from the paired roots (radices) of the dorsal aorta to the caudal artery. Kimmel et al, 1995.[TAO]
The artery in vertebrate embryos that transports blood from the aortic arches to the trunk and limbs. In adult fish it is a major artery that carries oxygenated blood from the efferent branchial arteries to branches that supply the body organ. In adult tetrapods it arises from the systemic arch
relationship loss: part_of axial vasculature (TAO:0001073)[TAO]
A delimited region of dense mesenchyme within looser mesenchyme.
Cell condensation that is an aggregation of mesenchymal cells that are committed to differentiate into chondroblasts and chondrocytes.
isa cell condensation in VSAO; has_part chondroblast in AEO
A delimited region of dense mesenchyme within looser mesenchyme whose cells are committed to become chondroblasts.
A closely packed aggregation of mesenchymal cells just prior to their differentiation into embryonic cartilage.
the paired ventral prominences formed by bifurcation of the first pharyngeal arches in the embryo; the two prominences unite ventrally and fuse to form the mandible and lower lip
An indentation of the olfactory placode which ends when the pits hollows out to form the nasopharynx[GO].
we represent the relationship as develops from, though in fact the pit is formed as an indentation in the placode
By the upgrowth of the surrounding parts the olfactory areas are converted into pits, the nasal pits or olfactory pits, which indent the fronto-nasal process and divide it into a medial and two lateral nasal processes[Wikipedia:Nasal_pit].
Anatomical cluster that is located in the posterior region of the cranium and forms the margin of the foramen magnum and occipital condyles.
An anatomical cluster that is located in the posterior region of the neurocranium and forms the margin of the foramen margin and occipital condyles.[AAO]
Anatomical cluster that is located in the posterior region of the cranium and forms the margin of the foramen magnum and occiptal condyle.[TAO]
Organ with organ cavity, which has as parts a serous membrane and a serous cavity . Examples: pleural sac, pericardial sac, tendon sheath, bursa.[FMA]
Epithelium that derives from the endoderm. Examples: urothelium, transitional epithelium of ureter, epithelium of prostatic gland.[FMA]
Subdivision of skeleton which consists of cranial skeleton, set of all vertebrae, set of all ribs and sternum[FMA, modified].
Skeletal subdivision of the central body axis including the cranium, vertebrae, notochord, ribs, and sternum.[VSAO]
Anteriosuperior, smooth-walled portion of the cavity of the right ventricle, beginning at the supraventricular crest and terminating in the pulmonary trunk
Anterosuperior fibrous portion of the left ventricle that connects to the ascending aorta.
Any of the arteries or veins that supply blood to the heart or return blood from the heart muscles to the circulation
Anatomical structure embedded in or located in the integument that is part of the integumental system. Examples: hair, follicles, skin glands, claws, nails, feathers.
add subclasses based on resolution of CARO tracker item. Also check: adnexal gland. Note that MP implicitly includes hypodermis.
the tissue or structures associated with or embedded in the skin such as hair and hair follicles, sweat glands, sebaceous glands and claws or nails[MP:0010678]
The mesonephric capsule is the tough fibrous layer surrounding the mesonephros, covered in a thick layer of perinephric adipose tissue.
The spiral septum that separates the truncus arteriosus into a ventral pulmonary trunk and the dorsal aorta[MP]. The aorticopulmonary septum is developmentally formed from neural crest, specifically the cardiac neural crest, and actively separates the aorta and pulmonary arteries and fuses with the interventricular septum within the heart during development. The actual mechanism of septation of the outflow tract is poorly understood, but is recognized as a dynamic process with contributions from contractile, hemodynamic, and extracellular matrix interactions.
The thin bilaminar membrane derived from the prechordal plate that is devoid of mesoderm and formed by the apposition of the stomodeal ectoderm with the foregut endoderm; after the embryonic head fold has evolved it lies at the caudal limit of the stomodeum, forming a septum between the primitive mouth and pharynx; the membrane eventually disappears, and thus a communication is established between the mouth and the future pharynx.
The membrane that covers the embryonic cloaca, formed by the union of proctodeal (anal pit) ectoderm and cloacal endoderm, with no intervening mesoderm; the urorectal septum joins the cloacal membrane and divides it into an anal membrane and a urogenital membrane; the point where the urorectal septum intersects the cloacal membrane is the future site of the perineal body; proliferation of mesoderm and ectoderm around the cloacal membrane produces primordial tissues of the external genitalia in both sexes: the genital tubercle, genital folds, and genital swellings.
A membrane that separates the proctodeum and the hindgut in the early embryo. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Vertebrates:_Comparative_Anatomy, p.497, see_Kardong_KV][VHOG]
In mammals, the cloaca exists as an embryonic structure that undergoes septation to become distinct urethral, anal, and genital orifices.[well established][VHOG]
PMID:11830557 De Santa Barbara P, Roberts DJ, Tail gut endoderm and gut/genitourinary/tail development: a new tissue-specific role for Hoxa13. Development (2002)
facio-acoustic VII-VIII preganglion complex
An anatomical junctions that overlaps the foregut and midgut.
Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[well established][VHOG]
The embryonic precursor of the brain and the set of mature brain structures that derive from it (CUMBO)
An anatomical junctions that overlaps the mouth and foregut.
The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord.
TODO - check ordering; awaiting confirmation from JB
The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. [Carson_JL, Dehart_DB, Developmental_Dynamics_(1994)_201:_260-278, Gesteland_K_and_Schoenwolf_GC, Inagaki_T, Morphogenesis_of_the_murine_node_and_notochordal_plate, The_prechordal_plate, Vrablic_T, see_Mueller_F_and_O'Rahilly_R, the_rostral_end_of_the_notochord_and_nearby_median_features_in_staged_human_embryos._Cells_Tissues_Organs_(2003)_173:_1-20_and_Sulik_K][VHOG]
A midline cellular cord formed from the migration of mesenchymal cells from the primitive knot
The notochordal process grows cranially until it reaches the prechordal plate, the future site of the mouth. In this area the ectoderm is attached directly to the endoderm without intervening mesoderm. This area is known as the oropharyngeal membrane, and it will break down to become the mouth. At the other end of the primitive streak the ectoderm is also fused directly to the endoderm; this is known as the cloacal membrane (proctodeum), or primordial anus.
the pair of depressions of thickened otic placode epithelium, that further develops into the otic vesicles
A depression appearing in each otic placode, marking the beginnning of embryonic development of the internal ear. [TFD][VHOG]
Multi-tissue structure that is part of the heart tube and will become the cardiac ventricle.
presumptive cardiac ventricle heart tube
The embryonic ventricle or primitive ventricle of the developing heart gives rise to the trabeculated parts of the left and right ventricles. In contrast, the smooth parts of the left and right ventricles originate from the embryological bulbus cordis. The primitive ventricle becomes divided by a septum, the septum inferius or ventricular septum, which grows upward from the lower part of the ventricle, its position being indicated on the surface of the heart by a furrow. Its dorsal part increases more rapidly than its ventral portion, and fuses with the dorsal part of the septum intermedium. For a time an interventricular foramen exists above its ventral portion, but this foramen is ultimately closed by the fusion of the aortic septum with the ventricular septum[WP]
See: https://github.com/obophenotype/mouse-anatomy-ontology/issues/13 and https://github.com/obophenotype/uberon/issues/693 -- consider merging into trigeminal ganglion, as this complicates the model
A segment of the eyeball that is filled with refractive media
Body substance in a liquid or semi-solid state in the eyeball which serves to refract light.
Liquid components of living organisms. includes fluids that are excreted or secreted from the body as well as body water that normally is not.
A nucleus of brain that is part of a brainstem.
An artery that connects two larger arteries.
A portion of organism substance that secreted_by a zone of skin.
A portion of organism substance that is secreted by a female reproductive gland.
female reproductive system fluid/secretion
A portion of organism substance that secreted_by a respiratory system.
A tube in the kidney that collect and transport urine.
in ZFA this is defined as part of mesonephros
A tube that is part of a excretory system.
The pharynx is the part of the digestive system immediately posterior to the mouth[GO].
currently this is an extremely generic class, encompassing both protostomes and deuterostomes.
Tunica media of artery which is continuous with the myocardium of right ventricle.[FMA]
A urethral meatus that is part of a female urethra[Automatically generated definition].
The external urethral orifice (urinary meatus) is the external opening of the urethra, from which urine is ejected during urination. It is placed about 2.5 cm behind the glans clitoridis and immediately in front of that of the vagina; it usually assumes the form of a short, sagittal cleft with slightly raised margins. To its left and right are the openings of the Skene's ducts.
ostium urethrae externum (urethra feminina)
A myocardium that is part of a left ventricle of a heart.
Myocardium of ventricle which is continuous with the tunica media of aorta.
A myocardium that is part of a right ventricle of a heart.
Myocardium of ventricle which is continuous with the tunica media of the pulmonary trunk.
The pectinate line (anocutaneous line, dentate line, anorectal junction) is a line which divides the upper 2/3rds and lower 1/3rd of the anal canal. Developmentally, this line represents the hindgut-proctodeum junction. It is an important anatomical landmark, and several distinctions can be made based upon the location of a structure relative to this line:
FMA also has FMA:29321 but it's not clear how this differs
Presumptive structure of the blastula that will develop into endoderm.
Portion of embryonic tissue determined by fate mapping to become a structure.
Presumptive structure of the blastula that will develop into ectoderm.
Presumptive structure of the blastula that will develop into mesoderm.
A muscle layer that is part of a fallopian tube.
A region of muscle in many organs in the vertebrate body, adjacent to the submucosa membrane. It is responsible for gut movement such as peristalsis.
currently this class conflates a generic layer of muscle and a specific layer found lining the digestive tract (the muscularis externa), typically composed of circular and longitudinal layers (although this varies)
An outer layer of smooth muscle surrounding a hollow or tubular organ as the bladder, esophagus, large intestine, small intestine, stomach, ureter, uterus, and vagina that often consists of an inner layer of circular fibers serving to narrow the lumen of the organ and an outer layer of longitudinal fibers serving to shorten its length[BTO].
typically smooth muscle, but there may be exceptions - in the upper esophagus, part of the externa is skeletal muscle, rather than smooth muscle.
An anatomical boundary that adjacent_to a epithelium.
the edge of the cornea where it joins the sclera; the limbus is a common site for the occurrence of corneal epithelial neoplasm
This location has parts such as blood vessels etc. See PMC2868485, http://www.ncbi.nlm.nih.gov/pubmed/2695343
An epithelium that is composed primarily of secretory cells.
consider splitting epithelium from epithelial tissue
Structural framework that provides support to the nasal sacs and ducts.
An anatomical space that surrounded_by a trachea.
A muscular coat that is part of a ureter.
The distalmost portion of the digestive tract, derived from the hindgut, and terminating with the anus.
this class is the superclass of 'rectum', which is currently reserved for the vertebrate structure. May be merged in future.
A head mesenchyme that develops_from a mesoderm.
merged in 'head mesoderm' from XAO/AAO and EFO here. Partially implements https://github.com/obophenotype/uberon/wiki/The-neural-crest NC meeting scheme
Mesenchyme that is part of a mandibular prominence.
An anatomical space that surrounded_by a digestive tract.
The thick, high squamous-stratified epithelium that covers the lips. It contains abundant melanocytes, many mucous cells and has well differentiated taste buds.[TAO]
An epithelium characterised by its most superficial layer consisting of squamous epithelial cells.
FBbt:00007028 (squamous epithelium) A type of epithelium that is made up of flattened cells which are arranged with their long axes in the plane of the epithelium
Multilaminar epithelium which consists of more than one layer of squamous cells only one layer of which is in contact with a basement membrane. Examples: keratinized stratified squamous epithelium, epithelium of wall of esophagus.[FMA]
A squamous epithelium that is part of a stomach.
The squamous epithelium of the cervical portio is similar to that of the vagina, except that it is generally smooth and lacks rete pegs. Colposcopically, it appears featureless except for a fine network of vessels which is sometimes visible. The relative opacity and pale pink coloration of the squamous epithelium derives from its multi-layered histology and the location of its supporting vessels below the basement membrane.
A squamous epithelium that is part of a vagina.
A glandular epithelium that lines the stomach. The stomach's glandular epithelium is characterized by the presence of gastric glands.
we follow Kardong in treating the glandular epithelium as a distinct entity, and thus as an epithelium which has glands; FMA has 'epithelium of gastric gland', which is part of the gastric gland.
Any gland that is part of the digestive system.
Simple columnar epithelium that constitutes the secretory part of a gland. Examples: epithelium of stomach, luminal epithelium of lactiferous duct.[FMA]
stomach mucosa that is lined with glandular epithelium and part of a stomach glandular region.
stomach glandular region glandular mucous membrane
Simple columnar epithelium made up of cells specialized to serve as sensory cells for the reception of external stimuli, as the sensory cells of the cochlea, vestibule, nasal mucosa, and tongue.
note that the definition sourced from Dorlands say 'simple columnar', but FMA says atypical
the epithelial cell layer containing the sensory hair cells and their associated sensory nerve terminals
The vascular cord is the primordial vasculature that will develop into blood vessels by the process of tubulogenesis[GO]. The vascular cord is composed of angioblast or vascular endothelial cells in a solid linear mass called a cord. The cord then undergoes tubulogenesis to form the lumen of the vessels[ZFA].
A capillary that is part of the coronary system.
A two dimensional anatomical structure that is the boundary between an anatomical structure and an anatomical substance, an anatomical space or the organism's environment. Examples include the surface of your skin, the surface of the lining of your gut; the surface of the endothelium of you aorta that is in contact with blood.n
Old definition: 'Non-material anatomical entity of two dimensions, that is demarcated by anatomical lines or points on the external or internal surfaces of anatomical structures.' Note, in the new definition, the space referred to is not necessarily an anatomical space. It may be the outside of an organism.
The splanchnic mesoderm in the cardiogenic region where the heart develops; it gives rise to endocardial heart tubes that fuse to form the primordial cardiac tube, the heart primordium[web]. Two migratory heart primordia that move ventrally during the course of neurulation, and then fuse[XAO].
consider FBbt:00005541 ! cardiogenic mesoderm
A multicellular organism that is at the juvenile stage.
Whole organism that is not fully grown or sexually mature.[TAO]
A multicellular organism that existence_ends_with a post-juvenile adult stage and existence_starts_with a post-juvenile adult stage.
Whole organism that is fully grown or sexually mature.[TAO]
The endodermal cells generate only the lining of the digestive tube and its glands; mesodermal mesenchyme cells will surround this tube to provide the muscles for peristalsis
Cranial neural crest that migrates into the mandibular arch.
Cranial neural crest that migrates into the hyoid arch.
A hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood or analogs[GO,modified].
note we reserve the subclass 'heart' from the vertebrate multi-chambered heart. 'The first heart-like organ is believed to have appeared 500my ago in an ancestral bilaterian'. Amniotes: four-chambered heart. Amphibians: two atria, one ventricle, pulmonary; fish: single atrium and ventricle; amphioxus: tubular, non-striated, closed, unidirectional; ascidians: tubular, striated, open, bidirectional; arthropods: tubular, open; C elegans: contractile pharynx; Cnideria: striated muscle cells associated with gastrodermis
An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section.
An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section. Kimmel et al, 1995.[TAO]
An anatomical cavity that surrounded_by a midgut.
An anatomical cavity that surrounded_by a hindgut.
An anatomical cavity that surrounded_by a anal canal.
An anatomical cavity that surrounded_by a colon.
A serous membrane that is part of a uterine tube infundibulum.
serosa of infundibulum of fallopian tube
A muscle layer that is part of a uterine tube infundibulum.
muscle layer of infundibulum of fallopian tube
muscularis of infundibulum of uterine tube
muscle layer of infundibulum of uterine tube
The structure from the trachea, bronchi, and bronchioles that forms the airways that supply air to the lungs. The lining of the tracheobronchial tree consists of ciliated columnar epithelial cells.
Mesenchyme that develops_from a cranial neural crest.
head mesenchyme from cranial neural crest
mesenchyme derived from head neural crest
Mesenchyme that develops_from a trunk neural crest.
mesenchyme derived from trunk neural crest
relationship to Meckel's cartilage to be added
A tunica media that is part of a artery.
A tunica adventitia that is part of a artery.
A tunica adventitia that is part of a vein.
Gray matter of the central nervous system which is a collection of clustered nuclei.
Any of the nuclei that comprise the superior olivary complex (superior olive). This includes both the primary nuclei such as the lateral and medial nuclei, as well as periolivary nuclei.
this class exists largely for consistency with the FMA. It is defined trivially with respect to the SOC. The class may be removed in future.
A pre-cartilage condensation that is part of a trachea.
Any collection of muscles that is part of a pectoral appendage.
Any collection of muscles that is part of a pelvic appendage.
Musculature that is part of the pelvic fin.[TAO]
Any collection of muscles that is part of an appendage.
Skeletal subdivision consisting of the anterior appendicular limb skeleton, excluding the pectoral girdle.
The collection of all skeletal elements in a pelvic appendage region.
The rhombencephalon (or hindbrain) is a developmental categorization of portions of the central nervous system in vertebrates. The rhombencephalon can be subdivided in a variable number of transversal swellings called rhombomeres. In the human embryo eight rhombomeres can be distinguished, from caudal to rostral: Rh7-Rh1 and the isthmus (the most rostral rhombomere). A rare disease of the rhombencephalon, 'rhombencephalosynapsis' is characterized by a missing vermis resulting in a fused cerebellum. Patients generally present with cerebellar ataxia. The caudal rhombencephalon has been generally considered as the initiation site for neural tube closure.
The embryonic rhombencephalon can be subdivided in a variable number of transversal swellings called rhombomeres. Rhombomeres Rh7-Rh4 form the myelencephalon that will give the medulla oblongata. Rhombomeres Rh3-Rh1 form the metencephalon that will form the pons and the cerebellum[NPX:PDR].
A presumptive structure that has the potential to develop into a endocardium.
Portion of tissue that is part of the heart tube and will become the endocardium.[TAO]
Embryonic structure that gives rise to the midbrain hindbrain boundary.
A presumptive structure that has the potential to develop into a presomitic mesoderm.
A presumptive structure that has the potential to develop into a neural plate.
Region of the gastrula which gives rise to the neural plate.[TAO]
The part of the blastula that has the potential to develop into a paraxial mesoderm.
A presumptive structure that has the potential to develop into a pronephric mesoderm.
A blood vessel that is part of a pectoral appendage.
A blood vessel that is part of a limb/fin.
A vasculature that is part of a pectoral appendage.
A vasculature that is part of a chordate pharynx.
A vasculature that is part of a limb/fin.
The epidermis is the entire outer epithelial layer of an animal, it may be a single layer that produces an extracellular material (e.g. the cuticle of arthropods) or a complex stratified squamous epithelium, as in the case of many vertebrate species[GO].
this grouping class exists primarily to align with GO - see GO:0008544.
Portion of the dermis characterized by a well-arranged, plywood-like, collagenous network.
Portion of the dermis characterized by a well-arranged, plywood-like, collagenous network. Le Guellec et al, 2004.[TAO]
relationship loss: develops_from collagenous dermal stroma (TAO:0001186)[TAO]
connective tissue in the skin is usually diffuse and irregular, although in some species collagen bundles are arranged in a distinct ordered layer in the dermis
Outermost layer of cells surrounding the embryo.
Outermost monolayer of cells surrounding the embryo that become very flattened in the blastula and give rise to the periderm. Sometimes used synonymously with periderm. Kimmel et al, 1995.[TAO]
relationship loss: develops_from superficial blastomere (TAO:0001484)[TAO]
Originally this tissue is one cell layer thick but in most vertebrates it soon becomes a two layered structure. The outer layer gives rise to the periderm.
A cartilage tissue that is part of a paired limb or fin.
Cartilage which is part of one of the paired fins.[TAO]
A cartilage tissue that is part of a pectoral appendage.
Cartilage which is part of the pectoral fin.[TAO]
A cartilage tissue that is part of a pelvic appendage.
Cartilage which is part of the pelvic fin.[TAO]
A nucleus of brain that spans a midbrain tegmentum.
this class groups together any nuclei in the tegmentum region, possibly including disparate structures across species
An epithelial tube that is open at one end only.
An epithelial tube open at both ends that allows fluid flow.
Mesenchyme with little extracellular matrix.
this class will be an important part of the NC reorganization
A ciliated columnar epithelium that is part of a oviduct.
A cuboidal epithelium that is part of a oviduct.
Simple columnar epithelium in which the luminal side of the cells bears cilia. Examples: epithelium of trachea, epithelium of uterine tube.[FMA]
In humans, Ciliated columnar epithelial cells are found mainly in the tracheal and bronchial regions of the pulmonary system and also in the fallopian tubes of the female reproductive system
Ciliated columnar epithelium in the pulmonary system is interspersed with goblet cells that secrete mucous to form a mucosal layer apical to the epithelial layer. The rowing-like action of epithelial cilia work in tandem with goblet cells to propel mucus away from the lungs, preventing particulate matter from causing infection[http://www.bio.davidson.edu/people/kabernd/berndcv/lab/epithelialinfoweb/ciliated%20columnar%20epithelium.html]
Epithelium bearing vibratile cilia on the free surface.
A thin, loose vascular connective tissue that makes up the membranes surrounding joints and the sheaths protecting tendons (particularly flexor tendons in the hands and feet) where they pass over bony prominences. Synovial tissue contains synovial cells, which secrete a viscous liquid called synovial fluid; this liquid contains protein and hyaluronic acid and serves as a lubricant and nutrient for the joint cartilage surfaces[BTO]. Synovial tissue can be found in tendons (tissues that connect muscle to bone), bursae (fluid-filled, cushioning sacs found in spaces between tendons, ligaments, and bones), and the cavity (hollow enclosed area) that separates the bones of a freely movable joint, such as the knee or elbow[BTO].
An anatomical cavity that surrounded_by a synovial joint.
cavitas articularis (junctura synovialis)
epithelial layer of the retina, ciliary body, or iris composed of cells containing pigment granules.
A neural nucleus that is part of a medulla oblongata.
The sensory trigeminal nerve nuclei are the largest of the cranial nerve nuclei, and extend through the whole of the midbrain, pons and medulla. There is also a distinct trigeminal motor nucleus that is medial to the chief sensory nucleus[WP].
in MA and FMA this is part of the pons / pontime tegmentum. We weaken this to overlaps to avoid inconsistency. In NIF this is a composite structure spanning multiple regions, which is more appropriate.
An anatomical structure that connects two structures
region of the embryo into the area in which the kidney rudiment will develop.
Anlagen are populations of contiguous cells, typically arranged in one plane, that are morphologically indistinct, but that already correspond in extent to a later organ/tissue.
relation conflict: ZFA vs EHDAA2. Note EHDAA2 term renamed to 'early PA endoderm'
The minute opening of a taste bud on the surface of the oral mucosa through which the gustatory hairs of the specialised neuroepithelial gustatory cells project.
A bone that is part of a reproductive organ.
Any bodily fluid that has passed through a membrane such as the capillary wall, as a result of unbalanced hydrostatic and osmotic forces
characteristically low in protein and cellular content (unless there has been secondary concentration)
Anatomical system that consists of all blood and lymph vessels.
The cardiovascular and lymphatic systems, collectively[ncithesaurus:Vascular_System].
in both MA and BTO, the arterial system and venous sytem are subtypes of the vascular system
Adipose tissue that is located in the abdominal region. This includes any subcutaneous fat, visceral fat or encapsulated adipose tissue depots.
The anteriormost subdivision of the body that includes the head, jaws, pharyngeal region and the neck (if present). In vertebrates this is the subdivision that includes the cervical vertebrae.
An organism subdivision that encompasses the region containing the pectoral or pelvic girdle. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc).
An organism subdivision that encompasses the region containing the pectoral or pelvic girdle. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). There are only two instances of appendage girdle regions per organism.[VSAO]
A bone that is part of a appendage girdle region.
A bone that is part of a pectoral girdle region.
A bone element or fused bone that is part of pelvic girdle.
check sacrum, coccyx (MA does NOT include these)
typically the ilium, ischium and pubis. These can alternately be considered individual bones, or zones of a single fused bone
A subdivision of a limb or fin skeleton consisting of bones which connects the upper limb or fin to the axial skeleton on each side. It consists of the clavicle and scapula in humans and, in those species with three bones in the pectoral girdle, the coracoid. Some mammalian species (e.g. the dog and the horse) have only the scapula. In humans, the only joints between the shoulder girdle and axial skeleton are the sternoclavicular joints on each side. No joint exists between each scapula and the rib cage; instead the muscular connection between the two permits relatively great mobility of the shoulder girdle in relation to the pelvic girdle. In those species having only the scapula, no joint exists between the forelimb and the thorax, the only attachment being muscular[WP]. Examples: There are only two instances, right and left pectoral girdle skeletons.
Anatomical cluster of paired dermal and endochondral bones that attaches to the dorso-posterior part of the cranium, and support the radials and pectoral fin. It consists of two components: the primary pectoral girdle consisting of the endochondral coracoid, scapula and mesocoracoid bones, and the secondary pectoral girdle consisting of the dermal posttemporal, supracleithrum, cleithrum and poscleithrum(thra) bones.[TAO]
Girdle skeleton consisting of a set of bones linking the axial series to the forelimb/fin skeleton and offering anchoring areas for forelimb/fin and caudal musculature.[VSAO]
Skeletal structure immediately behind the head attached to the vertebral column by muscles and supporting the forelimbs.[AAO]
The pectoral girdle is clearly of dual origin, composed of dermal as well as endochondral bones. The endochondral component, the scapulocoracoid, evolved by fusion or enlargment of several basal fin elements. (...) The dermal component of the shoulder girdle evolved from dermal bones of the body's surface. (...) Like endochondral bones, these dermal bones were passed along to tetrapods (...).[well established][VHOG]
Note that the VSAO and many ontologies use the label 'pectoral girdle' to denote the skeletal region specifically.
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.336 and Figure 9.18
Skeletal subdivision consisting of a set of bones linking the axial series to the hindlimb zeugopodium and offering anchoring areas for hindlimb and caudal musculature.
need to resolve whether this is a paired structure or a single belt (Paired in FMA - implicitly paired in VSAO)
Anatomical cluster by which the hind limbs are supported and attached to the vertebral column.[AAO]
Anatomical cluster that consists of the paired basipterygia which support the pelvic fin.[TAO]
Girdle skeleton consisting of a set of bones linking the axial series to the hindlimb/fin skeleton and offering anchoring areas for hindlimb/fin and caudal musculature.[VSAO]
The pelvic girdle is never joined by contributions of dermal bone. From its first appearance in placoderms, the pelvic girdle is exclusively endoskeletal. It arose from pterygiophores, perhaps several times, in support of the fin.[well established][VHOG]
Note that the VSAO and many ontologies use the label 'pelvic girdle' to denote the skeletal region specifically. We place the EHDAA2 class here, note that this includes the pre-cartilage condensation as parts
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.333
Bone element that arises as a result of intramembranous ossification.
Bone element that arises as a result of intramembranous ossification.[VSAO]
Intramembranous bone that forms deep in the organism.[TAO]
Skeletal element that is composed of cartilage tissue and may be permanent or transient.
Connective tissue, which consists of fibroblasts, the intercellular matrix of which contains a regular network of collagen and elastic fiber bundles. Examples: bone (tissue), cartilage (tissue), dense regular connective tissue.
the connective tissue hierarchy largely follows FMA with definitions from VSAO. Note that in FMA, loose-CT is irregular-CT. This means regular-CT is necessarily equivalent to dense-regular-CT (assuming a JEPD classification).
Connective tissue that is dominated by collagen fibres organized into a definitive pattern (e.g., parallel to one another), with comparatively fewer cells (mostly fibroblasts).
Connective tissue that is dominated by collagen fibres organized into a definitive pattern (e.g., parallel to one another), with comparatively fewer cells (mostly fibroblasts).[VSAO]
Regular connective tissue, the intercellular matrix of which consists predominantly of collagen fiber bundles arranged in parallel arrays.[FMA]
dense regular collagenous connective tissue
typus regularis (textus connectivus collagenosus compactus)
A bone that is part of a craniocervical region.
A skeletal joint that is part of a appendage girdle region.
A anatomical surface that is part of a cartilage element.
A bone that is hollow or contains many air cells, such as the mastoid process of the temporal bone[TMD].
subclasses of this should be checked for taxonomic consistency
Skeletal pneumaticity is the presence of air spaces within bones. Skeletal pneumaticity exists only in synapsids and archosaurs. It is generally produced during development by excavation of bone by pneumatic diverticula (air sacs) from an air-filled space such as the lungs or nasal cavity. Pneumatization is highly variable between individuals, and bones not normally pneumatized can become pneumatized in pathological development. Pneumatization occurs in the skulls of mammals, crocodilians and birds among extant groups, as well as extinct archosaurs including the dinosaurs and pterosaurs. Pneumatic spaces include the paranasal sinuses and some of the mastoid cells[WP]. [Wikipedia:Skeletal_pneumaticity]
Any muscle organ that is part of a pectoral girdle region.
EMAPA has both non-skeletal and skeletal types, with the non-skeletal also including a chest muscle, so we place the skeletal class here as the most accurate
The part of the ventral body cavity that is within the pelvis.
Musculature system of the pharyngeal and head regions.
in MA this is restricted to skeletal muscles
An endothelium that is part of a heart [Automatically generated definition].
this class includes any endothelia that are part of the heart. This might include the endocardial epithelia, as well as endothelia of vessels that are considered strictly part of the heart (e.g. outflow tract). As a grouping class, this may lack utility, and pending review this class may be obsoleted. For annotation consider a more specific class.
Any muscle organ that is part of an nose.
A transient embryonic complex that comprises the pharyngeal arches, bulges of tissues of mesoderm and neural crest derivation through which pass nerves and pharyngeal arch arteries. The arches are separated internally by pharyngeal pouches, evaginations of foregut endoderm, and externally by pharyngeal clefts, invaginations of surface ectoderm. The development of the system ends when the stucture it contributes to are forming, which may include (depending on species) the thymus, thyroid, parathyroids, maxilla, mandible, aortic arch, cardiac outflow tract, external and middle ear[GO,modified].
Currently defined in a vertebrate specific manner. The arch system has origins in basal deuterostomes, consider generalizing
A brain that develops_from a neural tube.
a reasoner should automatically classify all the vertebrate ontology brain classes here
The smooth muscle layer of the stomach wall that functions to churn and mix food and gastric secretions as well as to move food along the digestive tract to the intestines
the muscularis externa in the stomach differs from that of other GI organs in that it has three layers of smooth muscle instead of two
Any skeletal muscle organ in the hypodermis / superficial fascia
We follow MP and treat this as part of the hypodermis, although some sources may consider the hypodermis to be superficial to this
The part of the cardiovascular system consisting of all pulmonary arteries and all pulmonary veins.
Subdivision of cardiovascular system which has as its parts the pulmonary arterial and venous tree organs.[FMA]
Subdivision of endoskeleton derived from pharyngeal arches
Anatomical cluster that is part of the cranium and consists of the jaws, hyoid and branchial arches.[TAO]
Anatomical cluster that is part of the cranium and consists of the jaws, hyoid, and branchial arches.[AAO]
The part of the skull derived from the embryonic pharyngeal arches. [Biology_Online][VHOG]
The skull of ancestral tetrapods has the three basic components that we have been considering: (1) chondrocranium, (2) splanchnocranium, and (3) dermatocranium (reference 1); Each part of the skull arises from a separate phylogenetic source. The most ancient part is the splanchnocranium (visceral cranium), which first arose to support pharyngeal slits in protochordates (reference 2).[well established][VHOG]
VSAO labels this term 'pharyngeal arch' (2012-06-01) - however, it clearly means pharyngeal arch skeleton.
many sources define this as the part of the endoskeletal that is from pharyngeal arches - this would make it part-disjoint from dermatocranium. However, there are many bones in AOs that have part-paths to both
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.242, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.235
A pharyngeal arch that is posterior to the hyoid arch. i.e. any pharyngeal arch with a number 3 or higher.
Posterior-most stream of cranial neural crest, which sub-divides during migration.[AAO]
Skeletal element that forms superficially in the organism, usually in association with the ectoderm[VSAO].
Intramembranous bone that forms superficially in the organism.[TAO]
other AOs are not yet in sync with this classification
Bone element that is adjacent to the notochord.
We go with the latest VSAO in making this a subtype of bone, and add a logical definition based on the textual definition in VSAO. We also include the subtyping under 'replacement bone', for consistency with ZFA
Replacement bone that forms within the connective tissue surrounding the notochord.[TAO]
System pertaining to blood vessels in the brain.
Any portion of tissue that surrounds a urethra.
An artery that supplies blood to the urinary bladder.
Vein that drains left lung and returns blood to the heart.
A vein that returns oxygenated blood from the left lung to the left atrium of the heart[ncithesaurus:Left_Pulmonary_Vein].
Vein that drains right lung and returns blood to the heart.
A vein that returns oxygenated blood from the right lung to the left atrium of the heart[ncithesaurus:Right_Pulmonary_Vein].
An organism containing a developing embryo, fetus, or unborn offspring within the body.
A gonad prior to differentiating into a definitive testis or ovary.
typically part of the embryo - however, in male tammar wallabies the gonads are indifferent at the neonatal stage[8827321]
Rostralmost epibranchial placode. Associated with 1st branchial cleft.
Taxonomic equivalence to EHDAA2 class made on basis of shared development: gives rise to geniculate ganglion
Epibranchial placode between geniculate and nodose. Associated with 2nd branchial cleft.
Taxonomic equivalence to EHDAA2 class made on basis of shared development: gives rise to glossopharyngeal ganglion
Cranial ganglion which develops from an epibranchial placode.
Epibranchial ganglia orchestrate the development of the cranial neurogenic crest
A vein that is part of a craniocervical region.
consider adding new class (EMAPA:16097) for mesenchyme of embryo (some mesenchyme is extraembryonic - e.g. amnion mesoderm)
A nephric duct is a tube that drains a primitive kidney[GO].
Mesenchyme that is part of a otic placode.
An ectoderm that is part of a buccopharyngeal membrane.
An endoderm that is part of a buccopharyngeal membrane.
Mesenchyme that is part of a foregut-midgut junction.
associated mesenchyme of foregut-midgut junction
A portion of mesenchymal tissue associated with an individual pharyngeal arch.
this represents a part of the entire arch mesenchyme (UBERON:0010046), and is therefore a superclass of the individual arch mesenchyme classes. Alternate definition: primordial embryonic connective tissue associated with the branchial arches, consisting of mesenchymal cells supported in interlaminar jelly, that derive mostly from the mesoderm and contribute to facial and cranial nerve-associated structures.
An epithelium that is part of a foregut-midgut junction.
Anatomical region that surrounds the otic vesicle.
Mesenchyme that is part of a developing hindgut.
Mesenchyme that is part of a developing trachea.
An endoderm that is part of a anal region.
An endoderm that is part of a foregut-midgut junction.
A submucosa that is part of a intestine.
A sulcus limitans of neural tube that is part of a future spinal cord.
spinal cord lateral wall sulcus limitans
A sulcus limitans of neural tube that is part of a future medulla oblongata.
A sulcus limitans of neural tube that is part of a future metencephalon.
A sulcus limitans of neural tube that is part of a future myelencephalon.
Mesenchyme that is part of a 1st arch mandibular component.
mesenchymal region of mandibular component of first pharyngeal arch
Mesenchyme that is part of a developing left lung.
Mesenchyme that is part of a developing right lung.
A neural plate that develops_from a presumptive midbrain.
A neural plate that develops_from a presumptive hindbrain.
TODO - developmental relationships for lines
midbrain-hindbrain boundary neural plate
midbrain hindbrain boundary neural plate
A presumptive structure that has the potential to develop into a midbrain.
Bilateral mesenchymal mesoderm parallel and immediately adjacent to the neural tube/notochord; it generates a subset of extra-ocular, and other head, muscles.
A major contributor to neurocranium [PMID:16313393]
A basement membrane that is part of a bronchus.
MA classifies as type of connective tissue: https://github.com/obophenotype/mouse-anatomy-ontology/issues/108
A basement membrane that is part of a trachea.
An anatomical space that surrounded_by a embryonic cloaca.
An anatomical space that surrounded_by a rectum.
Any endocardium that is part of the right ventricle of the heart.
Endocardium of ventricle which is continuous tricuspid valve, pulmonary valve and with the tunica intima of the pulmonary trunk.
Any endocardium that is part of the left ventricle of the heart.
Endocardium of ventricle which is continuous with mitral valve, aortic valve, atrioventricular septum and the tunica intima of the aorta.
An anatomical cavity that surrounded_by a stomodeum.
The embryonic connective tissue made up of loosely aggregated mesenchymal cells, supported by interlaminar jelly, that gives rise to the developing cardiac structures
decide whether to merge with cardiac mesoderm. In EHDAA2 this lasts CS12->unbounded, includes mesenchyme of individual components as parts
A ganglion that is part of a abdominal segment of trunk.
The many-lobed berry cluster of cells that is the terminous of a gland where the secretion is produced is acinar in form.
An anatomical space that surrounded_by a primitive urogenital sinus.
Mesenchyme that surrounds primitive urogenital sinus.
Androgen receptor (AR) activation releases instructive signals from UGM that acts on UGS epithelium (UGE) to stimulate cell proliferation, form prostate ductal progenitors (prostatic buds), and regulate cell adhesion dynamics to permit prostatic bud outgrowth
An epithelium that is part of a embryonic cloaca.
Branch or outpocketing of the digestive tract.
A division of the stomach. The stomach can be divided based on mucosal histology (glandular epithelium and gastric glands) and the relative position and type of gastric gland.
We follow Kardong in defining stomach regions by gland, but we also include 'body of stomach'. In future we may want to have different partitions of the stomach
A specific region of the lateral mesoderm that will form the majority of the mesodermal component of the right ventricle, arterial pole (outflow tract) and venous pole (inflow tract).
extra-cardiac population of mesodermal progenitors that gives rise to the right ventricle and outflow tract[PMID:17276708].
In general, the two studies in chick concluded that the contribution of the SHF was to the outflow tract, whereas the mouse work suggested that the second lineage contributed more broadly to the heart, including the outflow tract and much or all of the right ventricle [11-14]. These different conclusions may represent differences in the experimental approaches used or may represent bona fide differences in the contribution of the second lineage to the hearts of birds compared to mammals [11]. Alternatively, the secondary/anterior heart fields described in the chick may represent a subset of a broader field that makes a more substantial contribution to the heart, as the mouse studies suggested
in mouse has left ventricular identity[PMID:22855565]
Mesenchyme that is part of a developing face.
An anatomical wall that is part of a ureter.
The smooth muscle tissue surrounding the epithelium of the ureter
A multicellular organism that existence_starts_with a post-embryonic stage.
Cranial ectodermal placode with potential to develop into a component of the nervous system, such as nerves or ganglia.
Includes: trigeminal, otic, lateral line and epibranchial placodes.
While some sensory placodes (otic and olfactory) may have homologues in basal chordates (Wada et al., 1998), the so-called neurogenenic placodes (trigeminal, otic, lateral line and epibranchial placodes) appear to have emerged at a later time (Shimeld and Holland, 2000)
A anatomical space that is enclosed by a urinary bladder.
The junction between the ureter and the renal pelvis of the kidney
The valve-like structure found at the site of entry of the ureter into the urinary bladder, normally displays an oblique angulation through the detrusor to avoid reflux of urine up the ureters and the kidney
An anatomical structure that has more than one cell as a part.
A small cluster of cells of various types which form a discrete structure, largely delimited by a morphological boundary and whose components work together to make the whole structure capable of a specific function.
Mesenchyme that is part of a pharyngeal arch 6.
An organ of the digestive tract that is capable of retaining and storing food
This is a very broad functionally defined grouping class that collects disparate structures from insects to vertebrates
Mesenchyme that is part of a pharyngeal arch 1.
The sum total of mesenchymal tissue in the pharyngeal arch region. Pharyngeal mesenchyme is undifferentiated, loose connective tissue derived mostly from mesoderm, and also contains ectodermally derived neural crest cells.
associated mesenchyme of pharyngeal region
entire branchial arch associated mesenchyme
entire pharyngeal arch associated mesenchyme
Gland of the epithelium lining the oral cavity. The most common are the salivary glands.
Note that Kardong classifies lacrimal glands here. EHDAA2 includes pituitary primordium, as this develops from oral mucosa
An epithelium consisting of cuboidal epithelial cells.
TODO - coordinate with CL, add cuboidal cell
Mesenchyme that has the potential to develop into a dermis.
A developing anatomical structure that has the potential to develop into a metencephalon.
A developing anatomical structure that has the potential to develop into a myelencephalon.
A gray matter that has the potential to develop into a facial nucleus.
A gray matter that has the potential to develop into a superior salivatory nucleus.
Any portion of cardiac muscle tissue that is part of the conducting system of heart or the Purkinje fibers.
any of the organized aggregations of cells that function as secretory or excretory organs and that release hormones in response to neural stimuli
A mucous secretion that is produced by glands in the epidermis.
An anatomical cavity that surrounded_by a blood vessel.
An urethral gland that is part of a female urethra.
the paired arterial structures of the embryo that supplies each developing somite via efferent segmental arteries; the dorsal aortae articulate with the umbilical arteries, which return mixed blood to the villi of the chorion for reoxygenation
One of the laterally paired arteries that supply the gonads.
An anatomical boundary that corresponds to some physical discontinuity.
One might argue that all boundaries are actually fiat in the sense that there must be some fiat element at a fine enough scale of granularity. This ontology choses to ignore this issue as below the level of granularity relevant to anatomy. (DOS121102)
Apparatus located between the lungs and the buccal cavity. This apparatus is composed of a pair of arytenoid cartilages that are supported by the cricoid ring.
check this. See also https://github.com/obophenotype/uberon/wiki/The-axial-skeleton
Many sources say: thyroid cartilage from arch 4 other laryngeal cartilage (cricoid/arytenoid) from 6?
The core globe-shaped component of the camera-type eye.
Mesenchyme that develops_from a neural crest and is part of a 1st arch mandibular mesenchyme.
1st arch mandibular mesenchyme from neural crest
Mesenchyme that develops_from a neural crest and is part of a 2nd arch mesenchyme.
pharyngeal arch 2 mesenchyme from neural crest
branchial arch 2 mesenchyme from neural crest
Mesenchyme that develops_from a neural crest and is part of a 4th arch mesenchyme.
4th pharyngeal arch mesenchyme derived from neural crest
mesenchyme derived from neural crest of mesenchyme of 4th arch
pharyngeal arch 4 mesenchyme from neural crest
branchial arch 4 mesenchyme from neural crest
Mesenchyme that develops_from a neural crest and is part of a 6th arch mesenchyme.
pharyngeal arch 6 mesenchyme from neural crest
branchial arch 6 mesenchyme from neural crest
Mesenchyme that develops_from a rhombencephalon neural crest.
mesenchyme from rhombencephalic neural crest
Mesenchyme that develops_from a neural crest and is part of a 1st arch mesenchyme.
mesenchyme derived from neural crest of mesenchyme of 1st arch
pharyngeal arch 1 mesenchyme from neural crest
branchial arch 1 mesenchyme from neural crest
Portion of tissue that is dorsolateral to the floor plate and part of the midbrain.
Portion of neural tube that gives rise to the midbrain.
we follow ZFA in temporally dividing midbrain NT from presumptive midbrain, but in future this may be collapsed
An endothelium that is part of a sclera.
Mesenchyme surrounding the developing optic cup which develops into the sclera.
The mesenchyme surrounding the developing optic cup differentiates into the sclera, the dense fibrous coat of the eye.. http://www.ncbi.nlm.nih.gov/pubmed/16496288
An epithelium that is part of a extraembryonic structure.
Stratified squamous epithelium is a stratified squamous epithelium, the cells of which synthesizes but does not accumulate keratin. Examples: epithelium of vagina, epithelium of wall of esophagus.
epithelium stratificatum squamosum noncornificatum
nonkeratinizing stratified squamous epithelium
stratified squamous non-keratinized epithelium
stratified squamous nonkeratinizing epithelium
non-keratinized stratified squamous epithelium
Developing anatomical structure that develops into the eyeball and associated structures.
Multi-tissue structure that consists of the structures that develop into the retina and lens.[TAO]
An anatomical structure that develops from the neural crest.
An anatomical structure that has some part that develops from the neural crest.
structure with developmental contribution from neural crest
A skeletal element that is part of a orbital region.
Skeletal subdivision of the head including skull (cranium plus mandible), pharyngeal and/or hyoid apparatus.
we use 'cranial skeletal system', so that we can include the skull, which has joints/sutures as parts (recall, we follow FMA in distinguishing between the skeleton and skeletal system - only the latter includes joints)
that the cranial skeleton includes the pharyngeal arch skeleton. It is thus more inclusive that the cranium itself, and extends beyond the head in tetrapods. The AAO class called 'skull' belongs here, as it includes the whole splanchnocranium
Bony structure that encases the central nervous system and the primary sense organs of sight, olfaction, hearing, and equilibrium.[AAO]
Skeletal system which is part of the skull, including the splanchnocranium, chondrocranium, and dermatocranium.[TAO]
Mesenchyme that is part of a limb/fin bud.
Mesenchyme that develops_from a neural crest and is part of a mandibular process mesenchyme.
mandibular process mesenchyme from neural crest
Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a mandibular process mesenchyme.
mandibular process mesenchyme from head mesenchyme
Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 1st arch mandibular mesenchyme.
1st arch mandibular mesenchyme from head mesenchyme
Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 1st arch mesenchyme.
mesenchyme derived from head mesoderm of mesenchyme of 1st arch
1st arch mesenchyme from head mesenchyme
Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 2nd arch mesenchyme.
head mesenchyme derived arch 2 mesenchyme
mesenchyme derived from head mesoderm of mesenchyme of 2nd arch
pharyngeal arch 2 mesenchyme from head mesenchyme
branchial arch 2 mesenchyme from head mesenchyme
2nd arch mesenchyme from head mesenchyme
Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 4th arch mesenchyme.
head mesenchyme derived arch 4 mesenchyme
mesenchyme derived from head mesoderm of mesenchyme of 4th arch
pharyngeal arch 4 mesenchyme from head mesenchyme
branchial arch 4 mesenchyme from head mesenchyme
4th arch mesenchyme from head mesenchyme
Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 6th arch mesenchyme.
head mesenchyme derived arch 6 mesenchyme
pharyngeal arch 6 mesenchyme from head mesenchyme
branchial arch 6 mesenchyme from head mesenchyme
6th arch mesenchyme from head mesenchyme
Mesenchyme that develops_from a neural crest and is part of a entire pharyngeal arch associated mesenchyme.
branchial arch mesenchyme from neural crest
Partially implements https://github.com/obophenotype/uberon/wiki/The-neural-crest NC meeting scheme
pharyngeal arch mesenchyme from neural crest
Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a entire pharyngeal arch associated mesenchyme.
branchial arch mesenchyme from head mesenchyme
pharyngeal arch mesenchyme from head mesenchyme
Skeletal subdivision that undergoes indirect development and includes elements that develop as a replacement or substitution of other elements or tissues.
An endoskeleton is an internal support structure of an animal, composed of mineralized tissue. Endoskeleton develops within the skin or in the deeper body tissues. The vertebrate is basically an endoskeleton made up of two types of tissues (bone and cartilage). During early embryonic development the endoskeleton is composed of notochord and cartilage. The notochord in most vertebrates is replaced by vertebral column and cartilage is replaced by bone in most adults. In three phyla and one subclass of animals, endoskeletons of various complexity are found: Chordata, Echinodermata, Porifera, and Coleoidea. An endoskeleton may function purely for support (as in the case of sponges), but often serves as an attachment site for muscle and a mechanism for transmitting muscular forces. A true endoskeleton is derived from mesodermal tissue. Such a skeleton is present in echinoderms and chordates. The poriferan 'skeleton' consists of microscopic calcareous or siliceous spicules or a spongin network. The Coleoidae do not have a true endoskeleton in the evolutionary sense; here, a mollusk exoskeleton evolved into several sorts of internal structure, the 'cuttlebone' of cuttlefish being the best-known version. Yet they do have cartilaginous tissue in their body, even if it is not mineralized, especially in the head, where it forms a primitive cranium. The endoskeleton gives shape,support and protection to the body and provides a mean of locomotion.[Wikipedia:Endoskeleton]t
A skeletal element that has the potential to participate in endochondral ossification, and may participate in intramembranous ossification.
Skeletal subdivision that undergoes direct development and includes elements that either develop in association with the basement membrane of the ectoderm or are homologous with such elements; includes dermatocranium, components of the appendicular skeleton, teeth and tooth-like elements of the oropharynx, and integumentary elements.
This ontology covers metazoa, so we do not use exoskeleton as primary label, as in VSAO
Epithelium composed of cells that develops from the ectoderm[FMA,modified].
Mesenchyme that develops_from a somatopleure.
the way this class is defined also includes extraembryonic mesenchyme such as the amniotic mesenchyme; in future this may be restricted to embryonic derivatives
Mesenchyme that develops_from a splanchnopleure.
An organ cavity that is part of a urethra.
The integrated unit (of the eye) that consists of the conjunctiva, the corneal surface, and the ocular mucosal adnexa including the lid margins and the meibomian gland openings, the lacrimal glands and the lacrimal drainage system, all which are critical to maintain ocular surface integrity and provide protection from external antigens and pathogenic microorganisms.
An orifice that is part of a lower urinary tract.
The ciliary processes are formed by the inward folding of the various layers of the choroid, i.e. , the choroid proper and the lamina basalis, and are received between corresponding foldings of the suspensory ligament of the lens.
A bone that is shaped as a broad flat plate and composed of two thin layers of compact tissue enclosing between them a variable quantity of cancellous tissue, which is the location of red bone marrow.
In an adult mammal, most red blood cells are formed in flat bones
Flat bones are those bones which are found where the principal requirement is either extensive protection or the provision of broad surfaces for muscular attachment
Examples: cranium, the ilium, sternum, rib cage, the sacrum and the scapula; the occipital, parietal, frontal, nasal, lacrimal, vomer, scapula, os coxC&, sternum, and ribs
A simple columnar epithelium that looks stratified but is not, because its cells are arranged with their nuclei at different levels.
Pseudostratified epithelia function in secretion or absorption. If a specimen looks stratified but has cilia, then it is a pseudostratified ciliated epithelium, since stratified epithelia do not have cilia.
glandular in NCIT; we consider the two NCIT terms synonymous
Epithelium composed of a single layer of cells, appearing as layered because the column-shaped cells vary in height so the nuclei are at different levels. The basal portions of all the cells are in contact with the basement membrane. It lines the respiratory system and the male reproductive tract. The cilia in the respiratory tract are motile, while the stereocilia in the male reproductive tract are immobile.
epithelium pseudostratificatum columnare ciliatum (trachea et bronchi)
pseudostratified ciliated columnar epithelium
Skeletal element that forms as a replacement or substitution of another element or tissue.
A vessel of the microcirculature, lying between the arterioles and venules; includes capillaries (blood and lymphatic), metarterioles and arteriovenous anastomoses.
An organ cavity that surrounded_by a bone.
An organism subdivision that includes both an appendage and its associated girdle region. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc).
It is still called a complex when one of the two parts is missing (?) There are fossil fishes with only an outgrowth (no record of a girdle), including thelodonts (which have a suprabranchial fin) as well as some anaspids which have a distinctive 'paired fin' (with differing published assertions on whether it's homologous to a pec fin or pelvic fin or both or neither). There are many fishes and other vertebrates with only a girdle and no outgrowth.[VSAO]
Anatomical group that consists of the soft and skeletal tissues of the appendicular region of the body and the appendage proper.[VSAO]
note that the FMA uses the term 'limb' to refer to the entire appendage complex (free limb plus girdle region)
Appendage girdle complex that when present, encompasses the pectoral appendicular skeleton and the pectoral girdle.
Appendage girdle complex that when present, encompasses the pectoral appendage and half of the pectoral girdle.[VSAO]
note that the FMA uses the terms 'upper limb' and 'lower limb' to refer to the entire appendage complex (free limb plus girdle region)
pectoral girdle plus anterior limb or fin
pectoral girdle plus pectoral limb or fin
Appendage girdle complex that when present, encompasses the pelvic appendicular skeleton and the pelvic girdle.
Appendage girdle complex that when present, encompasses the pelvic appendage and the pelvic girdle.[VSAO]
note that the FMA uses the terms 'upper limb' and 'lower limb' to refer to the entire appendage complex (free limb plus girdle region). Note the MA class 'hindlimb' may also belong here
pelvic girdle plus posterior limb or fin
The subdivision of the skeleton of either the pectoral or pelvic girdle.
Skeletal subdivision that is part of the appendage girdle region.[VSAO]
relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: part_of subdivision of skeleton (UBERON:0010912)[VSAO]
relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: proximally_connected_to subdivision of skeleton (UBERON:0010912)[VSAO]
A bone that is part of an appendage girdle complex (i.e. any bone in a limb, fin or girdle).
A bone that is part of a pectoral complex. Examples: scapula, manus phalanx, any carpal bone, any bone of the pectoral fin.
considering adding pectoral and pelvic complex skeleton classes
note that the MA class includes girdle parts so it belongs here;
bone of forelimb or pectoral fin or pectoral girdle
A bone that is part of a pelvic complex. Examples: pubis, ischium, fot phalanx, any tarsal bone, any bone of the pelvic fin or girdle.
the MA class called 'hindlimb bone' belongs here, as it includes bones in the pelvic girdle
Muscles of the pelvic girdle, hindlimb or pelvic fin.
Muscles of the pelvic girdle, thigh, leg (crus), and foot (pes).[AAO]
A muscle of a pectoral girdle, pectoral fin or anterior limb.
the MA class belongs here, based on its current child classes
Muscles of the pectoral girdle, arm, forearm, and hand (brachium, antebrachium, manus respectively).[AAO]
Anatomical cluster consisting of the skeletal elements (i.e. bone elements, cartilage elements, cartilage condensations) that are part of an individual subdivision of the organism. Excludes joints.
Anatomical cluster consisting of the skeletal elements that are part of the skeleton.[VSAO]
Any muscle organ that is part of either the head or the neck.
A cartilage element that is part of a splanchnocranium.
A skeleton of pelvic girdle that is part of a right pelvic girdle region.
A skeleton of pelvic girdle that is part of a left pelvic girdle region.
A pelvic girdle region that is in the right side of a multicellular organism.
A pelvic girdle region that is in the left side of a multicellular organism.
A synovial joint that is part of a pelvic girdle region.
A synovial joint that is part of a pectoral girdle region.
in FMA, these are part of the bony pectoral girdle
A skeletal joint that connects a laryngeal cartilage.
Joint in which the articulating bones or cartilages are connected by ligaments or fibrocartilage without an intervening synovial cavity. Examples: sagittal suture, inferior tibiofibular syndesmosis, costochondral joint, pubic symphysis.
Subdivision of the skeletal system which consists of the axial skeleton plus associated joints.
Subdivision of the skeletal system which consists of the postcranial axial skeleton plus associated joints.
Subdivision of urinary system which consists of the kidney and the ureters.
Gland of the lamina epithelialis mucosae which perforate the lamina muscularis, with their adenomeres located in the submucosal connective tissue.
Subdivision of skull that consists of the facial bones.
The skull can be divided into two: the neurocranium and the facial skeleton
primary subdivision of cranial skeletal system
A bone that is part of a neurocranium [Automatically generated definition].
A muscle layer that is part of a large intestine.
A multi cell part structure that is part of a central nervous system.
central nervous system cell part cluster
Muscles within the eye (bulbus oculi).[AAO]
Synovial sac which surrounds parts of one or more tendons. Examples: synovial tendon sheath of manual digit 2, radial bursa.
Alternate def: A synovial sheath is a layer of a tendon sheath containing tendons in the hand and foot. They lie internal to the fibrous tendon sheaths. An example is the common synovial sheath for the flexor tendons. [Wikipedia:Synovial_sheath]
synovial membrane of synovial tendon sheath
fibrous membrane of synovial tendon sheath
Subdivision of the skeletal system which consists of the appendicular skeleton plus associated joints.
Skeletal system which consists of the appendicular skeleton plus associated joints.[VSAO]
The part of the trunk that is in the dorsum[cjm].
In humans, the subdivision of trunk which is demarcated from the trunk proper by the external surface of the posterolateral part of the rib cage, the anterior surface of the thoracic vertebral column and the posterior axillary lines, the external surface of the posterior abdominal wall; together with the trunk proper, it constitutes the trunk[FMA]
compare with 'stratum basale of epidermis'. This class is the source for many adult structures - see WP2062. See also: 'enveloping layer of ectoderm'
The submucous layer of the wall of the uterine tube.
A blood vasculature that is part of a head.
Blood vessel part of cranial vasculature.[TAO]
A tube lumen that is part of a mesonephric duct.
The collection of all skeletal elements in an individual limb or fin.
Skeletal subdivision that is part of the paired limb/fin.[VSAO]
Anatomical structure that is an aggregation of similar cells from which cartilages and bones form, and from which chondrogenesis and osteogenesis are initiated during repair and/or regeneration. (Hall and Miyake 1995).
consider obsoleting, coordinate with VSAO
A subdivision of the head that corresponds to the jaw skeleton, containing both soft tissue, skeleton and teeth (when present). The jaw region is divided into upper and lower regions.
An epithelium that develops_from a ectoderm and is part of a oral epithelium.
A major subdivision of an organism that divides an organism along its main body axis (typically anterio-posterior axis). In vertebrates, this is based on the vertebral column.
Ideally this would be disjoint with analagous class for appendicular axes, but currently 'appendages' like antennae, horns cause a problem
subdivision of organism along main body axis
A cardiovascular system that is part of a conceptus.
The left nerve is longer than the right, because it crosses under the arch of the aorta at the ligamentum arteriosum.[WP]
vagus X nerve left recurrent laryngeal branch
vagus X nerve right recurrent laryngeal branch
An anatomical space that is part of a bone of lower jaw.
A cranial nerve nucleus that is associated with a vagus nerve.
A neural nucleus that is part of the spinal cord.
Ectodermal placode that does not develop into a component of the nervous system.
Connective tissue, which consists of a population of connective tissue cells, the intercellular matrix of which contains an irregular network of collagen and elastic fiber bundles. Examples: areolar tissue, mucoid tissue, connective tissue of peritoneum, connective tissue of fibrous pericardium.
Irregular connective tissue is an irregular connective tissue, the intercellular matrix of which contains a dense irregular network of collagen and elastic fiber bundles. Examples: connective tissue of peritoneum, connective tissue of fibrous pericardium.
Tissue characterized by a thick, random arrangement of collagen and elastin fibers with very few cells. The majority of the cells are fibroblasts, but mast cells and macrophages may also be seen. It is found in the dermis, periosteum, perichondrium, capsules of organs and sheaths of nerves and muscles[NCIT]
typus irregularis (textus connectivus collagenosus compactus)
Dense connective tissue is mainly composed of collagen type I. Crowded between the collagen fibers are rows of fibroblasts, fiber-forming cells, that manufacture the fibers. Dense connective tissue forms strong, rope-like structures such as tendons and ligaments. Tendons attach skeletal muscles to bones; ligaments connect bones to bones at joints. Ligaments are more stretchy and contain more elastic fibers than tendons. Dense connective tissue also make up the lower layers of the skin (dermis), where it is arranged in sheets
our OWL definition states that this is differentiated from other connective tissue types by virtue of the fact that the collage fiber component predominates, as opposed to cells and fluid.
Connective tissue in which the fibrous component predominates. The cells, ground substance, and tissue fluid represent a minor component[NCIT]
Irregular connective tissue, the intercellular matrix of which contains a sparse irregular network of collagen and elastic fiber bundles. Examples: areolar tissue, neuroglial tissue, mucoid tissue.
An acinus that is part of a exocrine gland.
the FMA class specifically refers to ureter
The connective tissue bundles in the extracellular matrix of aorta tissue that are composed of collagen, and play a role in tissue strength and elasticity
The connective tissue bundles in the extracellular matrix of pulmonary tissue that are composed of collagen, and play a role in tissue strength and elasticity
The connective tissue bundles in the extracellular matrix of bone tissue that are composed of collagen, and play a role in tissue strength and elasticity
The connective tissue bundles in the extracellular matrix of tendon tissue that are composed of collagen, and play a role in tissue strength and elasticity
Front (ventral) portion of the vascular, pigmentary, or middle coat of the eye, including the ciliary body and the iris.
A organ cavity that is part of a vagina.
Epimysium is a layer of connective tissue which ensheaths the entire muscle. It is composed of dense irregular connective tissue. It is continuous with fascia and other connective tissue wrappings of muscle including the endomysium, and perimysium. It is also continuous with tendons where it becomes thicker and collagenous.
The Epimysium also protects muscles from friction against other muscles and bones
A region of the stomach that is lined with glandular epithelium.
as currently defined, this would include the cardiac antrum; however, the intent may be to exclude the cardiac glands and in mice for this to be part of the region distal to the margo plicatus
The aggregate of the coelemic cavity lumen plus the membranes that line the lumen.
EHDAA2 distingsuishes between the lumen, the lining, and the 'coelomic cavity', which despire it's name, is not a space - it is the aggregate of space plus lining.
The central cavity within the mesoderm is the paired primary or embryonic coelom. Parts of the embryonic coelom often become enclosed in the mesoderm, forming a myocoel within the epimere, a nephrocoel within the mesomere, and simple coelom (body cavity) within the lateral plate mesoderm.[well established][VHOG]
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.166 and Figure 5.6
Bone that forms as a replacement of another structural tissue.
Bone that forms as a replacement of another structural tissue.[TAO]
This class was introduced to be consistent with the ZFA hierarchy. The corresponding TAO term was obsoleted, and never introduced into VSAO. Note that VSAO does have replacement element.
An anatomical cavity that is part of a bronchus.
Anatomical system that consists of the integumental system plus all mucosae and submucosae.
A primordium that has the potential to develop into a stomach.
facio-acoustic ganglion complex VII-VIII
facio-acoustic VII-VIII ganglion complex
acoustico-facial VII-VIII ganglion complex
A zone of skin that is part of a craniocervical region.
network of tubes that carries blood through the distensible musculomembranous organ that serves to collect and store urine excreted by the kidneys[MP]
external opening or orifice of the urethra through which urine and seminal fluid (in males only) leave the body; in males the meatus presents as a vertical slit normally positioned at the tip of glans penis; in females the meatus is located between the clitoris and the vagina in the vulvular vestibule of the female genitalia[MP].
the usually crescent-shaped opening of the urinary bladder into the urethra, placed at the anteroinferior angle (apex) of the urinary bladder trigone
internal urethral orifice of urinary bladder
mucus-secreting glands in the mucosa of the uterine cervix
Lining of the head of the uterus (cervix); contains large branched glands; does not undergo sloughing.
The part of the cervix uteri that protrudes into the vagina and is lined with stratified squamous epithelium.
distinction between two FMA classes not clear - we merge them here
A glandular epithelium that is part of a uterine cervix.
The 'glandular' or columnar epithelium of the cervix is located cephalad to the squamocolumnar junction. It covers a variable amount of the ectocervix and lines the endocervical canal. It is comprised of a single layer of mucin-secreting cells. The epithelium is thrown into longitudinal folds and invaginations that make up the so-called endocervical glands (they are not true glands). These infolding crypts and channels make the cytologic and colposcopic detection of neoplasia less reliable and more problematic. The complex architecture of the endocervical glands gives the columnar epithelium a papillary appearance through the colposcope and a grainy appearance upon gross visual inspection. The single cell layer allows the coloration of the underlying vasculature to be seen more easily. Therefore, the columnar epithelium appears more red in comparison with the more opaque squamous epithelium.
A epithelium that is part of a ectocervix.
The glandular epithelium that lines the endocervix.
Region of cervical epithelium where columnar epithelium of endocervic and the stratified non-keratinising squamous epithelium of the ectocervic meet
squamo-columnar junction of uterine cervix
squamocolumnar junction of uterine cervix
Site of 90% of lower genital tract neoplasia. This junction is presumed, but not proven, to be the embryologic junction of the Müllerian and urogenital sinus epithelia.
An artery that originates from the abdominal aorta
An epithelium that consists of columnar epithelial cells. Columnar epithelia are epithelial cells whose heights are at least four times their width. Columnar epithelia are divided into simple (or unilayered), and the rarer stratified (or multi-layered).[WP, modified]
Epithelium that derives from the mesoderm. [Automatically generated definition].
The nasal glands are the seromucous glands in the respiratory region of the nasal mucous membrane. The three major types of nasal glands are anterior serous glands, seromucous glands, and Bowman glands.
One of the pair of mesenchymal swellings (folds) located on either side of the cloacal membrane during the indifferent stage of embryonic development; cranial to the cloacal membrane the folds unite to form the genital tubercle; caudally the folds are subdivided into urogenital folds anteriorly and anal folds posteriorly
We presume this is distinct from AAO:0001003, an external integumentary structure - check with amphibian anatomy ontology developers. AO notes: the text def states mesenchymal swelling, EHDAA2 splits into mesenchymal and epithelial parts
One of five swellings formed during the development of the face
The median slit located inferior and posterior to the external urethral orifice in the female; the exit for menstrual flow and birth and the entrance for the penis during sexual intercourse; the size and appearance of the vaginal orifice varies inversely with that of the hymen (G. membrane), a thin fold of mucous membrane that surrounds the vaginal orifice
The deep cervical artery (Profunda cervicalis) is an artery of the neck.
A bone element that is part of a jaw region.
A muscle layer that is part of an intestine.
A muscular coat that is part of a urinary bladder.
respiratory system arterial smooth muscle
A smooth muscle tissue that is part of a respiratory system venous blood vessel.
The sclera and cornea form the fibrous tunic of the bulb of the eye; the sclera is opaque, and constitutes the posterior five-sixths of the tunic; the cornea is transparent, and forms the anterior sixth.
A anatomical space that is enclosed by a cloaca.
the ZFA class belongs here as it is an anatomical space. See https://sourceforge.net/p/obo/zebrafish-anatomy-zfa-term-requests/102/
The opening of the cloacal chamber to the outside of the organism. Birds maintain a single cloacal opening throughout their lives.
A anatomical space that is enclosed by a terminal part of digestive tract.
includes the cloacal lumen, in species where this is present
lumen of terminal part of digestive tract
An anatomical space with no opening to another space or to the exterior.
The collection of all skeletal elements in a pectoral complex - i.e. the combination of free limb or fin plus pectoral girdle.
skeleton of anterior limb/fin and girdle
The collection of all skeletal elements in a pelvic complex - i.e. the combination of free limb or fin plus pelvic girdle.
skeleton of posterior limb/fin and girdle
A mucosa that is part of a cloaca [Automatically generated definition].
cloacal epithelium (cle) (syn: cloacal endoderm) (TS17-TS20): the cloacal epithelium is derived from endoderm and lines the cloacal cavity. It is marked by Shh and Cdh1 and lines the cloacal lumen. The cloacal epithelium gives rise to the urogenital sinus epithelium, hindgut epithelium and the urethral plate epithelium.
A submucosa that is part of a cloaca [Automatically generated definition].
A serous membrane that is part of a cloaca [Automatically generated definition].
A muscular coat that is part of a cloaca.
A muscular coat that is part of a colon.
A muscular coat that is part of a anal canal.
A serous membrane that is part of a fallopian tube.
TODO mirror representation of abdominal aorta
this class groups all veins that are in the abdomen. The term 'abdominal vein' may have specific meanings in different contexts. The lateral abdominal veins are present in fishes but usually merged or absent in tetrapods; in amphibians, the L&R abdominal veins merge into the ventral abdominal vein
Any vein within the general circulation that transports blood back to the right atrium of the heart.
A gland that is part of a foregut-midgut junction.
The secretory unit of a serous gland. The acinar portion is composed of serous secreting cells.
In humans, the urethral groove is a temporary linear indentation on the underside (ventral side) of the male penis during embryonic development. It typically appears around 8 weeks of gestation and becomes closed into a normal male urethra by the 12th week
Anatomical cavity that is the lumen of the skull and contains the brain.
A blood vessel endothelium that is part of a lung [Automatically generated definition].
A section through the tube or network of tubes that connects the ovaries to the outside of the body.
FMA class may only represent the uterine portion
The anatomical space that is enclosed by a stomach.
Organ cavity which is bound by the internal surface of the wall of stomach. Examples: There is only one cavity of stomach[FMA:14585].
A anatomical cavity that is part of a ear vesicle.
Anatomical space that is an opening in a bone of the skull.
An anatomical space which is the lumen of some anatomical conduit and connects two or more spaces together[FMA,modified].
Vascular endothelium found in blood vessels of the blood-brain-barrier.
Vascular endothelium found in colon blood vessels.
Musculature of the head and neck, spine, and ribs.
A principle subdivision of an organism that includes all structures along the primary axis, typically the anterior-posterior axis, from head to tail, including structures of the body proper where present (for example, ribs), but excluding appendages.
The region of the organism associated with the visceral organs.
Cardinal body part, which consists of a maximal set of diverse subclasses of organ and organ part spatially associated with the vertebral column and ribcage. Examples: There is only one body proper[FMA:231424].
A tubular passage that extends from the primitive pit into the head process during the early stages of embryonic development in mammals. It perforates the splanchnopleure layer so that the yolk sac and the amnion are connected temporarily.
Fluid contained within the notochordal canal
A organ component layer that is part of a integumental system.
One of two openings in the uterine cervix.
Opening of uterine cervix into the vagina.
The external orifice of the uterus (or ostium of uterus, or external os) is a small, depressed, somewhat circular aperture on the rounded extremity of the vaginal portion of the cervix. Through this aperture, the cervical cavity communicates with that of the vagina. The external orifice is bounded by two lips, an anterior and a posterior. The anterior is shorter and thicker, though it projects lower than the posterior because of the slope of the cervix. Normally, both lips are in contact with the posterior vaginal wall. Prior to pregnancy, the external orifice has a rounded shape when viewed through the vaginal canal (as through a speculum). Following parturition, the orifice takes on an appearance more like a transverse slit or is 'H-shaped'[Wikipedia:External_orifice_of_the_uterus].
The cavity formed by the walls of the cervix.
Any of the organs or elements that are part of the digestive system. Examples: tongue, esophagus, spleen, crop, lunge feeding organ, tooth elements.
Great vessels is a term used to refer collectively to the large vessels that bring blood to and from the heart.
Groupings may vary - typically pulmonary vessels and aorta and vena cavae
A organ cavity that is part of a uterus.
Mesenchyme that develops_from the neural crest[Automatically generated definition].
Any member of the network of tubes that return blood from the renal tissues to the systemic circulation.
we follow MA and MP in distinguishing the venous blood vessel from the vein. The kidney cortex vein is not considered a renal vein, nor is the vasa recta
Subcutaneous adipose tissue that is located in the abdominal region.
Subdivision of skeletal system that consists of all skeletal elements in the thoracic region of the trunk. In most vertebrates this is the rib cage and sternum.
A unilaminar epithelium that develops_from a ectoderm and is part of a anal region.
The secretory unit of a mucous gland. The acinar portion is composed of mucous secreting cells.
A neuromere that is part of the presumptive midbrain
A neuromere that is part of the presumptive spinal cord
Any muscle organ that is part of a cloaca.
Any collection of muscles that is part of a pelvic complex. The pelvic complex comprises the pelvic girdle and the associated limb or fin.
Any collection of muscles that is part of a pectoral complex. The pectoral complex comprises the pectoral girdle and the associated limb or fin.
Any muscle organ that is part of a pectoral appendage (forelimb or pectoral fin).
Any muscle organ that is part of a pelvic appendage (hindlimb or pelvic fin).
A muscle organ that consists of skeletal muscle tissue ensheathed in epimysium, that develops from myotome and that is innervated by some somatic motor neuron. Skeletal muscles are typically attached (via a tendon) to a bone but there are exceptions (e.g. intrinsic tongue muscles).
A portion of tissue that will develop into vasculature.
A gland that is typically found in or near the orbital region, in or around either the medial or lateral canthi, and is typically associated with secretions onto the eyeball or associated ducts. Includes the Harderian, nictitans and lacrimal glands.
the only orbital gland found in anuran amphibians is either the Harderian or the lacrimal; if it is a lacrimal, then a progressive lateral migration of the lacrimal glands must occur through the amniotes[PMID:7559104]
the only orbital gland found in anuran amphibians is the Harderian[PMID:8843648]
An eye consisting of multiple light-sensing organs
present on mantle edge in arcacean Bivalvia
The eyes (optic cushions) on the oral surface of Asteroida (Echinodermata), close to the base of the terminal tentacles, are also composed of a number of simple ocelli - as many as 80-200 in certain species
A blood vessel that is part of a endometrium.
A region of somite adjacent to presomitic mesoderm.
Epithelium located in the intersomitic region.
Any structure that is placed on one side of the left-right axis of a bilaterian.
This class is primarily to implement taxon constraints. It may be removed in the future.
A hollow, muscular organ, which, by contracting rhythmically, contributes to the circulation of lymph, blood or analogs. Examples: a chambered vertebrate heart; the tubular peristaltic heart of ascidians; the dorsal vessel of an insect; the lymoh heart of a reptile.
A basement membrane of epithelium that is part of a respiratory system.
A epithelium that is part of a anal canal.
A smooth muscle tissue that is part of a hypodermis.
muscle layer in fatty layer of subcutaneous tissue
stratum musculosum panniculi adiposi telae subcutaneae
smooth muscle layer in fatty layer of subcutaneous tissue
Any anatomical conduit which is part of the upper respiratory tract
Anatomical cluster which consists a segment of the upper respiratory tract[FMA:265132].
An anatomical chamber that is part of the olfactory apparatus, consisting of cavity walls (nasal epithelium and mucosal layers) and the space bounded anteriorly by the nares and posteriorly by the choanae, when these structures are present.
see also, 'facial nerve muscle', which is not precisely equivalent. We include this grouping to accomodate the MA class, which includes masticatory muscle as a subtype; note the masticatory muscle is noy innervated by the facial nerve, unlike the facial muscles proper
A epithelium that is part of a camera-type eye.
is the sensory system for the sense of hearing.
Auditory system is general anatomical term in FMA
Luminal space of the right ventricle of the heart.
luminal space of the left ventricle of the heart.
A epithelium that is part of a female urethra.
The external part of the developing pharynx that is made of ectoderm. During vertebrate development, pockets form in pharyngeal ectoderm between the pharyngeal arches.
A layer of of the central nervous system that is part of gray matter.
central nervous system gray matter layer
mucus produced in the respiratory tract.
Any mucus produced by a mucosae of the respiratory system. This includes the mucus produced in the nasal cavity (nasal mucus) and mucus produced in the respiratory tract (phlegm).
An roughly circular indentation in a surface.
Primordium that develops into the central nervous system
Primordium that develops into the nervous system
Epithelium lining the distalmost portion of the digestive tract.
epithelium of terminal part of digestive tract
Any muscle tissue of the distalmost portion of the digestive tract.
muscle tissue of terminal part of digestive tract
The part of the conceptus that may be lost before birth or will be discarded at birth, or when the embryo becomes an independent organism.
An embryonic anatomical entity that will turn into one or more other anatomical entities, perhaps with other anatomical entities, later in development.
A mesenchyme-derived anatomical entity undergoing a transtion to become another structure.
A muscle layer that is part of the rectum
Any portion of smooth muscle tissue that is part of the rectum
A renal pelvis that is part of a left ureter.
A renal pelvis that is part of a right ureter.
A zone of skin that is part of a lower lip.
Added for consistency with MA EMAPA and EHDAA2. See https://github.com/obophenotype/mouse-anatomy-ontology/issues/104
Any portion of submucosa that lines the digestive tract.
Any organ component layer that consists of muscle tissue.
NCITA class may refer to smooth muscle only
A muscular coat that is part of a digestive tract.
responsible for gut movement, such as peristalsis
Foramen that allows the passge of the glossopharyngeal nerve (cranial nerve IX).
A Z-shaped canal running through the temporal bone from the internal acoustic meatus to the stylomastoid foramen. It is located within the middle ear region, according to its shape it is divided into three main segments: the labyrinthine, the tympanic, and the mastoidal segment .
The anatomical space within the intestine.
see notes in inclusivity in class 'intestine'
Muscle innervated by the trigeminal nerve (Cranial Nerve V).
muscle innervated by the trigeminal nerve
muscles innervated by the trigeminal nerve
An interconnected tubular multi-tissue structure that contains fluid that is actively transported around the heart.
A membranous sac in animals that serves as the receptacle of a liquid or contains gas.
Adipose tissue which is located throughout skeletal muscle and is responsible for the marbling seen in certain cuts of beef. In humans, excess accumulation of intramuscular fat is associated with insulin resistance and type 2 diabetes.
Any region of epithelium that is part of a skin region.
The part of the eye that consists of both the retina and the optic choroid
An exocrine gland that is part of a integumental system.
The spinal accessory nucleus lies within the cervical spinal cord (C1-C5) in the ventral horn. The nucleus ambiguus is classically said to provide the 'cranial component' of the accessory nerve. However, the very existence of this cranial component has been recently questioned and seen as contributing exclusively to the vagus nerve. The terminology continues to be used in describing both human anatomy, and that of other animals.
accessory nucleus of anterior column of spinal cord
nucleus accessorius columnae anterioris medullae spinalis
See also: http://en.wikipedia.org/wiki/Spinal_accessory_nucleus
A blood vessel that supplies or drains an ear.
A portion of organism substance that is secreted by a reproductive gland.
Single layer of a laminar structure, identified by different density, arrangement or size of cells and processes arranged in flattened layers or lamina[CUMBO].
this is currently used to group some cellular layers that may not strictly conform to the CARO definition of cell-part layer. Consider genericisizing and introducing subtypes for cellular layer, fibrous layer and cell soma layer
Serous membrane layer that is adjacent to and lines an organ.
Serous membrane layer that lines to a body cavity.
The layer of endometrial epithelium adjacent to the uterine cavity.
A specific region of the foregut into the area in which the lung will develop.
An embryonic or larval epithelium that is committed to form part of the nervous system.
An epithelium that is undergoing proliferation to provide large numbers of neuronal cells.
A neuroepithelium some of whose cells are undergoing terminal differentiation to become neuronal cells.
spinal cord lateral wall ventricular layer
Any of the cranial nerves, or their central nervous system analogs (the optic tract, the epiphyseal tract). These analogs are not true nerves, and are instead evaginated sensory afferents emanating from the brain
A taste bud that is located external to the digestive tube, on the head or body, as found in species such as goldfish.
A taste bud that is located on the skin of the head.
A taste bud that is located in the pharynx.
A taste bud that is located on the skin of the trunk.
The autonomic nerve is a small nerve which carries postganglionic sympathetic and parasympathetic neurons from the zygomaticotemporal nerve; a branch of the maxillary nerve, to the lacrimal nerve; a branch of the ophthalmic nerve. These neurons derive from the superior cervical ganglion and the pterygopalatine ganglion respectively. They will travel to the lacrimal gland via the lacrimal nerve. Parasympathetic will induce lacrimation and vice versa.
Any substance in the body or expelled from the body that is in a gaseous state.
Any portion of gas located in a part of the respiratory system that is composed primarily of air.
the area of axial mesoderm that develops into the prechordal plate
An multicellular anatomical structure that has subparts of multiple organs as a part.
A cluster of cells, largely surrounded by a morphological boundary.
A collection of anatomical structures that are alike in terms of their morphology or developmental origin.
resolve if this should be a subclass of disconnected anatomical group. Some collections (e.g. the skeleton or skull) are arguably connected
Any organ component layer that consists of smooth muscle tissue.
organ region with floating fiat boundary
Any portion of gas located in a part of the respiratory system.
Mesenchyme that is part of a developing jaw [Automatically generated definition].
Any material entity that is located in the digestive tract. This includes undigested food and liquid as well as unexcreted waste products. It also includes other entities such as ingested stones used to aid digestion. Any microbial cells or cell populations are also included.
Note that we treat any material entity that is ingested as an anatomical structure by defintion, although this may be expanding the CARO usage somewhat
Anatomical surface, which is the external surface of the whole body. Examples: There is only one body surface.
The organ of hearing located on the right side of the head.
The organ of hearing located on the left side of the head[ncit,modified].
The part of the circulatory system that lies within the subcutaneous tissue layers close to the surface of the skin.
Any of the veins carrying deoxygenated blood from the subcutaneous tissue layers.
The part of the circulatory system that lies deep beneath the subcutaneous tissue layers away from the surface of the skin.
A blood vessel carrying deoxygenated blood far beneath the skin usually accompanying an artery.
Any chamber of the left side of the heart
Any chamber of the right side of the heart
The parts of the orbital region that are outside of the the eyeball, including the lacrimal apparatus, the extraocular muscles and the eyelids, eyelashes, eyebrows and the conjunctiva
The primordial mouth region of the developing head.
A muscle layer that is part of the sigmoid colon
The sum of epicardial and paracardial fat deposits.
Any fat deposit surrounding a visceral organ.
The part of the ventral body cavity that is within the abdominal segment of the trunk, which encompasses the abdomen proper plus pelvic cavity.
respiratory primordium associated mesenchyme
An region of the mesoderm that includes anterior lateral mesoderm of the first heart field plus contiguous pharyngeal mesoderm that gives rise to second-heart-field-derived regions of the heart and branchiomeric muscles.
An anatomical junction that is between the sigmoid colon and rectum.
Material anatomical entity that forms the outermost boundary of an anatomical structure.
A bodily fluid that is located in the coelom.
he coelomic fluid serves several functions; it acts as a hydroskeleton, it allows free movement and growth of internal organs, it serves for transport of gases, nutrients and waste products between different parts of the body, it allows storage of sperm and eggs during maturation and it acts as a reservoir for waste[https://en.wikipedia.org/wiki/Coelom#Coelomic_fluid]
Any gland that is part os the respiratory system.
A notochord that has persisted beyond the embryonic stage.
Fluid that lines the vaginal walls that consists of multiple secretions that collect in the vagina from different glands.
The zygomaticotemporal nerve or zygomaticotemporal branch (temporal branch) is derived from the maxillary branch of the trigeminal nerve (Cranial nerve V). It runs along the lateral wall of the orbit in a groove in the zygomatic bone, receives a branch of communication from the lacrimal, and passes through zygomaticotemporal foramen in the zygomatic bone to enter the temporal fossa. It ascends between the bone, and substance of the Temporalis muscle, pierces the temporal fascia about 2.5 cm. above the zygomatic arch, and is distributed to the skin of the side of the forehead, and communicates with the facial nerve and with the auriculotemporal branch of the mandibular nerve. As it pierces the temporal fascia, it gives off a slender twig, which runs between the two layers of the fascia to the lateral angle of the orbit.
ramus zygomaticotemporalis (Nervus zygomaticus)
ramus zygomaticotemporalis nervus zygomatici
zygomaticotemporal branch of zygomatic nerve
Wall of ventricle which is continuous with the wall of aorta.
Wall of ventricle which is continuous with the wall of pulmonary trunk.
Region of wall of right ventricle which is continuous with the lateral and septal walls of right ventricle.
myocardium of anterior wall of left ventricle
myocardium of anterior wall of right ventricle
A mucosa that is part of a lip region [Automatically generated definition].
The upper tract of the renal system. The renal pelvis is the large cavity in the middle of each kidney. Urine drains from each kidney through a long tube called the ureter, into the bladder, where it is stored until it is passed from the body through the urethra.
vasculature of central nervous system plus retina
A zone of skin that is part of the face.
Cartilage which is part of the axial skeleton.
This class was sourced from an external ontology (teleost_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon
Non neural ectoderm that surrounds the presumptive neural plate and gives rise to neurogenic placodes.
Structures of the dermis, epidermis, glands and pigment cells recognizable on the external surfaces of the integument.
This class was sourced from an external ontology (amphibian_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon
Not clear how this differs from parent class. See https://github.com/obophenotype/uberon/issues/1305
Dermal, epidermal, glandular and pigment structures of the external head integument.
Dermal, epidermal, glandular and pigment structures of the body integument.
An anatomical surface that is part of a bone
surface of bone
A unit which is a standard measure of the distance between two points.
A unit which is a standard measure of the amount of matter/energy of a physical object.
A unit which is a standard measure of the dimension in which events occur in sequence.
A unit which is a standard measure of the average kinetic energy of the particles in a sample of matter.
A unit which is a standardised quantity of an element or compound with uniform composition.
A unit which represents a standard measurement of how much of a given substance there is mixed with another substance.
A unit which is a standard measure of the amount of space occupied by any substance, whether solid, liquid, or gas.
A unit which is a standard measure of the number of repetitive actions in a particular time.
A unit which is a standard measure of the volume of fluid which passes through a given surface per unit time .
A unit which represents a standard measurement occurrence of a process per unit time.
A vaccine is a processed material with the function that when administered, it prevents or ameliorates a disorder in a target organism by inducing or modifying adaptive immune responses specific to the antigens in the vaccine.
Many vaccines are developed to protect against infectious pathogens that causes infectious diseases. Many vaccines are also being developed against other diseases such as cancer, allergy, and autoimmune diseases.
a role that inheres in a prepared material entity that is designed to induce protection or treament for a diease or infection in vivo.
A bacterial vaccine that prevents against Escherichia coli infection.
A bacterial vaccine that prevents Neisseria meningitidis infection.
A Mycobacterium vaccine that protects against Mycobacterium tuberculosis.
a vaccine adjuvant that is formed as a mineral salt.
a vaccine adjuvant that contains microbial derived material.
an aluminum vaccine adjuvant that contains aluminum hydroxide.
an aluminum vaccine adjuvant that is aluminum phosphate.
a mineral salt vaccine adjuvant composed of calcium phosphate.
an emulsion vaccine adjuvant that consists of a water-in-oil emulsion of aqueous antigen in paraffin (mineral) oil of low specific gravity and low viscosity. It is named after Jules T. Freund (1890-1960), Hungarian-born American immunologist. It is a water in oil emulsion.
is a Freund's emulsfied oil adjuvant that contains inactivated and dried mycobacteria, usually Mycobacterium tuberculosis (the pathogenic agent of tuberculosis).
a Freud's adjuvant that does not contain the mycobacterial components.
A microbial derivative vaccine adjuvant consisting of cholera toxin (CT) from Vibrio cholerae.
A microbial derivative vaccine adjuvant that is the P40 particulate fraction isolated from Corynebacterium.
Corynebacterium-derived P40 vaccine adjuvant
an adjuvant role that inheres in a vaccine component which is added as part of a vaccine and induces enhanced adaptive immune response to the vaccine antigen.
The Latin "adjuvans" means to help, particularly to reach a goal. Adjuvant therapy for cancer is surgery followed by chemotherapy or radiation to help decrease the risk of the cancer recurring (coming back). An adjuvant is a substance that helps and enhances the pharmacological effect of a drug or increases the ability of an antigen to stimulate the immune system.
A vaccine that targets against a bacterial disease.
a processed material that is output of the vaccine preparation and part of a vaccine.
A microbial derivative vaccine adjuvant made from bacterial lipopolysaccharide (LPS) of gram-negative bacteria.
a synthetic vaccine adjuvant formulated to correspond to a component found in a water-soluble extract of cell walls of mycobacteria used in complete Freund's adjuvant (CFA).
an emulsion vaccine adjuvant that contains an organic polymer with some antigenic epitopes which might be shared with other organic polymers acting as immunostimulators.
a synthetic vaccine adjuvant that is an emulsifier called Arlacel A.
a montanide vaccine adjuvant that is Montanide 103.
a microbial derivitive vaccine adjuvant that contains components from killed Bordetella pertussis. The killed B. pertussis has a strong adjuvant effect on the diphtheria and tetanus toxoids in the DPT vaccines.
Bordetella pertussis component vaccine adjuvant
vaccine function is a function that inheres in a vaccine that induces protective immune response against a disease. It is realized in the immunization process in the host.
PERSPN: Oliver He: There has been hot discussion about whether we use 'vaccine function' or 'vaccine role'. Vaccine role may not be the good term to use. Vaccine is designed to be 'vaccine', so it should be vaccine function. One special case is cowpox virus. The cowpox virus can be mixed with some liquid like water and used as a smallpox vaccine. In this case, people often say: the cowpox virus has a 'vaccine role'. However, the cowpox virus vaccine is a processed material of a mix of the virus with water. The virus is a virus, it is not a vaccine per se. Therefore, vaccine role may not be an accurate term.
A synthetic vaccine adjuvant that is PCPP salt.
polyidi (carboxylatophenoxy) lphosphazene
a vaccine adjuvant that contains particles made up of concentric lipid membranes containing phospholipids and other lipids in a bilayer configuration separated by aqueous compartments. It is a relatively stable but non-covalently-bound complex of saponin adjuvant Quil-A, cholesterol and amphipathic antigen in a molar ratio of approximately 1:1:1. The spectrum of viral capsid antigens and non-viral amphipathic antigens of relevance for human vaccination, incorporated into ISCOMs, comprises influenza, measles, rabies, gp340 from EB-virus, gp120 from HIV, Plasmodium falciparum and Trypanosoma cruzi. Ref: http://www.vaccination.inoz.com/adjuvants.html.
IL-15 plasmid vaccine adjuvant
a microbial derivative vaccine adjuvant that is derived from E. coli heat labile toxin LT.
E. coli LT toxin derived vaccine adjuvant
Page 73, Chapter 6, Vaccine, 5th Edition. EXPERT CONSULT by Plotkin SA., et. al. 2008
a role inheres in a material entity, that has been added into a vaccine's formulation by the manufacture for a specific purpose. For example: adjuvant to enhance the effect of immunogen, perservatives, stablizers and those materials added for affecting PH and isotonicity.
Protective antigen is an antigen that stimulates protective immunity when used in vivo.
E. coli O157:H7 subunit vaccine expressing Esps and Tir
E. coli vaccine using intimin polypeptide
immunization is a processual entity that primes or modifies an adaptivie immune response to some antigens.
WEB: http://en.wikipedia.org/wiki/Immunization
Active immunization is an immunization process that entails the introduction of a foreign molecule into the body, which causes the body itself to generate adaptive immunity against the target.
Active immunization entails the introduction of a foreign molecule into the body, which causes the body itself to generate immunity against the target. This immunity comes from the T cells and the B cells with their antibodies. Active immunization can occur naturally when a person comes in contact with, for example, a microbe. If the person has not yet come into contact with the microbe and has no pre-made antibodies for defense (like in passive immunization), the person becomes immunized. The immune system will eventually create antibodies and other defenses against the microbe. The next time, the immune response against this microbe can be very efficient; this is the case in many of the childhood infections that a person only contracts once, but then is immune. Artificial active immunization is where the microbe, or parts of it, are injected into the person before they are able to take it in naturally. If whole microbes are used, they are pre-treated, Attenuated vaccine. (Wikipedia)
artificial active immunization is an active immunization that occurs when a person or animal is vaccinated with a specific vaccine.
a synthetic vaccine adjuvant, adamantylamide dipeptide (AdDP) is the desmuramyl analog of MDP.
adamantylamide dipeptide vaccine adjuvant
a vaccine component that is chemical substance added to vaccine and enhance and direct immune response to protective antigen. Many of vaccine adjuvants cause a range of serious side-effects.
immunization objective is the specification of an objective to achieve immunization.
vaccine preparation is a manufacturing process to produce a vaccine.
A bacterial vaccine that protects against Mycobacterium bacterial infection.
A bacterial vaccine that protects against Yersinia bacterial infection.
A vaccine that targets against a viral disease.
a role that inheres in a material entity that becomes an ingredient of a vaccine.
vaccine component role
An E. coli vaccine that uses subunit antigen type.
E. coli subunit vaccine
A bacteria vaccine that prevents against Yersinia pestis infection that causes plague.
a Streptococcal vaccine that is used against S. pneumoniae infection, which causes pneumococcal diseases.
WEB: http://www.who.int/vaccines/en/pneumococcus.shtml
A viral vaccine that protects against infection with Pseudorabies virus.
A particulate antigen delivery system, ISCOM is a vaccine adjuvant that consists of an assembly of antigens in multimeric form and presents an antigen to induce specific immunologic responses. The assembly is attached to a matrix with a built-in adjuvant, saponin. ISCOMs induce strong serum antibody responses, and are used as highly immunogenic forms of subunit vaccines. MeSH term: D20.215.894.860.449.
A bacterial vaccine that prevents streptococcal infections.
A Y. pestis subunit vaccine that uses recombinant Y. pestis V antigen. PMID: 7622205.
recombinant Y. pestis YopD protein vaccine
a mineral salt vaccine adjuvant that is composed of aluminum salt.
Aluminum vaccine adjuvant is a vaccine adjuvant that is composed of some aluminum compound.
"XG is derived from Xanthomonas campestris, has a pentasaccharide repeating unit structure, and its terminus contains a mannose moiety which acts as a toll-like receptor 2 agonist." REF: Mucoadhesive liposomes for intranasal immunization with an avian influenza virus vaccine in chickens, by Chiou C. et al. Biomaterials, Volume 30, Issue 29, October 2009, Pages 5862-5868, ISSN 0142-9612, 10.1016/j.biomaterials.2009.06.046. (http://www.sciencedirect.com/science/article/pii/S0142961209006371)
a cytokine vaccine adjuvant that includes IL-12.
IL-12 vaccine adjuvant is a vaccine adjuvant that contains IL-12.
an E. coli subunit vaccine that uses E. coli FimH adhesin protein as teh antigen, and uses the complete Freund's adjuvant (CFA) in the first vaccination and the incomplete Freund's adjuvant (IFA) in the boost vaccination.
PubMed: http://www.ncbi.nlm.nih.gov/pubmed/9110982
E. coli FimH with CFA and then IFA
A microbial derivative vaccine adjuvant compsed of CpG DNA.
Ribi vaccine adjuvant is an emulsion vaccine adjuvant that is a stable oil-in-water emulsion.
a synthetic vaccine adjuvant named RC529 that is a lipid A mimetic.
An aluminum vaccine adjuvant that is aluminum potassium sulfate (AlK(SO4)2).
An aluminum hydroxide vaccine adjuvant that is a gel that is made by precipitation of aluminum hydroxide Al(OH)3 under alkaline conditions.
A microbial derivative vaccine adjuvant made of the B subunit of the cholera toxin from Vibrio cholerae.
an aqueous formula of the synthetic vaccine adjuvant RC529.
RC529-AF can be obtained from Corixa Corporation (Seattle, WA). Reference: PMID: 15308371
RC529 vaccine adjuvant in an aqueour formulation
A microbial derivative vaccine adjuvant derived from the lipopolysaccharide (LPS) of Salmonella minnesota R595.
3-O-deacylated monophosphoryl lipid A vaccine adjuvant
A microbial derivative vaccine adjuvant that is a mutant form of LT containing a Ser-Lys substitution in position 63 which has been shown to be totally devoid of toxicity stable to protease treatment and able to act as mucosal adjuvant.
LTK63 is an enzymatically inactive mutant of the heat-labile enterotoxin of Escherichia coli. It can be used as a potent mucosal adjuvant.
A microbial derivative vaccine adjuvant derived from heat-killed Corynebacterium parvum.
killed Corynebacterium parvum vaccine adjuvant
Titermax Gold is an emulsion vaccine adjuvant which is a water-in-oil adjuvant with CRL-8300 (a block copolymer), squalene, and sorbitan monooleate.
It's a water-in-oil emulsion adjuvant. Reference: http://www.titermax.com/i_gold4.htm.
URL: http://www.titermax.com/i_gold4.htm
a synthetic vaccine adjuvant that is dimethyldioctadecylammonium bromide (DDA), a lipophilic quaternary ammonium salt known as a good adjuvant when co-administered systemically or nasally with an antigen.
A liposome-based vaccine adjuvant that have a positive surface charge.
cationic liposomal vaccine adjuvant DDA:TDB
a tenosactive compound vaccine adjuvant that contains purified extract from the bark of the South American tree Quillaja saponaria Molina.
A combination vaccine adjuvant comprised of monophosphoryl lipid A (MPL), QS21 and an oil in water emulsion.
monophosphoryl lipid A (MPL), QS21 and an oil in water emulsion.
AS04 is a combination vaccine adjuvant that is a combination of 50 μg of the immunoenhancer MPL (3-O-desacyl-4′-monophosphoryl lipid A) with 500 μg of aluminium salt.
VSA-3 is an emulsion vaccine adjuvant which is an emulsion plus DDA.
a tensoactive compound vaccine adjuvant that is derived from saponin, a compound that is an immunostimulator found in the plant P. senega.
A Montanide vaccine adjuvant that is formulated as water-in-oil emulsions and induces high antibody titers in several animal species. It is a vaccine adjuvant composed of metabolizable oil and a surfactant system designed to make a water-in-oil emulsion. It has been used since 1992 in more than 50 clinical trials related to therapeutic vaccines against various diseases such as cancer and malaria.
WEB: http://www.seppic.com/human-health/vaccine-adjuvant/montanide-isa-720-@/view-1044-seproduit.html?menuid=,979,&lang=en
a montanide vaccine adjuvant that is a mineral oil adjuvant.
A montanide vaccine adjuvant that is a vaccine adjuvant composed of a light mineral oil and a surfactant system designed to make a water-in-oil emulsion.
WEB: http://www.seppic.com/human-health/vaccine-adjuvant/montanide-isa-51-@/view-1042-seproduit.html?menuid=,979,&lang=en
An emulsion vaccine adjuvant developed by Montanide (http://www.montanide.com/).
B subunit of E. coli heat-labile enterotoxin
A microbial derivative vaccine adjuvant composed of the B subunit of E. coli heat-labile toxin.
A synthetic vaccine adjuvant with the tradename Polygen.
URL: http://www.mvp-technologies.com/adjuvants/Polygen%20Final%20Technical%20Bulletin.pdf
a role of host that contains vaccine. It is a role that inheres in an organism that is the target of a vaccine administration (vaccination process).
A nonantigenic carbohydrate adjuvant, which enhances both humoral and cell-mediated immunity to oligopeptides in experimental animal models.
A suspension of 1-2μm ovoids of immune stimulant gamma inulin (g-IN) in which alum is embedded as a carrier for protein or other anionic antigens.
a synthetic vaccine adjuvant that is Bay R1005 (N-(2-Deoxy-2-L-leucylamino β-D-glucopyranosyl)-N-octadecyldodecanoylamide hydroacetate ).
N-( 2-Deoxy-2-L-leucylamino-β-D-glucopyranosyl)-N-octadecyldodecanoylamide hydroacetate
A synthetic vaccine adjuvant that is N, N-dioctadecyl-N′, N′-bis( 2-hydroxyethyl) propanediamine (Avridine).
N, N-dioctadecyl-N′, N′-bis( 2-hydroxyethyl) propanediamine
a calcium phosphate vaccine adjuvant that is a gel prepared by precipitating soluable calcium and phosphate salts.
A microbial derivative vaccine adjuvant composed of the CTA1-DD fusion protein.
Cholera toxin A1-subunit-ProteinA D-fragment fusion protein
A mineral salt vaccine adjuvant that is composed of Deoxycholic acid sodium salt (DOC) complexed with aluminum hydroxide.
gamma inulin is a carbohydrate adjuvant that is a highly specific activator of the alternative pathway of complement in vitro and in vivo, and is composed of linear (unbranched) b-D-(2-1) polyfructofuranosyl-a-D-glucose.
Gerbu adjuvant is a combination vaccine adjuvant that is comprised of a mixture of GMDP, DDA, and Zinc L-proline salt complex (ZnPro8).
a cytokine vaccine adjuvant that includes GM-CSF.
A synthetic vaccine adjuvant containing GMDP, a higly effective primary adjuvant.
an IFN-gamma vaccine adjuvant that is composed of recombinant hIFN-gamma.
recombinant hIFN-gamma/Interferon-g vaccine adjuvant
a cytokine vaccine adjuvant that includes IL-1b.
a cytokine vaccine adjuvant that includes IL-2.
a cytokine vaccine adjuvant that includes IL-7.
a synthetic vaccine adjuvant loxoribine is a guanosine analog derivatized at position N7 and C8, and activates TLR-7.
An emulsion vaccine adjuvant consisting of an oil (squalene)-in-water nano emulsion.
MTP-PE liposomes are a liposome-based vaccine adjuvant that consists of liposomes containing the synthetic lipophilic analog of muramyl dipeptide, muramyl tripeptide phosphatidylethanolamine (MTP-PE).
a synthetic vaccine adjuvant made of murametide that has adjuvant activity similar to MDP.
a synthetic vaccine adjuvant called murapalmitine.
Nac-Mur-L-Thr-D-isoGIn-sn-glyceroI dipalmitoyl
a synthetic adjuvant that is an MDP analog called D-Murapalmitine.
Nac-Mur-D-Ala-D-isoGln-sn-glycerol dipalmitoyl
a synthetic vaccine adjuvant that is composed of neuraminidase-galactose oxidase (NAGO) a mixture of mixture of the two enzymes-neuraminidase and galactose oxidase.
a synthetic vaccine adjuvant consisting of multi-lamellar vesicles comprising a mixture of non-ionic surfactant (e.g., 1-monopalmitoyl-rac-glycerol), cholesterol and dicetyl phosphate used as a primary vaccine adjuvant for entrapped antigen.
a synthetic vaccine adjuvant made from the emulsion polymerization of methyl methacrylate.
a synthetic vaccine adjuvant synthesized from stable protein phospholipid-calcium precipitates.
a tensoactive compound vaccine adjuvant that is composed of extracts from the bark of the Quillaja saponaria Molina tree.
An aluminum vaccine adjuvant that is a synthetic oxyhydroxide of aluminum (aluminum hydroxide) prepared by acid-base precipitation.
An aluminum hydroxide vaccine adjuvant that is a low visosity aluminum hydroxide gel.
a cytokine vaccine adjuvant that contains the 163-171 peptide of IL-1β.
Specon is an emulsion vaccine adjuvant that is a water-in-oil emulsion that is used as an adjuvant and has immunostimulating properties similar to Freund's complete adjuvant (FCA).
SPT is an emulsion vaccine adjuvant that is an emulsion of squalane (5%), Tween 80( 0.2%), Pluronic L121( 1.25%), phosphate-buffered saline pH 7.4, and antigen.
a synthetic vaccine adjuvant stearyl tyrosine is considered an "organic equivelant" of aluminum hydroxide.
a synthetic vaccine adjuvant called Theramide that is composed of N-acetylglucosaminyl-N-acetylinuramyl-L-Ala-D-isoGlu-L-Ala-dipalmitoxy propylamide (DTP-DPP).
a synthetic vaccine adjuvant that is a copolymer (CRL1005), based on a 12 kDa polyoxypropylene (POP) core with 5% POE.
Nanoemulsion vaccine adjuvant is an emulsion vaccine adjuvant and is made from non-toxic lipid droplets a few hundred nanometers in diameter and made from surfactants approved for human consumption and common food substances that are 'Generally Recognized as Safe' (GRAS) by the FDA.
AS03 is an emusion vaccine adjuvant that contains α-tocopherol and squalene, two biodegradable polyprenyls, in an oil-in-water emulsion.
A microbial deriviative vaccine adjuvant that is a mutant form of E.coli heat-labile toxin.
A microbial derivative vaccine adjuvant containing E. coli heat-labile toxin.
An aluminum vaccine adjuvant that is a a proprietary aluminum hydroxyphosphate sulfate formulation that is both physically and functionally distinct from traditional aluminum phosphate and aluminum hydroxide adjuvants.
amorphous aluminum hydroxyphosphate sulfate adjuvant (AAHSA)
a synthetic vaccine adjuvant contiaing imiquimod a imidazoquinoline.
a synthetic vaccine adjuvant, resiquimod is a chemical analog of imiquimod.
An emulsion vaccine adjuvant containing 2.5% squalene.
A microbial derivative vaccine adjuvant composed of flagellin from gram-negative bacteria.
a synthetic vaccine adjuvant containing Poly(I:C), a synthetic double stranded analog of RNA.
WEB: http://en.wikipedia.org/wiki/Polyinosinic:polycytidylic_acid
a particulate antigen delivery system that is a vaccine adjuvant comprising cholesterol, phospholipid and saponin but without antigen.
ISCOMATRIX is identical to ISCOMs except that it does not contain antigen. Ref: PMID: 17336431.
a tensoactive compound vaccine adjuvant that is made from highly purified saponins.
WEB: http://www.isconova.com/products/abisco-research-reagent/abisco-100.aspx
a particulate antigen delivery system that is albumin-heparin microparticles vaccine adjuvant that is prepared from albumin and heparin stabilized by cross-linking reaction with EDC.
albumin-heparin microparticles vaccine adjuvant
SmithKline Beecham adjuvant system 2 (AS-2) is a combination vaccine adjuvant and is based on the combination of Monophosphoryl Lipid A(MPL), QS21 (a purified fraction of Saponin extracted from Quillarja Saponaria), and a proprietary oil in water emulsion.
a cytokine vaccine adjuvant that includes B7-2.
a synthetic vaccine adjuvant that is a local anaesthetic drug belonging to the amino amide group, and is used as a vaccine adjuvant in DNA vaccines.
PMID: 15246629, WEB: http://en.wikipedia.org/wiki/Bupivacaine
A liposome-based vaccine adjuvant that is composed of virus sized liposomes that contain a DNA plasmid.
a synthetic vaccine adjuvant that is DHEA, which is relatively stable and can be directly incorporated into vaccine formulations.
a synthetic vaccine adjuvant that is PLGA, which has been used in the controlled delivery of peptide drugs.
Polyester poly (DL-lactide-co-glycolide)
DL-PGL (Polyester poly (DL-lactide-co-glycolide)) vaccine adjuvant
a cytokine vaccine adjuvant that uses the adjuvant effect of cytokine IL-15.
immunoliposomes containing antibodies to costimulatory molecules is a liposome-based vaccine adjuvant which is prepared from dehydration-rehydration vesicles (DRVs).
immunoliposomes containing antibodies to costimulatory molecules
A microbial derivative vaccine adjuvant that is a mutant form of heat-labile Escherichia coli enterotoxin (LT) that contains a substitution Ala → Arg in position 72 of the A subunit.
A microbial derivative vaccine adjuvant containing MPL and squalene.
A microbial derived vaccine adjuvant made of E112K mC, a mutated CT created by substituting a single amino acid in the ADP-ribosyltransferase active centre, glutamate to lysine at position 112.
non-toxic mutant E112K of Cholera Toxin mCT-E112K
a microbial derivative vaccine adjuvant that is derived from cholera toxin.
SAF-1 is a combination vaccine adjuvant that is composed of threonyl-MDP (0.05-1%) in an emulsion vehicle [5% squalane, 2.5% Pluronic® L121, 0.2% Polysorbate 80 and phosphate buffered saline (pH 7.4)].
A liposome-based vaccine adjuvant that includes the glycoproteins of Sendai virus.
Sendai Proteoliposomes, Sendai-containing Lipid Matrices
a synthetic vaccine adjuvant that is threonyl muramyl dipeptide (TMDP).
N-acetyl muramyl-L-threonyl-D-isoglutamine
threonyl muramyl dipeptide (TMDP) vaccine adjuvant
A microbial derivative vaccine adjuvant made of virus like particles (VLPS) containing the yeast retrotransposon Ty which has the amino acids 1-381 of the pI protein encoded.
a vaccine adjuvant that contains active cytokine compound.
a vaccine adjuvant that is composed of differnt compounds under more than one category.
a vaccine adjuvant that serves as a particulate antigen delivery system.
A vaccine aduvant that contains synthetic material.
a vaccine adjuvant that includes tensioactive material. Tensioactive materials, surfactants or active surface agents are chemical substances with a polar-non polar structure. These substances have a tendency to locate themselves at the surface creating an adsorbed monomolecular layer on the interface.
WEB: http://www.citt.ufl.edu/team/sepulveda/html/en_tensioactivos.htm
a vaccine adjuvant that is primarily composed of carbohydrates.
a cytokine vaccine adjuvant that includes IFN-gamma.
The objective that intends to produce vaccine via the vaccine preparation process.
A vaccine that protects against Listeria monocytogenes.
Listeria monocytogenes vaccine
A CpG DNA vaccine adjuvant that is a short, synthetic, unmethylated CpG oligodeoxynucleotide (CpG ODN) with immunostimulatory activity.
ISS 1018 is a short, synthetic, unmethylated CpG oligodeoxynucleotide (CpG ODN) with immunostimulatory activity. ISS 1018 signals through Toll-like receptor 9 (TLR9) to induce the production of immunoglobulin by B cells and interferon (IFN) -alpha, IFN-beta, interleukin-12 (IL-12), and tumor necrosis factor - alpha (TNF-alpha) by plasmacytoid dendritic cells (pDC). ISS 1018 CpG ODN promotes antigen presentation and co-stimulatory molecule expression. ISS 1018 is currently being investigated in combination with HBsAg vaccine as a prophylactic treatment for to prevent Hepatitis B in adults. It is also being investigated in combination with rituximab for treatment of b-cell or non-hodgkin's lymphoma.
ISS 1018 CpG ODN vaccine adjuvant
L. monocytogenes DNA Vaccine encoding hly
Psuedorabies DNA vaccine encoding IE180 protein
M. tuberculosis DNA Vaccine encoding KatG
Herpes simplex virus type 1 and 2 protein
VP35 expressed from alphavirus replicons induced a protective immune response in C57BL/6 mice when challenged with Ebola virus Zaire [PMID:11485406].
VP35 expressed from alphavirus replicons induced a protective immune response in C57BL/6 mice when challenged with Ebola virus Zaire [PubMed: 11485406].
Protegen ID: 16; NCBI Gene GI: 911827; NCBI Protein GI: 10313992; NCBI Protein Accession: NP_066244; NCBITaxon: 186538
MAb BA5 protected animals against plague, neutralized the Y. pestis type III secretion pathway and promoted opsonophagocytic clearance of bacteria in blood. LcrV residues 196-225 were necessary and sufficient for MAb BA5 binding. These results identify LcrV residues 196-225 as a linear epitope that is recognized by the murine immune system to confer plague protection [PMID:20005318].
MAb BA5 protected animals against plague, neutralized the Y. pestis type III secretion pathway and promoted opsonophagocytic clearance of bacteria in blood. LcrV residues 196-225 were necessary and sufficient for MAb BA5 binding. These results identify LcrV residues 196-225 as a linear epitope that is recognized by the murine immune system to confer plague protection [PubMed: 20005318].
Protegen ID: 44; NCBI Gene GI: 1172676; NCBI Protein GI: 16082719; NCBI Protein Accession: NP_395165; NCBITaxon: 214092
An LcrV variant lacking amino acid residues 271 to 300 (rV10) elicited immune responses that protected mice against a lethal challenge with Y. pestis [PMID:16041032].
An LcrV variant lacking amino acid residues 271 to 300 (rV10) elicited immune responses that protected mice against a lethal challenge with Y. pestis [PubMed: 16041032].
Protegen ID: 45; NCBI Gene GI: 1149310; NCBI Protein GI: 31795491; NCBI Protein Accession: NP_857946; NCBITaxon: 187410
Study evaluated the humoral immune response of mice that survived lethal Y. pestis aerosol challenge after antibiotic treatment. Results indicated that one of the predominant antibody response of mice surviving pneumonic plague after treatment with antibiotics was to pla [PMID:10085037].
Study evaluated the humoral immune response of mice that survived lethal Y. pestis aerosol challenge after antibiotic treatment. Results indicated that one of the predominant antibody response of mice surviving pneumonic plague after treatment with antibiotics was to pla [PubMed: 10085037].
Protegen ID: 48; NCBI Gene GI: 1172643; NCBI Protein GI: 16082686; NCBI Protein Accession: NP_395233; NCBITaxon: 214092
The type III secretion apparatus encoded on the low-calcium response (LCR) virulence plasmid, pCD1 in strain KIM5, of Y. pestis is a conserved virulence mechanism that is absolutely required for virulence of Y. pestis. YscF is a surface localized protein required both to secrete Yops and to translocate toxins into eukaryotic cells. YscF polymerization is possibly required for a YscF needle to puncture eukaryotic cell membranes. It is also likely that YscF and its homologs function to provide a base that a translocon complex is built upon, or that YscF builds a conduit from the bacterium to the eukaryotic membrane - this suggestion seems more likely given that other proteins such as YopB, YopD, and LcrV are also required for translocation into eukaryotic cells. YscF is thought to be a surface-expressed protein in Y. pestis and is required for virulence. YscF has been found to function as a protective antigen against experimental plague infection [PMID:15978133].
The type III secretion apparatus encoded on the low-calcium response (LCR) virulence plasmid, pCD1 in strain KIM5, of Y. pestis is a conserved virulence mechanism that is absolutely required for virulence of Y. pestis. YscF is a surface localized protein required both to secrete Yops and to translocate toxins into eukaryotic cells. YscF polymerization is possibly required for a YscF needle to puncture eukaryotic cell membranes. It is also likely that YscF and its homologs function to provide a base that a translocon complex is built upon, or that YscF builds a conduit from the bacterium to the eukaryotic membrane - this suggestion seems more likely given that other proteins such as YopB, YopD, and LcrV are also required for translocation into eukaryotic cells. YscF is thought to be a surface-expressed protein in Y. pestis and is required for virulence. YscF has been found to function as a protective antigen against experimental plague infection [PubMed: 15978133].
Protegen ID: 49; NCBI Gene GI: 1172673; NCBI Protein GI: 16082716; NCBI Protein Accession: NP_395162; NCBITaxon: 214092
Mice and rabbits were immunized with recombinant HCR/A1 (rHCR/A1) from the classical type A-Hall strain (ATCC 3502) (BoNT/A1) and rHCR/E from BoNT serotype E Beluga (BoNT/E(B)). The protection elicited by rHCR/A1 to BoNT/A1 and BoNT/A2 and by rHCR/E(B) to BoNT/E(A) indicate that immunization with receptor binding domains elicit protection within sub-serotypes of BoNT [PMID:16177380].
Mice and rabbits were immunized with recombinant HCR/A1 (rHCR/A1) from the classical type A-Hall strain (ATCC 3502) (BoNT/A1) and rHCR/E from BoNT serotype E Beluga (BoNT/E(B)). The protection elicited by rHCR/A1 to BoNT/A1 and BoNT/A2 and by rHCR/E(B) to BoNT/E(A) indicate that immunization with receptor binding domains elicit protection within sub-serotypes of BoNT [PubMed: 16177380].
Protegen ID: 448; NCBI Gene GI: 5398487; NCBI Protein GI: 153936924; NCBI Protein Accession: YP_001386738; NCBITaxon: 441771
The DNA replicon vaccine (pSCARSBHc) encoding the Hc domain of BoNT/B (BHc) induced better responses and protection against BoNT/B mouse challenge than conventional DNA vaccine. Recombinant SFV particle VRP-BHc protected mice from high-dose BoNT/B challenge [PMID:28869522]. The production of ciBoNT/B1 HP, ciBoNT/C1 HP, ciBoNT/E1 HP and ciBoNT/F1 HP suggest the ciBoNT HP vaccines exhibit superior potency after single vaccinations.[PMID:28869522]
The DNA replicon vaccine (pSCARSBHc) encoding the Hc domain of BoNT/B (BHc) induced better responses and protection against BoNT/B mouse challenge than conventional DNA vaccine. Recombinant SFV particle VRP-BHc protected mice from high-dose BoNT/B challenge [PubMed: 19712769].
Protegen ID: 449; NCBI Gene GI: 6030102; NCBI Protein GI: 169834607; NCBI Protein Accession: YP_001693307; NCBITaxon: 498213
The heterologous prime-boost strategy of live Salmonella vaccine expressing Mycobacterium tuberculosis fusion antigen Age5B-ESAT6 (esxA) from the chromosome followed by a systemic boost of antigen and adjuvant reduced the levels of M. tuberculosis bacteria in the lungs and spleen to the same extent as BCG. Additionally, this vaccination regimen was observed to be statistically equivalent in terms of protection to immunisation with BCG [PMID:16751377]. In a prophylactic vaccine model, immunization with the Mycobacterium tuberculosis protein ESAT-6 with LANAC adjuvant elicited significant protective immunity against aerosol challenge with virulent M. tuberculosis [PMID:16751377].
The heterologous prime-boost strategy of live Salmonella vaccine expressing Mycobacterium tuberculosis fusion antigen Age5B-ESAT6 (esxA) from the chromosome followed by a systemic boost of antigen and adjuvant reduced the levels of M. tuberculosis bacteria in the lungs and spleen to the same extent as BCG. Additionally, this vaccination regimen was observed to be statistically equivalent in terms of protection to immunisation with BCG [PubMed: 19755145].
Protegen ID: 104; NCBI Gene GI: 886209; NCBI Protein GI: 57117165; NCBI Protein Accession: NC_000962.2; NCBITaxon: 1773
Mice immunized intranasally with recombinant Tir protein had a survival rate of 92.9% after challenge with EHEC 0157:H7 [PMID:26020530]. Immunization of calves with recombinant EHEC O157 EspA, intimin and Tir resulted in the generation of antibodies capable of cross-reacting with antigens from non-O157 EHEC serotypes, suggesting that immunization with these antigens may provide a degree of cross-protection against other EHEC serotypes [PMID:26020530]
Protegen ID: 199; NCBI Gene GI: 960860; NCBI Protein GI: 15804222; NCBI Protein Accession: NP_290261.1; NCBITaxon: 562
Systemic immunization of calves with a combination of EspA, intimin-531, and H7 flagellin resulted in a significant reduction in shedding of EHEC O157 to levels predicted to significantly impact on EHEC O157 cattle-to-cattle transmission [PMID:26020530]
EHEC strains produce intimin, an outer membrane adhesin encoded by the eae gene located in a chromosomal pathogenicity island termed the locus of enterocyte effacement [PubMed: 17258324].
Protegen ID: 93; NCBI Gene GI: 960862; NCBI Protein GI: 15804220; NCBI Protein Accession: NP_290259; NCBITaxon: 155864
FimH is a protective antigen [PMID:9110982] Of the vaccine preparations, Fusion, Fusion + CT, and FimH admixed with FliC and CT showed the best protection against UPEC (Asadi et al., 2016).
FimH is a protective antigen [PubMed: 9110982]
Protegen ID: 263; NCBI Gene GI: 3992235; NCBI Protein GI: 91213965; NCBI Protein Accession: YP_543951; NCBITaxon: 364106
The 10-kDa culture filtrate protein (CFP-10, esxB) and 6-kDa early secretory antigen of T cells (ESAT-6) are secreted in abundance by Mycobacterium tuberculosis. Study demonstrated that protective immunity is induced by CFP-10 DNA vaccination in C3H mice as measured by a CFU reduction in the lung and spleen 4 and 8 weeks after challenge with M. tuberculosis [PMID:18332205].
The 10-kDa culture filtrate protein (CFP-10, esxB) and 6-kDa early secretory antigen of T cells (ESAT-6) are secreted in abundance by Mycobacterium tuberculosis. Study demonstrated that protective immunity is induced by CFP-10 DNA vaccination in C3H mice as measured by a CFU reduction in the lung and spleen 4 and 8 weeks after challenge with M. tuberculosis [PubMed: 18332205].
Protegen ID: 121; NCBI Gene GI: 886194; NCBI Protein GI: 15611010; NCBI Protein Accession: NP_218391; NCBITaxon: 83332
Researchers have developed DNA vaccines expressing M. tuberculosis antigen 85A (Ag85A, fbpA) and cytokine granulocyte macrophage colony stimulating factor (GM-CSF). The immune strategy of BCG-prime and DNA vaccine boost induced mice to generate efficient immune protection against M. tuberculosis challenge [PMID:19450898].
Researchers have developed DNA vaccines expressing M. tuberculosis antigen 85A (Ag85A, fbpA) and cytokine granulocyte macrophage colony stimulating factor (GM-CSF). The immune strategy of BCG-prime and DNA vaccine boost induced mice to generate efficient immune protection against M. tuberculosis challenge [PubMed: 19450898].
Protegen ID: 122; NCBI Gene GI: 886132; NCBI Protein GI: 15610940; NCBI Protein Accession: NC_000962.2; NCBITaxon: 1773
Immunization with IutA protects against urinary tract colinization by E.coli CFT073 in the bladders of CBA/J mice [PMID:26729174]. We demonstrated for IutA, antigen-specific serum IgG represents a strong correlate of protection in vaccinated mice [PMID:26729174].
Immunization with IutA protects against urinary tract colinization by E.coli CFT073 in the bladders of CBA/J mice [PubMed: 19806177].
Protegen ID: 280; NCBI Gene GI: 1039578; NCBI Protein GI: 26249458; NCBI Protein Accession: NP_755498; NCBITaxon: 199310
Antibodies directed at the putative binding region of FimH (anti- s-FimH1-25) significantly reduced E. coli bladder infections in the experimental mouse model of urinary tract infections [PMID:9276729].
Antibodies directed at the putative binding region of FimH (anti- s-FimH1-25) significantly reduced E. coli bladder infections in the experimental mouse model of urinary tract infections [PubMed: 9276729].
Protegen ID: 281; NCBI Gene GI: 948847; NCBI Protein GI: 16132141; NCBI Protein Accession: NP_418740; NCBITaxon: 511145
Active immunization of BALB/c mice with IroN antigen in Freund's adjuvant protects mice from lethal challenge with ExPEC strain S26 [PMID:17145948].
Active immunization of BALB/c mice with IroN antigen in Freund's adjuvant protects mice from lethal challenge with ExPEC strain S26 [PubMed: 17145948 ].
Protegen ID: 282; NCBI Gene GI: 7379404; NCBI Protein GI: 222104801; NCBI Protein Accession: YP_002539290; NCBITaxon: 562
S. flexneri M90T is a colonisation-defective mutant with a transposon in fnr, which encodes a regulator of anaerobic metabolism. To establish whether FNR-mediated repression of spa32 and spa33 contributes to increased Shigella entry into cells in an anaerobic cabinet, recombinant M90T strains were constructed which contain spa32 and spa33 under the control of either their native promoters (M90Tp32/33) or promoters with disrupted FNR boxes (M90Tp#32/#33).The presence in M90T of spa32 and spa33 alleles that are not repressed by FNR led to IpaB secretion during anaerobic growth, and loss of the increased entry of Shigella into cells in an anaerobic cabinet [PMID:20436458].
S. flexneri M90T is a colonisation-defective mutant with a transposon in fnr, which encodes a regulator of anaerobic metabolism. To establish whether FNR-mediated repression of spa32 and spa33 contributes to increased Shigella entry into cells in an anaerobic cabinet, recombinant M90T strains were constructed which contain spa32 and spa33 under the control of either their native promoters (M90Tp32/33) or promoters with disrupted FNR boxes (M90Tp#32/#33).The presence in M90T of spa32 and spa33 alleles that are not repressed by FNR led to IpaB secretion during anaerobic growth, and loss of the increased entry of Shigella into cells in an anaerobic cabinet [PubMed: 20436458].
Protegen ID: 288; NCBI Gene GI: 876502; NCBI Protein GI: 13449098; NCBI Protein Accession: NP_085314; NCBITaxon: 424718
Oral immunization of mice with ZJ111/pcDNA3-SAG1 elicited specific humoral responses and stimulated proliferation of splenocytes (P<0.05). Mice immunized with ZJ111/pcDNA3-SAG1 displayed significant protection against an intraperitoneally challenge with 500 tachyzoite forms of T. gondii RH strain. Vaccination at 10(7) and 10(8)CFU per mice provided a 20% and 10% survival rate comparing 100% mortality of the non-immunized mice, exhibiting longer living time and better survival rate [PMID:18590785].
Oral immunization of mice with ZJ111/pcDNA3-SAG1 elicited specific humoral responses and stimulated proliferation of splenocytes (P<0.05). Mice immunized with ZJ111/pcDNA3-SAG1 displayed significant protection against an intraperitoneally challenge with 500 tachyzoite forms of T. gondii RH strain. Vaccination at 10(7) and 10(8)CFU per mice provided a 20% and 10% survival rate comparing 100% mortality of the non-immunized mice, exhibiting longer living time and better survival rate [PubMed: 18590785].
Protegen ID: 326; NCBI Gene GI: 7900172; NCBI Protein GI: 237839159; NCBI Protein Accession: XP_002368877; NCBITaxon: 508771
Modified yopD antigens were able to partially protect immunized mice at various levels against lethal challenge with Y. pestis KIM 1001 strain [PMID:18291562].
Modified yopD antigens were able to partially protect immunized mice at various levels against lethal challenge with Y. pestis KIM 1001 strain [PubMed: 18291562].
Protegen ID: 339; NCBI Gene GI: 1149313; NCBI Protein GI: 31795494; NCBI Protein Accession: NP_857949; NCBITaxon: 187410
Study tested the efficacy of 2 proteins, Psn and a portion of LcrV in protecting mice against virulent Yersinia pestis challenge. Results show that the truncated LcrV protein delivered by RASV is sufficient to afford a full protective immune response in a mouse model of bubonic plague and the Psn protein afforded partial protection in a non-optimized system [PMID:17966435].
Study tested the efficacy of 2 proteins, Psn and a portion of LcrV in protecting mice against virulent Yersinia pestis challenge. Results show that the truncated LcrV protein delivered by RASV is sufficient to afford a full protective immune response in a mouse model of bubonic plague and the Psn protein afforded partial protection in a non-optimized system [PubMed: 17966435].
Protegen ID: 351; NCBI Gene GI: 1147351; NCBI Protein GI: 22126288; NCBI Protein Accession: NP_669711; NCBITaxon: 187410
Study evaluated the humoral immune response of mice that survived lethal Y. pestis aerosol challenge after antibiotic treatment. Results indicated that one of the predominant antibody response of mice surviving pneumonic plague after treatment with antibiotics was to yopH [PMID:10085037].
Study evaluated the humoral immune response of mice that survived lethal Y. pestis aerosol challenge after antibiotic treatment. Results indicated that one of the predominant antibody response of mice surviving pneumonic plague after treatment with antibiotics was to yopH [PubMed: 10085037].
Protegen ID: 352; NCBI Gene GI: 1172712; NCBI Protein GI: 16082755; NCBI Protein Accession: NP_395201; NCBITaxon: 214092
Researchers constructed isogenic mutants of B. pertussis Tohama expressing the alleles ptxA1 or ptxA2 and prn1 or prn2 and compared the efficacies of an acellular pertussis vaccine against the mutants in a mouse model. While the vaccine was effective against all of the B. pertussis strains regardless of the allele expression pattern, the strain expressing ptxA1 and prn2 displayed a survival advantage over the other strains [PMID:20357056].
Researchers constructed isogenic mutants of B. pertussis Tohama expressing the alleles ptxA1 or ptxA2 and prn1 or prn2 and compared the efficacies of an acellular pertussis vaccine against the mutants in a mouse model. While the vaccine was effective against all of the B. pertussis strains regardless of the allele expression pattern, the strain expressing ptxA1 and prn2 displayed a survival advantage over the other strains [PubMed: 20357056].
Protegen ID: 378; NCBI Gene GI: 2664290; NCBI Protein GI: 33592195; NCBI Protein Accession: NP_879839; NCBITaxon: 257313
BALB/c mice were immunized with PTx vaccine on day 6 of life and then challenged with B. pertussis using the aerosol challenge model. These primed mice were significantly better protected against leukocytosis, weight loss, and proliferation of B. pertussis in the lungs following aerosol challenge than the nonprimed group. This protection correlated with levels of anti-PT antibody in serum present on the day of aerosol challenge [PMID:12117973].
BALB/c mice were immunized with PTx vaccine on day 6 of life and then challenged with B. pertussis using the aerosol challenge model. These primed mice were significantly better protected against leukocytosis, weight loss, and proliferation of B. pertussis in the lungs following aerosol challenge than the nonprimed group. This protection correlated with levels of anti-PT antibody in serum present on the day of aerosol challenge [PubMed: 12117973].
Protegen ID: 379; NCBI Gene GI: 2665068; NCBI Protein GI: 33594638; NCBI Protein Accession: NP_882282; NCBITaxon: 257313
Mice immunized with rLm/iglC were protected against lethal challenge with F. tularensis LVS administered by the intranasal route, a route chosen to mimic airborne infection, and, most importantly, against aerosol challenge with the highly virulent Type A F. tularensis SchuS4 strain [PMID:19126421].
Mice immunized with rLm/iglC were protected against lethal challenge with F. tularensis LVS administered by the intranasal route, a route chosen to mimic airborne infection, and, most importantly, against aerosol challenge with the highly virulent Type A F. tularensis SchuS4 strain [PubMed: 19126421].
Protegen ID: 470; NCBI Gene GI: 3191591; NCBI Protein GI: 56708413; NCBI Protein Accession: YP_170309; NCBITaxon: 177416
Immunization with WbtI(G191V) protected mice against a relatively low-dose intraperitoneal challenge with LVS (F. tularensis subspecies holarctica live vaccine strain), but was less protective against a high-dose challenge [PMID:17768257].
Immunization with WbtI(G191V) protected mice against a relatively low-dose intraperitoneal challenge with LVS (F. tularensis subspecies holarctica live vaccine strain), but was less protective against a high-dose challenge [PubMed: 17768257].
Protegen ID: 472; NCBI Gene GI: 5522688; NCBI Protein GI: 156502002; NCBI Protein Accession: YP_001428067; NCBITaxon: 458234
Anti-lpnA MAbs conferred significant, although not complete, protection of naïve C3H/HeN mice from lethal challenge with F. tularensis LVS when administered therapeutically [PMID:19176692].
Anti-lpnA MAbs conferred significant, although not complete, protection of nave C3H/HeN mice from lethal challenge with F. tularensis LVS when administered therapeutically [PubMed: 19176692].
Protegen ID: 477; NCBI Gene GI: 3191792; NCBI Protein GI: 56708002; NCBI Protein Accession: YP_169898; NCBITaxon: 177416
Rabbit antibody prepared against P2 from one strain was cross-reactive with P2 isolated from the other two heterologous strains by Western blot. This antibody passively protected infant rats against type b Haemophilus infection caused by the homologous organism, but not against challenge by a strain with the heterologous 36,500 mol wt P2 protein [PMID:6603479].
Rabbit antibody prepared against P2 from one strain was cross-reactive with P2 isolated from the other two heterologous strains by Western blot. This antibody passively protected infant rats against type b Haemophilus infection caused by the homologous organism, but not against challenge by a strain with the heterologous 36,500 mol wt P2 protein [PubMed: 6603479].
Protegen ID: 485; NCBI Gene GI: 3429565; NCBI Protein GI: 68248747; NCBI Protein Accession: YP_247859; NCBITaxon: 281310
BALB/c mice receiving a glycoprotein D1 (gD1, US5) DNA vaccine alone were 80% protected against a subsequent HSV-1 challenge. Results also indicate that the administration of NLX as an adjuvant improved protective immunity against HSV-1 [PMID:19174474].
BALB/c mice receiving a glycoprotein D1 (gD1, US5) DNA vaccine alone were 80% protected against a subsequent HSV-1 challenge. Results also indicate that the administration of NLX as an adjuvant improved protective immunity against HSV-1 [PubMed: 19174474].
Protegen ID: 501; NCBI Gene GI: 2703406; NCBI Protein GI: 9629447; NCBI Protein Accession: NP_044668; NCBITaxon: 10298
Protection against a lethal intraperitoneal challenge of HSV-1 (5 x 10(4) pfu) with gC or gE (US8) plasmid vaccination could be demonstrated if the inoculating dose of DNA was 250 microg. All mice immunized with vaccinia recombinants expressing either gC or gE survived HSV-1 challenge [PMID:9728527].
Protection against a lethal intraperitoneal challenge of HSV-1 (5 x 10(4) pfu) with gC or gE (US8) plasmid vaccination could be demonstrated if the inoculating dose of DNA was 250 microg. All mice immunized with vaccinia recombinants expressing either gC or gE survived HSV-1 challenge [PubMed: 9728527].
Protegen ID: 507; NCBI Gene GI: 2703448; NCBI Protein GI: 9629449; NCBI Protein Accession: NP_044670; NCBITaxon: 10298
A targeted fusion protein based on the CTA1-DD adjuvant and containing tandem repeats of the matrix protein 2 (M2e) ectodomain epitope derived from Influenza A virus (A/Puerto Rico/8/34(H1N1)), CTA1-3M2e-DD, confers strong protective immunity against a potentially lethal challenge infection with influenza virus in mice. The formulation was highly effective for mucosal immunizations and promoted high M2e-specific serum IgG and mucosal IgA antibody titers and an hitherto unknown anti-M2e CD4 T cell immunity [PMID:18243429].
A targeted fusion protein based on the CTA1-DD adjuvant and containing tandem repeats of the matrix protein 2 (M2e) ectodomain epitope derived from Influenza A virus (A/Puerto Rico/8/34(H1N1)), CTA1-3M2e-DD, confers strong protective immunity against a potentially lethal challenge infection with influenza virus in mice. The formulation was highly effective for mucosal immunizations and promoted high M2e-specific serum IgG and mucosal IgA antibody titers and an hitherto unknown anti-M2e CD4 T cell immunity [PubMed: 18243429].
M2 from Influenza A virus (A/Puerto Rico/8/34(H1N1))
Protegen ID: 524; NCBI Gene GI: 956528; NCBI Protein GI: 56583270; NCBI Protein Accession: NP_040979; NCBITaxon: 211044
Lewis rats were immunized with recombinant vaccinia virus (VV) expressing various proteins of measles virus (MV). VVP (Phosphoprotein) -immunized rats were partially protected from MV challenge [PMID:1833505].
Lewis rats were immunized with recombinant vaccinia virus (VV) expressing various proteins of measles virus (MV). VVP (Phosphoprotein) -immunized rats were partially protected from MV challenge [PubMed: 1833505].
Protegen ID: 580; NCBI Gene GI: 1489805; NCBI Protein GI: 9626947; NCBI Protein Accession: NP_056919; NCBITaxon: 11234
Lewis rats were immunized with recombinant vaccinia virus (VV) expressing various proteins of measles virus (MV). VVM (Matrix Protein) -immunized rats were partially protected from MV challenge [PMID:1833505].
Lewis rats were immunized with recombinant vaccinia virus (VV) expressing various proteins of measles virus (MV). VVM (Matrix Protein) -immunized rats were partially protected from MV challenge [PubMed: 1833505].
Protegen ID: 581; NCBI Gene GI: 1489803; NCBI Protein GI: 9626949; NCBI Protein Accession: NP_056921; NCBITaxon: 11234
A total of 11 meningococcal proteins that are necessary for establishing systemic infection were expressed as recombinant antigens and assessed for their ability to protect mice against live bacterial challenge against N. meningitidis; ExbB, which is required for iron acquisition, elicited protective immunity [PMID:15964482].
A total of 11 meningococcal proteins that are necessary for establishing systemic infection were expressed as recombinant antigens and assessed for their ability to protect mice against live bacterial challenge against N. meningitidis; ExbB, which is required for iron acquisition, elicited protective immunity [PubMed: 15964482].
Protegen ID: 601; NCBI Gene GI: 903370; NCBI Protein GI: 15677575; NCBI Protein Accession: NP_274732; NCBITaxon: 122586
Immunization with the pneumococcal proteins pneumolysin (Ply), choline binding protein A (CbpA), or pneumococcal surface protein A (PspA) elicits protective responses against invasive pneumococcal disease in animal models.[PMID:26245351]
The protective effects a pneumolysin mutant (DeltaA146 Ply) against pneumococcal infections in mice was evaluated. Vaccinated mice were challenged with pneumococcal strain D39 at 1,500 times the LD50 (1.5 x 105 CFU) and the vaccinated mice survived significantly longer than control mice after challenge [PubMed: 20038538].
Protegen ID: 607; NCBI Gene GI: 4441611; NCBI Protein GI: 116515376; NCBI Protein Accession: YP_817150; NCBITaxon: 373153
The protective effects of ATP-dependent caseinolytic protease (ClpP) was evaluated. Vaccinated mice were intraperitoneally and/or intranasally challenged with different pneumococcal strains. In intraperitoneal challenge models with pneumococcal strain D39 (serotype 2), clpP elicited some protection in mice [PMID:20038538].
The protective effects of ATP-dependent caseinolytic protease (ClpP) was evaluated. Vaccinated mice were intraperitoneally and/or intranasally challenged with different pneumococcal strains. In intraperitoneal challenge models with pneumococcal strain D39 (serotype 2), clpP elicited some protection in mice [PubMed: 20038538].
Protegen ID: 608; NCBI Gene GI: 4441476; NCBI Protein GI: 116516216; NCBI Protein Accession: YP_816144; NCBITaxon: 373153
Mice immunized with recombinant (r)PsrP(BR) had significantly less bacteria in their blood and improved survival versus controls following intranasal challenge [PMID:19627498].
Mice immunized with recombinant (r)PsrP(BR) had significantly less bacteria in their blood and improved survival versus controls following intranasal challenge [PubMed: 19627498].
Protegen ID: 613; NCBI Gene GI: 7329552; NCBI Protein GI: 221232510; NCBI Protein Accession: YP_002511663; NCBITaxon: 561276
Intraperitoneal immunization with recombinant SrtA was found to have conferred to mice protection against S. pneumoniae intraperitoneal challenge and the passive transfer of immune serum before intraperitoneal challenge was also protective. Moreover, by using the intranasal challenge model, significant reduction of bacteremia when mice were intraperitoneally immunized with SrtA was observed, while a moderate decrease of lung infection was achieved by intranasal immunization, even though no influence on nasopharynx colonization was seen [PMID:19433540].
Intraperitoneal immunization with recombinant SrtA was found to have conferred to mice protection against S. pneumoniae intraperitoneal challenge and the passive transfer of immune serum before intraperitoneal challenge was also protective. Moreover, by using the intranasal challenge model, significant reduction of bacteremia when mice were intraperitoneally immunized with SrtA was observed, while a moderate decrease of lung infection was achieved by intranasal immunization, even though no influence on nasopharynx colonization was seen [PubMed: 19433540].
Protegen ID: 615; NCBI Gene GI: 4442999; NCBI Protein GI: 116515518; NCBI Protein Accession: YP_816547; NCBITaxon: 373153
Mice were actively immunized with a fragment of choline binding protein A (CbpA; also known as PspC, Hic, and SpsA). CbpA was able to protect mice from intraperitoneal challenge with medium to very high doses of a highly virulent capsular type 2 pneumococcal strain, D39 [PMID:11553536].
Mice were actively immunized with a fragment of choline binding protein A (CbpA; also known as PspC, Hic, and SpsA). CbpA was able to protect mice from intraperitoneal challenge with medium to very high doses of a highly virulent capsular type 2 pneumococcal strain, D39 [PubMed: 11553536].
Protegen ID: 619; NCBI Gene GI: 4441159; NCBI Protein GI: 116515359; NCBI Protein Accession: YP_817402; NCBITaxon: 373153
Groups of BALB/c mice immunized with choline binding protein PspA were challenged with either D39 or WCH16. PspA elicited protection by using moderate challenge doses of S. pneumoniae [PMID:17088353].
Groups of BALB/c mice immunized with choline binding protein PspA were challenged with either D39 or WCH16. PspA elicited protection by using moderate challenge doses of S. pneumoniae [PubMed: 17088353].
Protegen ID: 620; NCBI Gene GI: 4441373; NCBI Protein GI: 116515876; NCBI Protein Accession: YP_815641; NCBITaxon: 373153
Mice vaccinated intraperitoneally (i.p.) with 10^7 p.f.u. of a vaccinia virus recombinant expressing either the glycoprotein (rVac-G) or nucleoprotein (rVac-N) of rabies virus 3 weeks before challenge were protected against peripheral lethal infection [PMID:8207400].
Mice vaccinated intraperitoneally (i.p.) with 10^7 p.f.u. of a vaccinia virus recombinant expressing either the glycoprotein (rVac-G) or nucleoprotein (rVac-N) of rabies virus 3 weeks before challenge were protected against peripheral lethal infection [PubMed: 8207400].
Protegen ID: 648; NCBI Gene GI: 1489853; NCBI Protein GI: 9627198; NCBI Protein Accession: NP_056793; NCBITaxon: 11292
To examine the response by IE180 more closely, a vaccine trial in mice with a vector DNA construct that contains the gene encoding for IE180, designated pcDNAIE180 was conducted. Seven months after immunization with pcDNAIE180, an overall 25% of BALB/c, C3H/HeJ, and C57BL/6 mice receiving a lethal PrV challenge were protected [PMID:9586695].
To examine the response by IE180 more closely, a vaccine trial in mice with a vector DNA construct that contains the gene encoding for IE180, designated pcDNAIE180 was conducted. Seven months after immunization with pcDNAIE180, an overall 25% of BALB/c, C3H/HeJ, and C57BL/6 mice receiving a lethal PrV challenge were protected [PubMed: 9586695].
Protegen ID: 658; NCBI Gene GI: 2952540; NCBI Protein GI: 51557548; NCBI Protein Accession: YP_068382; NCBITaxon: 10345
Study compared the handling of overlapping 24-mer peptides from HIV Nef either mixed or covalently linked in tandem in one protein. With adjuvant, overlapping peptides were capable of protecting Balb/c mice against lethal viral challenge with 3 × 108 plaque forming units of vv-nef, whereas the intact protein was less protective [PMID:19193636].
Study compared the handling of overlapping 24-mer peptides from HIV Nef either mixed or covalently linked in tandem in one protein. With adjuvant, overlapping peptides were capable of protecting Balb/c mice against lethal viral challenge with 3 108 plaque forming units of vv-nef, whereas the intact protein was less protective [PubMed: 19193636].
Protegen ID: 707; NCBI Gene GI: 156110; NCBI Protein GI: 28872818; NCBI Protein Accession: NP_057857; NCBITaxon: 11676
Antibodies generated against TcpF are protective against experimental V. cholerae infection in the infant mouse cholera model [PMID:16040956].
Antibodies generated against TcpF are protective against experimental V. cholerae infection in the infant mouse cholera model [PubMed: 16040956].
Protegen ID: 733; NCBI Gene GI: 2614504; NCBI Protein GI: 15640854; NCBI Protein Accession: NP_230485; NCBITaxon: 243277
Mice actively immunized using a recombinant V antigen (rVagHis, encoded by lcrV gene) of Y. enterocolitica were completely protected against challenge with both, Y. enterocolitica 0:8 and Y. pseudotuberculosis serotype III [PMID:10089162].
Mice actively immunized using a recombinant V antigen (rVagHis, encoded by lcrV gene) of Y. enterocolitica were completely protected against challenge with both, Y. enterocolitica 0:8 and Y. pseudotuberculosis serotype III [PubMed: 10089162].
Protegen ID: 790; NCBI Gene GI: 1449458; NCBI Protein GI: 32470278; NCBI Protein Accession: NP_863514; NCBITaxon: 630
Y. enterocolititica Subunit V Antigen Protein Vaccine
A vaccine that protects against Yersinia enterocolitica.
YopH from Y. pestis strain: CO92, biovar: Orientalis
Protegen ID: 51; NCBI Gene GI: 1172712; NCBI Protein GI: 16082755; NCBI Protein Accession: NP_395201; NCBITaxon: 214092
In a prophylactic vaccine model, immunization with the Mycobacterium tuberculosis protein ESAT-6 with LANAC adjuvant elicited significant protective immunity against aerosol challenge with virulent M. tuberculosis [PMID:16751377].
In a prophylactic vaccine model, immunization with the Mycobacterium tuberculosis protein ESAT-6 with LANAC adjuvant elicited significant protective immunity against aerosol challenge with virulent M. tuberculosis [PubMed: 16751377].
Protegen ID: 816; NCBI Gene GI: 886209; NCBI Protein GI: 57117165; NCBI Protein Accession: YP_178023; NCBITaxon: 83332
DNA vaccines encoding KatG antigen fused to TPA signal sequences evoked a significant protective response in mice aerogenically challenged with low doses of Mycobacterium tuberculosis Erdman 17 to 21 days after the final immunization [PMID:10456931].
DNA vaccines encoding KatG antigen fused to TPA signal sequences evoked a significant protective response in mice aerogenically challenged with low doses of Mycobacterium tuberculosis Erdman 17 to 21 days after the final immunization [PubMed: 10456931].
Protegen ID: 817; NCBI Gene GI: 885638; NCBI Protein GI: 15609045; NCBI Protein Accession: NP_216424; NCBITaxon: 83332
A selection of previously identified protective Mycobacterium tuberculosis DNA vaccines were re-formulated as proteins and administered with a Th1-inducing adjuvant to help stimulate the relevant immune responses necessary for protection. One candidate (Rv1806-1807) induced protection in the guinea pig aerosol infection model 30 days post-challenge on the basis of reducing the bacterial burden of M. tuberculosis in the lungs [PMID:16520093].
A selection of previously identified protective Mycobacterium tuberculosis DNA vaccines were re-formulated as proteins and administered with a Th1-inducing adjuvant to help stimulate the relevant immune responses necessary for protection. One candidate (Rv1806-1807) induced protection in the guinea pig aerosol infection model 30 days post-challenge on the basis of reducing the bacterial burden of M. tuberculosis in the lungs [PubMed: 16520093].
Protegen ID: 820; NCBI Gene GI: 885072; NCBI Protein GI: 57116920; NCBI Protein Accession: YP_177653; NCBITaxon: 83332
Purified preparations of HBHA were emulsified in a dimethyldioctadecylammonium bromide-monophosphoryl lipid A adjuvant and tested for the ability to reduce M. tuberculosis infection in the mouse aerosol challenge model for tuberculosis. The HBHA-containing vaccine gave a approximately 0.7-log reduction in CFU in both mouse lungs and spleens compared to adjuvant controls 28 days following challenge [PMID:15557600].
Purified preparations of HBHA were emulsified in a dimethyldioctadecylammonium bromide-monophosphoryl lipid A adjuvant and tested for the ability to reduce M. tuberculosis infection in the mouse aerosol challenge model for tuberculosis. The HBHA-containing vaccine gave a approximately 0.7-log reduction in CFU in both mouse lungs and spleens compared to adjuvant controls 28 days following challenge [PubMed: 15557600].
Protegen ID: 821; NCBI Gene GI: 5211814; NCBI Protein GI: 148660242; NCBI Protein Accession: YP_001281765; NCBITaxon: 25177
In an attempt to generate a subunit vaccine in this experimental disease model, eukaryotic plasmid DNA expression vectors containing genes encoding either the wild-type or modified forms of recombinant listeriolysin O (hly) were generated and used for genetic vaccination of naive mice. Results of these studies indicate that the intramuscular immunization of mice with specifically designed plasmid DNA constructs encoding recombinant forms of listeriolysin O (hly) stimulates peptide-specific CD8+ immune T cells that exhibit in vitro cytotoxic activity. More importantly, such immunization can provide protective immunity against a subsequent challenge with viable L. monocytogenes [PMID:10384131].
In an attempt to generate a subunit vaccine in this experimental disease model, eukaryotic plasmid DNA expression vectors containing genes encoding either the wild-type or modified forms of recombinant listeriolysin O (hly) were generated and used for genetic vaccination of naive mice. Results of these studies indicate that the intramuscular immunization of mice with specifically designed plasmid DNA constructs encoding recombinant forms of listeriolysin O (hly) stimulates peptide-specific CD8+ immune T cells that exhibit in vitro cytotoxic activity. More importantly, such immunization can provide protective immunity against a subsequent challenge with viable L. monocytogenes [PubMed: 10384131].
Protegen ID: 842; NCBI Gene GI: 987033; NCBI Protein GI: 16802248; NCBI Protein Accession: NP_463733; NCBITaxon: 169963
cervical carcinoma
宫颈癌
Bowel
adult alimentary canal
gut
intestines
成人消化道
肠(Bowel)
肠(intestines)
肠道
The fluid-feeding habit of adult mosquitoes is reflected in the structure and ultrastructure of the alimentary canal.
The tubular part of the alimentary canal that extends from the stomach to the anus.
从胃延伸到肛门的消化道的管状部分。
成年蚊子的摄食习惯反映在消化道的结构和超微结构上。
intestine
肠(intestine)
URI: http://www.ebi.ac.uk/cellline#intestine
RIKEN Cell Bank
example to be eventually removed
The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job
failed exploratory term
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
准备好发布
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
待最后审批
Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes.
core
placeholder removed
An editor note should explain what were the merged terms and the reason for the merge.
terms merged
This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use.
term imported
This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created.
term split
This is to be used if none of the existing instances cover the reason for obsolescence. An editor note should indicate this new reason.
We expect to be able to mine these new reasons and add instances as required.
other
Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents.
A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf
A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal
"definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal.
A named class expression is a logical expression that is given a name. The name can be used in place of the expression.
named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions
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
Transformation-ML
Transformation-ML file describing parameter transformations used in a GvHD experiment.
Transformation-ML is a format standard of a digital entity that is conformant with the Transformation-ML standard.(http://wiki.ficcs.org/ficcs/Transformation-ML?action=AttachFile&do=get&target=Transformation-ML_v1.0.26.pdf)
person:Jennifer Fostel
ACS
d06.acs, ACS1.0 data file of well D06 of plate 2 of part 1 of a GvHD experiment.
ACS is a format standard of a digital entity that is conformant with the Analytical Cytometry Standard. (http://www.isac-net.org/content/view/607/150/)
XML
RDF/XML file, OWL file, Compensation-ML file, WSDL document, SVG document
XML is a format standard of a digital entity that is conformant with the W3C Extensible Markup Language Recommendation.(http://www.w3.org/XML/)
RDF
A FOAF file, a SKOS file, an OWL file.
RDF is a format standard of a digital entity that is conformant with the W3C Resource Description Framework RDF/XML Syntax specification.(http://www.w3.org/RDF/)
zip
MagicDraw MDZIP archive, Java JAR file.
zip is a format standard of a digital entity that is conformant with the PKWARE .ZIP file format specification (http://www.pkware.com/index.php?option=com_content&task=view&id=59&Itemid=103/)
tar
Example.tar file.
tar is a format standard of a digital entity that is conformant with the tape archive file format as standardized by POSIX.1-1998, POSIX.1-2001, or any other tar format compliant with the GNU tar specification. (http://www.gnu.org/software/tar/manual/)
FCS
d01.fcs, FCS3 data file of well D06 of plate 2 of part 1 of a GvHD experiment.
FCS is a format standard of a digital entity that is conformant with the Flow Cytometry Data File Standard.(http://www.fcspress.com/)
Compensation-ML
compfoo.xml, Compensation-ML file describing compensation used in a GvHD experiment
Compensation-ML is a format standard of a digital entity that is conformant with the Compensation-ML standard. (http://wiki.ficcs.org/ficcs/Compensation-ML?action=AttachFile&do=get&target=Compensation-ML_v1.0.24.pdf)
Gating-ML
foogate.xml, Gating-ML file describing gates used in a GvHD experiment.
Gating-ML is a format standard of a digital entity that is conformant with the Gating-ML standard. (http://www.flowcyt.org/gating/)
OWL
OBI ontology file, Basic Formal Ontology file, BIRNLex file, BioPAX file.
OWL is a format standard of a digital entity that is conformant with the W3C Web Ontology Language specification.(http://www.w3.org/2004/OWL/)
An organization which supplies technology, tools and protocols for use in high throughput applications
Affymetrix
GenePattern module SVM is a GenePattern software module which is used to run a support vector machine data transformation.
GenePattern module KMeansClustering is a GenePattern software module which is used to perform a k Means clustering data transformation.
GenePattern module CARTXValidation is a GenePattern software module which uses a CART decision tree induction with a leave one out cross validation data transformations.
GenePattern module KNNXValidation is a GenePattern software module which uses a k-nearest neighbours clustering with a leave one out cross validation data transformations.
GenePattern module KNN is a GenePattern software module which perform a k-nearest neighbors data transformation.
GenePattern module HierarchicalClustering
GenePattern module HierarchicalClustering is a GenePattern software module which is used to perform a hierarchical clustering data transformation.
GenePattern module PCA is a GenePattern software module which is used to perform a principal components analysis dimensionality reduction data transformation.
GenePattern HeatMapViewer data visualization
The GenePattern process of generating Heat Maps from clustered data.
GenePattern HierarchicalClusteringViewer data visualization
The GenePattern process of generating hierarchical clustering visualization from clustered data.
A GenePattern software module which is used to generate a heatmap view of data.
GenePattern module HierarchicalClusteringViewer
A GenePattern software module which is used to generate a view of data that has been hierarchically clustered.
2009/09/28 Alan Ruttenberg. Fucoidan-use-case
The Edinburgh Handedness Inventory is a set of questions used to assess the dominance of a person's right or left hand in everyday activities.
PMID:5146491#Oldfield, R.C. (1971). The assessment and analysis of handedness: The Edinburgh inventory. Neuropsychologia, 9, 97-113
Advanced Instruments Inc. (AI Companies)
Nimblegen
An organization that focuses on manufacturing target enrichment probe pools for DNA sequencing.
Pacific Biosciences
An organization that supplies tools for studying the synthesis and regulation of DNA, RNA and protein. It developed a powerful technology platform called single molecule real-time (SMRT) technology which enables real-time analysis of biomolecules with single molecule resolution.
NanoString Technologies
An organization that supplies life science tools for translational research and molecular diagnostics based on a novel digital molecular barcoding technology. The NanoString platform can provide simple, multiplexed digital profiling of single molecules.
An organization that is an American multinational, biotechnology product development company, created in 2006 by the merger of Thermo Electron and Fisher Scientific.
Thermo Fisher Scientific
A histologic grade according to AJCC 7th edition indicating that the tumor cells and the organization of the tumor tissue appear close to normal.
A histologic grade according to AJCC 7th edition indicating that the tumor cells are moderately differentiated and reflect an intermediate grade.
A histologic grade according to AJCC 7th edition indicating that the tumor cells are poorly differentiated and do not look like normal cells and tissue.
A histologic grade according to AJCC 7th edition indicating that the tumor cells are undifferentiated and do not look like normal cells and tissue.
A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei are round, uniform, approximately 10um and that nucleoli are inconspicuous or absent.
A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei are slightly irregular, approximately 15um and nucleoli are evident.
A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei are very irregular, approximately 20um and nucleoli large and prominent.
A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei arei bizarre and multilobulated, 20um or greater and nucleoli are prominent and chromatin clumped.
A histologic grade for ovarian tumor according to a two-tier grading system indicating that the tumor is low grade.
A histologic grade for ovarian tumor according to a two-tier grading system indicating that the tumor is high grade.
A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is well differentiated.
A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is moderately differentiated.
A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is poorly differentiated.
A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is undifferentiated.
A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that there is no evidence of primary tumor.
A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating carcinoma in situ (intraepithelial or invasion of lamina propria).
A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor invades submucosa.
A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor invades muscularis propria.
A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor invades subserosa or into non-peritionealized pericolic or perirectal tissues.
A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor perforates visceral peritoneum.
A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor directly invades other organs or structures.
A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that there is no evidence of primary tumor.
A pathologic primary tumor stage for lung according to AJCC 7th edition indicating carcinoma in situ.
A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is 3 cm or less in greatest dimension, surrounded by lung or visceral pleura without bronchoscopic evidence of invasion more proximal than the lobar bronchus (i.e., not in the main bronchus).
A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is 2 cm or less in greatest dimension.
A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 2 cm but not more than 3 cm in greatest dimension.
A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 3 cm but not more than 7 cm or the tumor has any of the following features: involves main bronchus, 2 cm or more distal to the carina, invades visceral pleura, associated with atelectasis or obstructive pneumonitis that extends to the hilar region but does not involve the entire lung.
A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 3 cm but not more than 5 cm in greatest dimension.
A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 5 cm but not more than 7 cm in greatest dimension.
A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 7 cm or one that directly invades any of: parietal pleura, chest wall (including superior sulcus tumors), diaphragm, phrenic nerve, mediastinal pleura, parietal pericardiu or the tumor is in the main bronchus less than 2 cm distal to the carina but without involvement of the carina or there is associated atelectasis or obstructive pneumonitis of the entire lung or there is separate tumor nodule(s) in the same lobe as the primary.
A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor of any size that invades any of the following: mediastinum, heart, great vessels, trachea, recurrent laryngeal nerve, esophagus, vertebral body, carina or there is separate tumor nodule(s) in a different ipsilateral lobe to that of the primary.
A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that there is no evidence of primary tumor.
A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is 7 cm or less in greatest dimension and limited to the kidney.
A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is 4 cm or less.
A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 4 cm but not more than 7 cm.
A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 7 cm in greatest dimension and limited to the kidney.
A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 7 cm but not more than 10 cm.
A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 10 cm and limited to the kidney.
A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor extends into major veins or perinephric tissues but not into the ipsilateral adrenal gland and not beyond the Gerota fascia.
A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor grossly extends into the renal vein or its segmental (muscle containing) branches, or the tumor invades perirenal and/or renal sinus fat (peripelvic) fat but not beyond Gerota fascia.
A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor grossly extends into vena cava below diaphragm.
A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor grossly extends into vena cava above the diaphragm or Invades the wall of the vena cava.
A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor invades beyond Gerota fascia (including contiguous extension into the ipsilateral adrenal gland).
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that there is no evidence of primary tumor.
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to the ovaries (one or both).
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to one ovary; capsule intact, no tumor on ovarian surface and no malignant cells in ascites or peritoneal washings.
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to both ovaries; capsule intact, no tumor on ovarian surface and no malignant cells in ascites or peritoneal washings.
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to one or both ovaries with capsule ruptured, tumor on ovarian surface, or malignant cells in ascites or peritoneal washings.
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor involves one or both ovaries with pelvic extension.
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has extension and/or implants on uterus and/or tube(s) and no malignant cells in ascites or peritoneal washings.
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has extension to other pelvic tissues and no malignant cells in ascites or peritoneal washings.
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has pelvic extension with malignant cells in ascites or peritoneal washings.
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor involves one or both ovaries with microscopically confirmed peritoneal metastasis outside the pelvis and/or regional lymph node metastasis.
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has microscopic peritoneal metastasis beyond pelvis.
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has macroscopic peritoneal, metastatasis beyond pelvis, 2 cm or less in greatest dimension.
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has peritoneal metastasis beyond pelvis, more than 2 cm in greatest dimension and/or regional lymph node metastasis.
A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating no regional lymph node metastsis.
A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 1-3 regional lymph nodes.
A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 1 regional lymph node.
A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 2-3 regional lymph nodes.
A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating tumor deposit(s), i.e., satellites in the subserosa, or in non-peritonealized pericolic or perirectal soft tissue without regional lymph node metastasis.
A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 4 or more regional lymph nodes.
A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 4 to 6 regional lymph nodes.
A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 7 or more regional lymph nodes.
A pathologic lymph node stage for lung according to AJCC 7th edition indicating no regional lymph node metastasis.
A pathologic lymph node stage for lung according to AJCC 7th edition indicating metastasis in ipsilateral peribronchial and/or ipsilateral hilar lymph nodes and intrapulmonary nodes, including involvement by direct extension.
A pathologic lymph node stage for lung according to AJCC 7th edition indicating metastasis in ipsilateral mediastinal and/or subcarinal lymph node(s).
A pathologic lymph node stage for lung according to AJCC 7th edition indicating metastasis in contralateral mediastinal, contralateral hilar, ipsilateral or contralateral scalene, or supraclavicular lymph node(s).
A pathologic lymph node stage for kidney according to AJCC 7th edition indicating that there is no regional lymph node metastasis.
A pathologic lymph node stage for kidney according to AJCC 7th edition indicating that there is regional lymph node metastasis.
A pathologic lymph node stage for ovary according to AJCC 7th edition indicating that there is no regional lymph node metastasis.
A pathologic lymph node stage for ovary according to AJCC 7th edition indicating that there is regional lymph node metastasis.
A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that there are no symptoms or signs of distant metastasis.
A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that there is clinical evidence of distant metastases by history, physical examination, imaging studies, or invasive procedures, but without microscopic evidence of the presumed distant metastases.
A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is confined to one organ based on clinical assessment.
A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is in more than one organ or the peritoneum based on clinical assessment.
A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that there is microscopic evidence confirming distant metastatic disease.
A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is confined to one organ and histologically confirmed.
A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is in more than one organ or the peritoneum and histologically confirmed.
A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is no distant metastasis.
A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there are distant metastases based on clinical assessment.
A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that metastasis is based on clinical assessment and a separate tumor nodule(s) in a contralateral lobe; tumor with pleural nodules OR malignant pleural or pericardial effusion.
A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is a distant metastases based on clinical assessment.
A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is a distant metastases that is histologically confirmed.
A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that metastasis is histologically confirmed and a separate tumor nodule(s) in a contralateral lobe; tumor with pleural nodules OR malignant pleural or pericardial effusion.
A pathologic distant metastases stage for kidney according to AJCC 7th edition indicating that there is no distant metastasis.
A pathologic distant metastases stage for kidney according to AJCC 7th edition indicating that there are distant metastases based on clinical assessment.
A pathologic distant metastases stage for kidney according to AJCC 7th edition indicating that there is a distant metastases that is histologically confirmed.
A pathologic distant metastases stage for ovary according to AJCC 7th edition indicating that there is no distant metastasis.
A pathologic distant metastases stage for ovary according to AJCC 7th edition indicating that there is distant metastasis except peritoneal metastasis based on clinical assessment.
A pathologic distant metastases stage for ovary according to AJCC 7th edition indicating that there is distant metastasis except peritoneal metastasis that is histologically confirmed.
A clinical tumor stage group according to AJCC 7th edition indicating a small carcinoma, either asymptomatic or giving rise to metastases without symptoms due to the primary carcinoma.
A clinical tumor stage group according to AJCC 7th edition indicating a carcinoma in situ (or melanoma in situ for melanoma of the skin or germ cell neoplasia in situ for testicular germ cell tumors) and generally is considered to have no metastatic potential.
A clinical tumor stage group according to AJCC 7th edition indicating cancers that are smaller or less deeply invasive without regional disease or nodes.
A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent but less than in Stage III and with differing characteristics from IIB and IIC.
A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent but less than in Stage III and with differing characteristics from IIA and IIC.
A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent but less than in Stage III and with differing characteristics from IIA and IIB.
A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent greater than in Stage II and with differing characteristics from IIIB and IIIC.
A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent greater than in Stage II and with differing characteristics from IIIA and IIIC.
A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent greater than in Stage II and with differing characteristics from IIIA and IIIB.
A clinical tumor stage group according to AJCC 7th edition indicating cancers in patients who present with distant metastases at diagnosis and with differing characteristics from IVB.
A clinical tumor stage group according to AJCC 7th edition indicating cancers in patients who present with distant metastases at diagnosis and with differing characteristics from IVA.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating invasive carcinoma which can be diagnosed only by microscopy, with deepest invasion <5 mm and the largest extension <7 mm.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating measured stromal invasion of <3.0 mm in depth and extension of <7.0 mm.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating measured stromal invasion of >3.0 mm and not >5.0 mm with an extension of not >7.0 mm.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating clinically visible lesions limited to the cervix uteri or pre-clinical cancers greater than stage IA
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating clinically visible lesion limited to the cervix uteri or pre-clinical cancers greater than stage IA <4.0 cm in greatest dimension.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating clinically visible lesion limited to the cervix uteri or pre-clinical cancers greater than stage IA >4.0 cm in greatest dimension.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina without parametrial invasion.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina without parametrial invasion and clinically visible lesion <4.0 cm in greatest dimension.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina without parametrial invasion and clinically visible lesion >4.0 cm in greatest dimension.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina with obvious parametrial invasion.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating tumour involves lower third of the vagina, with no extension to the pelvic wall.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating extension to the pelvic wall and/or hydronephrosis or non-functioning kidney.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating spread of the growth to adjacent organs.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating spread to distant organs.
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1, N0, and M0.
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1a, N0, and M0.
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1b, N0, and M0.
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1c, N0, and M0.
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2, N0, and M0.
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2a, N0, and M0.
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2b, N0, and M0.
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2c, N0, and M0.
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of (T3, N0, and M0) or (T3,3a,3b, NX, and M0).
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T3a, N0, and M0 .
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T3b, N0, and M0 .
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of (T3c, N0,X and M0) or (any T, N1 and M0).
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of any T, any N, and M1.
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of (T0, N0, and M0) or (T1,1a-1c,2,2a-2c, NX, and M0) or (TX, N0,X, M0).
3: symptomatic in bed more than 50% of the day but not bed ridden
An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic and in bed for more than 50% of the day but is not bed ridden.
2: symptomatic but in bed less than 50% of the day
An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic but is in bed for less than 50% of the day.
An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic and is bed ridden.
An Eastern Cooperative Oncology Group score value specification indicating a patient is asymptomatic.
An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic but is fully ambulatory.
A Karnofsky score vaue specification indicating that a patient is asymptomatic.
A Karnofsky score vaue specification indicating that a patient is symptomatic but fully ambulatory.
60-70: symptomatic but in bed less than 50% of the day
A Karnofsky score vaue specification indicating that a patient is symptomatic but in bed less than 50% of the day.
40-50: symptomatic, in bed more than 50% of the day, but not bed ridden
A Karnofsky score vaue specification indicating that a patient is symptomatic, in bed more than 50% of the day, but not bed ridden.
## 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
A length unit which is equal to the length of the path traveled by light in vacuum during a time interval of 1/299 792 458 of a second.
A mass unit which is equal to the mass of the International Prototype Kilogram kept by the BIPM at Svres, France.
A time unit which is equal to the duration of 9 192 631 770 periods of the radiation corresponding to the transition between the two hyperfine levels of the ground state of the caesium 133 atom.
A length unit which is equal to one hundredth of a meter or 10^[-2] m.
A length unit which is equal to one thousandth of a meter or 10^[-3] m.
A length unit which is equal to one millionth of a meter or 10^[-6] m.
A length unit which is equal to one thousandth of one millionth of a meter or 10^[-9] m.
A length unit which is equal to 10 [-10] m.
A mass unit which is equal to one thousandth of a kilogram or 10^[-3] kg.
A mass unit which is equal to one thousandth of a gram or 10^[-3] g.
A mass unit which is equal to one millionth of a gram or 10^[-6] g.
A mass unit which is equal to one thousandth of one millionth of a gram or 10^[-9] g.
A mass unit which is equal to 10^[-12] g.
A temperature unit which is equal to one kelvin degree. However, they have their zeros at different points. The centigrade scale has its zero at 273.15 K.
A time unit which is equal to 60 seconds.
A time unit which is equal to 3600 seconds or 60 minutes.
A time unit which is approximately equal to the length of time of one of cycle of the moon's phases which in science is taken to be equal to 30 days.
A time unit which is equal to 12 months which is science is taken to be equal to 365.25 days.
A substance unit equal to a millionth of a mol or 10^[-6] mol.
A substance unit equal to one thousandth of one millionth of a mole or 10^[-9] mol.
A unit of concentration which expresses a concentration of 1 mole of solute per liter of solution (mol/L).
A unit of molarity which is equal to one thousandth of a molar or 10^[-3] M.
A unit of molarity which is equal to one millionth of a molar or 10^[-6] M.
A unit of molarity which is equal to one thousandth of one millionth of a molar or 10^[-9] M.
A unit of molarity which is equal to 10^[-12] M.
A volume unit which is equal to one millionth of a cubic meter or 10^[-9] m^[3], or to 1 ml.
A volume unit which is equal to one thousandth of a liter or 10^[-3] L, or to 1 cubic centimeter.
A volume unit which is equal to one thousandth of a cubic meter or 10^[-3] m^[3], or to 1 decimeter.
A volume unit which is equal to one thousand of a cubic meter or 10^[-3] m^[3], or to 1 L.
A volume unit which is equal to one millionth of a liter or 10^[-6] L.
A volume unit which is equal to one thousandth of one millionth of a liter or 10^[-9] L.
A volume unit which is equal to 10^[-12] L.
A frequency unit which is equal to 1 complete cycle of a recurring phenomenon in 1 second.
A dimensionless concentration unit which denotes the mass of a substance in a mixture as a percentage of the mass of the entire mixture.
A dimensionless concentration unit which denotes the mass of the substance in a mixture as a percentage of the volume of the entire mixture.
A dimensionless concentration unit which denotes the volume of the solute in mL per 100 mL of the resulting solution.
A mass unit density which is equal to mass of an object in grams divided by the volume in liters.
A mass unit density which is equal to mass of an object in milligrams divided by the volume in milliliters.
A temperature unit which is equal to 5/9ths of a kelvin. Negative 40 degrees Fahrenheit is equal to negative 40 degrees Celsius.
A dimensionless concentration notation which denotes the acidity of a solution in terms of activity of hydrogen ions (H+).
A volume per unit volume unit which is equal to one millionth of a liter of solute in one liter of solution.
A mass density unit which is equal to mass of an object in grams divided by the volume in deciliters.
A concentration unit which a measure of viable bacterial numbers in a given volume.
A volumetric flow rate unit which is equal to one microliter volume through a given surface in one minute.
A rate unit which is equal to one over one nanomolar second.
A rate unit which is equal to one over one molar second.
A rate unit which is equal to one over one nanomolar.
A rate unit which is equal to one over one molar.
A mass unit density which is equal to mass of an object in micrograms divided by the volume in liters.
the cell wall is disposed to filter chemicals in endocitosis and exocitosis
the cell wall is disposed to filter chemicals in endocytosis and exocytosis
BFO 2参考：倾向存在于强度连续体中。只有一小部分触发事件才能实现较弱的倾向形式。这些形式出现在相当数量的类似案例中。
(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]
如果b是一个可实现的实体，那么对于存在b的所有t时刻，b s-依赖_于t时刻的一个物质实体。 （BFO2公理标签参考：[063-002]）
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.
某些人有结肠癌的倾向
b是倾向方式：b是可实现的实体； b的持有人是一些物质实体； b是这样的，如果它不复存在，那么它的持有人发生了物理变化； b的实现发生在且因为这个持有者处于一些特殊的物理环境中；这种实现是由于持有者的物理构成而发生的。 （BFO2公理标签参考：[062-002]）
细胞壁被设置为过滤内吞作用和胞吐作用中的化学物质
倾向
元素X的原子具有衰减到元素Y的原子的倾向
Disposition
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])
disposition
孩子天生就倾向于以特定的方式对物体进行分类。
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])
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.
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 [89
To say that each spatiotemporal region s temporally_projects_onto some temporal region t is to say that t is the temporal extension of s. (axiom label in BFO2 Reference: [080-003])
To say that spatiotemporal region s spatially_projects_onto spatial region r at t is to say that r is the spatial extent of s at t. (axiom label in BFO2 Reference: [081-003])
For external terms/classes, the ontology from which the term was imported
引自
imported from
外部术语/类，术语引入的本体
A disposition of a pathogen becoming harmless or less virulent towards its host, when the pathogen is altered physically or genetically. This disposition is realized in the process of the pathogen-host interaction. It is host dependent, or host specific.
attenuated disposition
has_specified_input
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.
see is_input_of example_of_usage
has_specified_output
this person has role this investigator role (more colloquially: this person has this role of investigator)
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.
a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence
has role
has_role
MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z
GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z), e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity'
GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction'
This rule is dubious: added as a quick fix for expected inference in GO-CAM. The problem is most acute for transmembrane proteins, such as receptors or cell adhesion molecules, which have some subfunctions inside the cell (e.g. kinase activity) and some subfunctions outside (e.g. ligand binding). Correct annotation of where these functions occurs leads to incorrect inference about the location of the whole protein. This should probably be weakened to "... -> overlaps"
If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.
inferring direct reg edge from input to regulatory subfunction
inferring direct neg reg edge from input to regulatory subfunction
inferring direct positive reg edge from input to regulatory subfunction
effector input is compound function input
Input of effector is input of its parent MF
if effector directly regulates X, its parent MF directly regulates X
if effector directly positively regulates X, its parent MF directly positively regulates X
if effector directly negatively regulates X, its parent MF directly negatively regulates X
'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).
'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).